diff --git a/.gitignore b/.gitignore
index c47142fb..d6fa962d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,4 @@ distribute-*.egg
 dammit.egg-info/
 *.so
 *~
+.tags*
diff --git a/MANIFEST.in b/MANIFEST.in
index a9cbb482..50d8b3b2 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -3,5 +3,9 @@ include setup.cfg
 include LICENSE
 include distribute_setup.py
 include dammit/VERSION
-include bin/dammit
+include bin/dammit*
 recursive-include dammit .*.json
+recursive-include dammit/viewer/templates *.html
+recursive-include dammit/viewer/templates *.js
+recursive-include dammit/viewer/static *.css
+recursive-include dammit/viewer/static *.js
diff --git a/bin/dammit-view b/bin/dammit-view
new file mode 100644
index 00000000..3aaa7d62
--- /dev/null
+++ b/bin/dammit-view
@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+from flask import Flask, g
+from dammit import common
+from dammit.viewer import transcript_pane
+from dammit.viewer.database import db
+from dammit.viewer import static_folder, template_folder
+import os
+
+DIRECTORY = None
+ZODB_STORAGE = None
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--directory')
+    args = parser.parse_args()
+
+    DIRECTORY = os.path.abspath(args.directory)
+    ZODB_STORAGE = 'file://' + os.path.join(DIRECTORY, common.CONFIG['settings']['database_filename'])
+
+    app = Flask(__name__, static_folder=static_folder, template_folder=template_folder)
+    app.config.from_object(__name__)
+    app.register_blueprint(transcript_pane.views)
+    db.init_app(app)
+
+    app.run(host='0.0.0.0', port=5001, debug=True)
diff --git a/dammit/.config.json b/dammit/.config.json
index 07f4c813..bf7dfe5c 100644
--- a/dammit/.config.json
+++ b/dammit/.config.json
@@ -9,7 +9,9 @@
 		"dammit_dir": ".dammit",
 		"dep_dir": "dependencies",
         "db_dir": "databases",
-        
+        "summary_filename": "dammit.summary.json",
+        "database_filename": "dammit.database.fs",
+
         "blast": {
             "evalue": 0.000001,
             "params": ""
diff --git a/dammit/.databases.json b/dammit/.databases.json
index 564da0fb..84e82f7f 100644
--- a/dammit/.databases.json
+++ b/dammit/.databases.json
@@ -43,6 +43,13 @@
         "url": "ftp://cegg.unige.ch/OrthoDB8/Eukaryotes/Genes_to_OGs/ODB8_EukOGs_genes_ALL_levels.txt.gz"
     },
 
+    "ncbi.tax": {
+        "access": "download",
+        "db_type": "json",
+        "filename": "ncbi_taxonomy.json",
+        "url": "https://s3-us-west-1.amazonaws.com/json-taxonomies/ncbi_taxonomy.json"
+    },
+
     "busco": {
 
         "metazoa": {
diff --git a/dammit/__init__.py b/dammit/__init__.py
index a785c72e..91af3eed 100644
--- a/dammit/__init__.py
+++ b/dammit/__init__.py
@@ -7,16 +7,18 @@
 from .hits import BestHits
 from .crbl import CRBL
 
-import parsers
-import gff
-import blast
-import tasks
+import fileio
 
-import annotate
-import databases
-import dependencies
-import common
-import report
+from . import parsers
+from . import gff
+from . import blast
+from . import tasks
+
+from . import annotate
+from . import databases
+from . import dependencies
+from . import common
+from . import report
 
 import os
 rel_path = os.path.dirname(__file__)
diff --git a/dammit/annotate.py b/dammit/annotate.py
index 54eff343..a32a905d 100644
--- a/dammit/annotate.py
+++ b/dammit/annotate.py
@@ -6,11 +6,13 @@
 from platform import system
 import sys
 
+from doit.task import Task
+
 from . import common
 from .log import LogReporter
 #from .crbl import CRBL
 from .report import get_report_tasks
-from .tasks import get_transcriptome_stats_task, \
+from .tasks import get_summary_task, \
                    get_busco_task, \
                    get_group_task, \
                    get_link_file_task, \
@@ -24,6 +26,7 @@
                    get_sanitize_fasta_task, \
                    get_rename_transcriptome_task, \
                    get_transeq_task, \
+                   get_create_zodb_task, \
                    print_tasks
 
 logger = logging.getLogger(__name__)
@@ -61,16 +64,14 @@ def _init_filenames(self):
         else:
             out_dir = self.args.output_dir
         self.directory = os.path.abspath(out_dir)
-        
-        self.stats_fn = self.transcriptome_fn + '.stats.json'
 
         self.busco_basename = '{0}.{1}.busco.results'.format(self.transcriptome_fn,
                                                              self.args.busco_group)
         self.busco_dir = 'run_{0}'.format(self.busco_basename)
-        busco_summary_fn = 'short_summary_{0}'.format(self.transcriptome_fn)
+        busco_summary_fn = 'short_summary_{0}'.format(self.busco_basename)
         self.busco_summary_fn = os.path.join(self.busco_dir,
                                              busco_summary_fn)
-        
+
         self.translated_fn = '{0}.pep'.format(self.transcriptome_fn)
 
         self.transdecoder_dir = '{0}.transdecoder_dir'.format(self.transcriptome_fn)
@@ -81,13 +82,20 @@ def _init_filenames(self):
         self.transdecoder_pfam_fn = '{0}.pfam.tbl'.format(self.transdecoder_orf_fn)
         self.transdecoder_pep_fn = '{0}.transdecoder.pep'.format(self.transcriptome_fn)
         self.transdecoder_gff3_fn = '{0}.transdecoder.gff3'.format(self.transcriptome_fn)
-        
+
         self.pfam_fn = '{0}.pfam.csv'.format(self.transcriptome_fn)
         self.rfam_fn = '{0}.rfam.tbl'.format(self.transcriptome_fn)
 
         self.orthodb_fn = '{0}.x.orthodb.maf'.format(self.transcriptome_fn)
         self.uniref_fn = '{0}.x.uniref.maf'.format(self.transcriptome_fn)
 
+        self.final_gff3_fn = '{0}.dammit.gff3'.format(self.transcriptome_fn)
+        self.final_fasta_fn = '{0}.dammit.fasta'.format(self.transcriptome_fn)
+        self.final_transcript_fn = '{0}.dammit.json'.format(self.transcriptome_fn)
+        self.transcript_info_fn = '{0}.dammit.info.csv'.format(self.transcriptome_fn)
+        self.summary_fn = common.CONFIG['settings']['summary_filename']
+        self.database_fn = common.CONFIG['settings']['database_filename']
+
         self.user_pep_fn_dict = {}
 
 
@@ -117,8 +125,8 @@ def run_tasks(self, doit_args=['run']):
                 os.makedirs(self.directory)
             os.chdir(self.directory)
 
-            common.run_tasks(self.tasks, 
-                             doit_args, 
+            common.run_tasks(self.tasks,
+                             doit_args,
                              config=self.doit_config)
         finally:
             self.logger.debug('chdir: {0}'.format(cwd))
@@ -130,27 +138,17 @@ def rename_task(self):
                                              self.names_fn,
                                              self.args.name)
 
-    def stats_task(self):
-        '''Calculate assembly information. First it runs some basic stats like N50 and
-        number of contigs, and uses the HyperLogLog counter from khmer to
-        estimate unique k-mers for checking redundancy. Then it runs BUSCO to
-        assess completeness. These tasks are grouped under the 'assess' task.
-        '''
-
-        return get_transcriptome_stats_task(self.transcriptome_fn, 
-                                            self.stats_fn)
-   
     def busco_task(self):
         '''BUSCO assesses completeness using a series of curated databases of core
         conserved genes.
         '''
 
         busco_cfg = common.CONFIG['settings']['busco']
-        return get_busco_task(self.transcriptome_fn, 
-                              self.busco_basename, 
+        return get_busco_task(self.transcriptome_fn,
+                              self.busco_basename,
                               self.database_dict['BUSCO'],
-                              'trans', 
-                              self.args.n_threads, 
+                              'trans',
+                              self.args.n_threads,
                               busco_cfg)
 
     def transeq_task(self):
@@ -170,14 +168,14 @@ def transdecoder_tasks(self):
 
 
         orf_cfg = common.CONFIG['settings']['transdecoder']['longorfs']
-        yield get_transdecoder_orf_task(self.transcriptome_fn, 
+        yield get_transdecoder_orf_task(self.transcriptome_fn,
                                         orf_cfg)
 
-        yield get_hmmscan_task(self.transdecoder_orf_fn, 
+        yield get_hmmscan_task(self.transdecoder_orf_fn,
                                self.transdecoder_pfam_fn,
-                               self.database_dict['PFAM'], 
+                               self.database_dict['PFAM'],
                                self.args.evalue,
-                               self.args.n_threads, 
+                               self.args.n_threads,
                                common.CONFIG['settings']['hmmer']['hmmscan'])
 
         yield get_remap_hmmer_task(self.transdecoder_pfam_fn,
@@ -185,7 +183,7 @@ def transdecoder_tasks(self):
                                    self.pfam_fn)
 
         predict_cfg = common.CONFIG['settings']['transdecoder']['predict']
-        yield get_transdecoder_predict_task(self.transcriptome_fn, 
+        yield get_transdecoder_predict_task(self.transcriptome_fn,
                                             self.transdecoder_pfam_fn,
                                             predict_cfg)
 
@@ -196,26 +194,26 @@ def cmscan_task(self):
         '''
 
         cmscan_cfg = common.CONFIG['settings']['infernal']['cmscan']
-        return get_cmscan_task(self.transcriptome_fn, 
+        return get_cmscan_task(self.transcriptome_fn,
                                self.rfam_fn,
-                               self.database_dict['RFAM'], 
+                               self.database_dict['RFAM'],
                                self.args.evalue,
-                               self.args.n_threads, 
+                               self.args.n_threads,
                                cmscan_cfg)
 
     def orthodb_task(self):
         '''Run LAST to get homologies with OrthoDB. We use LAST here because
         it is much faster than BLAST+, and OrthoDB is pretty huge.
         '''
-        
+
         lastal_cfg = common.CONFIG['settings']['last']['lastal']
         orthodb = self.database_dict['ORTHODB']
-        return get_lastal_task(self.transcriptome_fn, 
-                               orthodb, 
-                               self.orthodb_fn, 
+        return get_lastal_task(self.transcriptome_fn,
+                               orthodb,
+                               self.orthodb_fn,
                                True,
                                self.args.evalue,
-                               self.args.n_threads, 
+                               self.args.n_threads,
                                lastal_cfg)
 
     def uniref_task(self):
@@ -243,17 +241,37 @@ def user_crb_tasks(self):
 
             fn = '{0}.x.{1}.crbb.tsv'.format(self.transcriptome_fn, key)
             self.user_pep_fn_dict[key] = fn
-            yield get_crb_blast_task(self.transcriptome_fn, 
-                                     key, 
-                                     fn, 
+            yield get_crb_blast_task(self.transcriptome_fn,
+                                     key,
+                                     fn,
                                      self.args.evalue,
-                                     crb_blast_cfg, 
+                                     crb_blast_cfg,
                                      self.args.n_threads)
 
+    def summary_task(self):
+        '''Calculate assembly information. First it runs some basic stats like N50 and
+        number of contigs, and uses the HyperLogLog counter from khmer to
+        estimate unique k-mers for checking redundancy. Then it runs BUSCO to
+        assess completeness. These tasks are grouped under the 'assess' task.
+        '''
+
+        return get_summary_task(self.final_fasta_fn,
+                                self.names_fn,
+                                self.directory,
+                                self.final_gff3_fn,
+                                self.busco_summary_fn,
+                                self.summary_fn,
+                                self.transcript_info_fn)
+
+    def create_zodb_task(self):
+        return get_create_zodb_task(self.final_gff3_fn,
+                                    self.transcript_info_fn,
+                                    self.database_fn)
+
     def get_tasks(self):
 
         yield self.rename_task()
-        yield self.stats_task()
+        #yield self.stats_task()
         yield self.busco_task()
         #yield self.transeq_task()
         for task in self.transdecoder_tasks():
@@ -265,10 +283,11 @@ def get_tasks(self):
         for task in self.user_crb_tasks():
             yield task
 
-        self.outputs, report_tasks = get_report_tasks(self.transcriptome_fn, 
-                                                      self,
-                                                      self.database_dict,
-                                                      n_threads=self.args.n_threads)
+        report_tasks = get_report_tasks(self.transcriptome_fn,
+                                        self,
+                                        self.database_dict,
+                                        n_threads=self.args.n_threads)
         for task in report_tasks:
             yield task
-
+        yield self.summary_task()
+        yield self.create_zodb_task()
diff --git a/dammit/app.py b/dammit/app.py
index b5cd0794..e416c265 100644
--- a/dammit/app.py
+++ b/dammit/app.py
@@ -22,7 +22,7 @@ def __init__(self, arg_src=sys.argv[1:]):
         self.meta = '{0}\n{1} {2}'.format(common.CONFIG['meta']['description'],
                                           ', '.join(common.CONFIG['meta']['authors']),
                                           common.CONFIG['meta']['date'])
-        
+
         self.parser = self.get_parser()
         self.args = self.parser.parse_args(arg_src)
 
@@ -40,7 +40,7 @@ def get_parser(self):
                      )
 
         parser.add_argument('--debug', action='store_true', default=False)
-        parser.add_argument('--version', action='version', 
+        parser.add_argument('--version', action='version',
                             version='%(prog)s ' +__version__)
         subparsers = parser.add_subparsers(title='dammit subcommands')
 
@@ -53,16 +53,16 @@ def add_common_args(parser):
             Args:
                 parser (object): The parser to which arguments will be added.
             '''
-            parser.add_argument('--database-dir', 
-                                default=None, 
+            parser.add_argument('--database-dir',
+                                default=None,
                                 help='Directory to store databases. Existing'\
                                      ' databases will not be overwritten.'\
                                      ' By default, the database directory is'\
                                      ' $HOME/.dammit/databases.'
                                 )
 
-            parser.add_argument('--full', 
-                                action='store_true', 
+            parser.add_argument('--full',
+                                action='store_true',
                                 default=False,
                                 help='Do complete run with uniref90. By default'\
                                      ' uniref90 is left out, as it is huge '\
@@ -70,7 +70,7 @@ def add_common_args(parser):
                                      ' time.'
                                 )
 
-            parser.add_argument('--busco-group', 
+            parser.add_argument('--busco-group',
                                 default='metazoa',
                                 choices=['metazoa', 'eukaryota', 'vertebrata',
                                          'arthropoda'],
@@ -79,6 +79,7 @@ def add_common_args(parser):
                                 )
             parser.add_argument('--verbosity',
                                 default=0,
+                                type=int,
                                 choices=[0,1,2],
                                 help='Verbosity level for doit tasks.'
                                 )
@@ -86,7 +87,7 @@ def add_common_args(parser):
         '''
         Add the databases subcommand.
         '''
-        desc = '''Check for databases and optionally download and prepare them 
+        desc = '''Check for databases and optionally download and prepare them
                for use. By default, only check their status.'''
         databases_parser = subparsers.add_parser(
                                'databases',
@@ -94,7 +95,7 @@ def add_common_args(parser):
                                 help=desc
                                 )
 
-        databases_parser.add_argument('--install', 
+        databases_parser.add_argument('--install',
                                       action='store_true',
                                       default=False,
                                       help='Install missing databases. Downloads'
@@ -107,8 +108,8 @@ def add_common_args(parser):
         '''
         Add the dependencies subcommand.
         '''
-        desc = '''Checks for dependencies on system PATH. Unlike with the 
-               databases, dependencies are not downloaded when missing and must 
+        desc = '''Checks for dependencies on system PATH. Unlike with the
+               databases, dependencies are not downloaded when missing and must
                be installed by the user.'''
         dependencies_parser = subparsers.add_parser(
                                   'dependencies',
@@ -120,10 +121,10 @@ def add_common_args(parser):
         '''
         Add the annotation subcommand.
         '''
-        desc = '''The main annotation pipeline. Calculates assembly stats; 
-               runs BUSCO; runs LAST against OrthoDB (and optionally uniref90), 
-               HMMER against Pfam, Inferal against Rfam, and Conditional Reciprocal 
-               Best-hit Blast against user databases; and aggregates all results in 
+        desc = '''The main annotation pipeline. Calculates assembly stats;
+               runs BUSCO; runs LAST against OrthoDB (and optionally uniref90),
+               HMMER against Pfam, Inferal against Rfam, and Conditional Reciprocal
+               Best-hit Blast against user databases; and aggregates all results in
                a properly formatted GFF3 file.'''
         annotate_parser = subparsers.add_parser(
                               'annotate',
@@ -132,7 +133,7 @@ def add_common_args(parser):
                               help=desc
                               )
 
-        annotate_parser.add_argument('transcriptome', 
+        annotate_parser.add_argument('transcriptome',
                                      help='FASTA file with the transcripts to be'\
                                           ' annotated.'
                                      )
@@ -154,22 +155,22 @@ def add_common_args(parser):
                                           ' searches.'
                                      )
 
-        annotate_parser.add_argument('-o', '--output-dir', 
+        annotate_parser.add_argument('-o', '--output-dir',
                                      default=None,
                                      help='Output directory. By default this will'\
                                           ' be the name of the transcriptome file'\
                                           ' with `.dammit` appended'
                                      )
 
-        annotate_parser.add_argument('--n_threads', 
-                                     type=int, 
+        annotate_parser.add_argument('--n_threads',
+                                     type=int,
                                      default=1,
                                      help='Number of threads to pass to programs'\
                                           ' supporting multithreading'
                                      )
 
-        annotate_parser.add_argument('--user-databases', 
-                                     nargs='+', 
+        annotate_parser.add_argument('--user-databases',
+                                     nargs='+',
                                      default=[],
                                      help='Optional additional protein databases. '\
                                           ' These will be searched with CRB-blast.'
@@ -187,7 +188,7 @@ def handle_databases(self):
 
         databases.DatabaseHandler(self.args).handle()
 
-        
+
     def handle_dependencies(self):
         common.print_header('submodule: dependencies', level=1)
 
@@ -203,5 +204,3 @@ def handle_annotate(self):
         db_handler.check_or_fail()
 
         annotate.AnnotateHandler(self.args, db_handler.databases).handle()
-
-
diff --git a/dammit/databases.py b/dammit/databases.py
index cbb42dbd..bf1db841 100644
--- a/dammit/databases.py
+++ b/dammit/databases.py
@@ -10,6 +10,7 @@
 from . import common
 from .log import LogReporter
 from .tasks import get_download_and_gunzip_task, \
+                   get_download_task, \
                    get_hmmpress_task, \
                    get_cmpress_task, \
                    get_download_and_untar_task, \
@@ -31,7 +32,7 @@ def __init__(self, args):
             except KeyError:
                 self.logger.debug('no DAMMIT_DB_DIR or --database-dir, using'\
                                   ' default')
-                directory = os.path.join(common.get_dammit_dir(), 
+                directory = os.path.join(common.get_dammit_dir(),
                                          common.CONFIG['settings']['db_dir'])
         else:
             directory = args.database_dir
@@ -59,7 +60,7 @@ def handle(self, doit_args=['run']):
 
         missing = self.check()
         print_tasks(self.tasks, logger=self.logger)
-        
+
         if self.args.install:
             if missing:
                 common.print_header('Installing databases', level=2)
@@ -104,8 +105,8 @@ def check(self):
         return missing
 
     def get_tasks(self):
-        '''Generate tasks for installing the bundled databases. 
-        
+        '''Generate tasks for installing the bundled databases.
+
         These tasks download the databases, unpack them, and format them for use.
         Current bundled databases are:
 
@@ -113,7 +114,7 @@ def get_tasks(self):
             * Rfam (RNA models)
             * OrthoDB8 (conserved ortholog groups)
             * uniref90 (protiens, if --full selected)
-        
+
         User-supplied databases are downloaded separately.
 
         Returns:
@@ -170,20 +171,28 @@ def get_tasks(self):
         BUSCO = os.path.join(self.directory, 'buscodb')
         tasks.append(
             # That top-level path is given to the download task:
-            get_download_and_untar_task(common.DATABASES['busco'][self.args.busco_group]['url'], 
+            get_download_and_untar_task(common.DATABASES['busco'][self.args.busco_group]['url'],
                                         BUSCO,
                                         label=self.args.busco_group)
         )
         # The untarred arhive has a folder named after the group:
         databases['BUSCO'] = os.path.abspath(os.path.join(BUSCO, self.args.busco_group))
 
+        NCBI_TAXA = os.path.join(self.directory,
+                                 common.DATABASES['ncbi.tax']['filename'])
+        tasks.append(
+            get_download_task(common.DATABASES['ncbi.tax']['url'],
+                              NCBI_TAXA)
+        )
+        databases['NCBI_TAXA'] = os.path.abspath(NCBI_TAXA)
+
         # Get uniref90 if the user specifies
         # Ignoring this until we have working CRBL
         if self.args.full:
-            UNIREF = os.path.join(self.directory, 
+            UNIREF = os.path.join(self.directory,
                                   common.DATABASES['uniref90']['filename'])
             tasks.append(
-                get_download_and_gunzip_task(common.DATABASES['uniref90']['url'], 
+                get_download_and_gunzip_task(common.DATABASES['uniref90']['url'],
                                              UNIREF)
             )
             tasks.append(
@@ -193,4 +202,3 @@ def get_tasks(self):
             databases['UNIREF'] = os.path.abspath(UNIREF)
 
         return databases, tasks
-
diff --git a/dammit/fileio/__init__.py b/dammit/fileio/__init__.py
new file mode 100644
index 00000000..1e9e9f8c
--- /dev/null
+++ b/dammit/fileio/__init__.py
@@ -0,0 +1 @@
+from . import maf
diff --git a/dammit/fileio/base.py b/dammit/fileio/base.py
new file mode 100644
index 00000000..9acc04b7
--- /dev/null
+++ b/dammit/fileio/base.py
@@ -0,0 +1,14 @@
+class BaseParser(object):
+
+    def __init__(self, filename):
+        self.filename = filename
+
+class ChunkParser(BaseParser):
+
+    def __init__(self, filename, chunksize=10000):
+        self.chunksize = chunksize
+        super(ChunkParser, self).__init__(filename)
+
+    def __iter__(self):
+        raise NotImplementedError()
+        yield
diff --git a/dammit/fileio/maf.py b/dammit/fileio/maf.py
new file mode 100644
index 00000000..65a0c1a3
--- /dev/null
+++ b/dammit/fileio/maf.py
@@ -0,0 +1,90 @@
+import pandas as pd
+import numpy as np
+from .base import ChunkParser
+
+class MafParser(ChunkParser):
+
+    def __init__(self, *args, **kwargs):
+        self.LAMBDA = None
+        self.K = None
+        super(MafParser, self).__init__(*args, **kwargs)
+
+    def __iter__(self):
+        '''Iterator yielding DataFrames of length chunksize holding MAF alignments.
+
+        An extra column is added for bitscore, using the equation described here:
+            http://last.cbrc.jp/doc/last-evalues.html
+
+        Args:
+            fn (str): Path to the MAF alignment file.
+            chunksize (int): Alignments to parse per iteration.
+        Yields:
+            DataFrame: Pandas DataFrame with the alignments.
+        '''
+        data = []
+        with open(self.filename) as fp:
+            while (True):
+                try:
+                    line = fp.next().strip()
+                except StopIteration:
+                    break
+                if not line:
+                    continue
+                if line.startswith('#'):
+                    if 'lambda' in line:
+                        meta = line.strip(' #').split()
+                        meta = {k:v for k, _, v in map(lambda x: x.partition('='), meta)}
+                        self.LAMBDA = float(meta['lambda'])
+                        self.K = float(meta['K'])
+                    else:
+                        continue
+                if line.startswith('a'):
+                    cur_aln = {}
+
+                    # Alignment info
+                    tokens = line.split()
+                    for token in tokens[1:]:
+                        key, _, val = token.strip().partition('=')
+                        cur_aln[key] = float(val)
+
+                    # First sequence info
+                    line = fp.next()
+                    tokens = line.split()
+                    cur_aln['s_name'] = tokens[1]
+                    cur_aln['s_start'] = int(tokens[2])
+                    cur_aln['s_aln_len'] = int(tokens[3])
+                    cur_aln['s_strand'] = tokens[4]
+                    cur_aln['s_len'] = int(tokens[5])
+
+                    # First sequence info
+                    line = fp.next()
+                    tokens = line.split()
+                    cur_aln['q_name'] = tokens[1]
+                    cur_aln['q_start'] = int(tokens[2])
+                    cur_aln['q_aln_len'] = int(tokens[3])
+                    cur_aln['q_strand'] = tokens[4]
+                    cur_aln['q_len'] = int(tokens[5])
+
+                    data.append(cur_aln)
+                    if len(data) >= self.chunksize:
+                        if self.LAMBDA is None:
+                            raise Exception("old version of lastal; please update")
+                        yield self._build_df(data)
+                        data = []
+
+        if data:
+            yield self._build_df(data)
+
+    def _build_df(self, data):
+
+        def _fix_sname(name):
+            new, _, _ = name.partition(',')
+            return new
+
+        df = pd.DataFrame(data)
+        df['s_name'] = df['s_name'].apply(_fix_sname)
+        setattr(df, 'LAMBDA', self.LAMBDA)
+        setattr(df, 'K', self.K)
+        df['bitscore'] = (self.LAMBDA * df['score'] - np.log(self.K)) / np.log(2)
+
+        return df
diff --git a/dammit/gff.py b/dammit/gff.py
index 91c70949..6bc8f6f4 100644
--- a/dammit/gff.py
+++ b/dammit/gff.py
@@ -28,11 +28,12 @@ def write_gff3_df(df, fp):
               index=False, header=False, quoting=csv.QUOTE_NONE)
 
 
-def maf_to_gff3_df(maf_df, tag, database=''):
+def maf_to_gff3_df(maf_df, tag='', database=''):
 
     gff3_df = pd.DataFrame()
     gff3_df['seqid'] = maf_df['q_name']
-    gff3_df['source'] = ['LAST'] * len(maf_df)
+    source = '{0}.LAST'.format(tag) if tag else 'LAST'
+    gff3_df['source'] = [source] * len(maf_df)
     gff3_df['type'] = ['translated_nucleotide_match'] * len(maf_df)
     gff3_df['start'] = maf_df['q_start'] + 1
     gff3_df['end'] = maf_df['q_start'] + maf_df['q_aln_len'] + 1
@@ -43,7 +44,7 @@ def maf_to_gff3_df(maf_df, tag, database=''):
     def build_attr(row):
         data = []
         data.append('ID=homology:{0}'.format(next(ID_GEN)))
-        data.append('Name={0}:{1}'.format(row.s_name, tag))
+        data.append('Name={0}'.format(row.s_name))
         data.append('Target={0} {1} {2} {3}'.format(row.s_name, row.s_start,
                                                  row.s_start + row.s_aln_len,
                                                  row.s_strand))
@@ -53,49 +54,16 @@ def build_attr(row):
         return ';'.join(data)
 
     gff3_df['attributes'] = maf_df.apply(build_attr, axis=1)
-    
-    return gff3_df
-
-
-def blast_to_gff3_df(blast_df, prog, RBH=False, database=''):
-
-    assert prog in ['BLASTX', 'TBLASTN', 'BLASTP']
-
-    gff3_df = pd.DataFrame()
-    gff3_df['seqid'] = blast_df['qseqid']
-    gff3_df['source'] = [prog] * len(blast_df)
 
-    ftype = 'protein_match'
-    if prog in ['BLASTX', 'TBLASTN']:
-        ftype = 'translated_nucleotide_match'
-    gff3_df['type'] = [ftype] * len(blast_df)
-
-    gff3_df['start'] = blast_df['qstart'] + 1
-    gff3_df['end'] = blast_df['qend']
-    gff3_df['score'] = blast_df['evalue']
-    gff3_df['strand'] = blast_df['qstrand']
-    gff3_df['phase'] = ['.'] * len(blast_df)
-
-    def build_attr(row):
-        data = []
-        data.append('ID=homology:{0}'.format(next(ID_GEN)))
-        data.append('Name={0}:{1}'.format(row.sseqid, tag))
-        data.append('Target={0} {1} {2} {3}'.format(row.sseqid, row.sstart,
-                                                    row.send, row.sstrand))
-        if database:
-            data.append('database={0}'.format(database))
-
-        return ';'.join(data)
-
-    gff3_df['attributes'] = blast_df.apply(build_attr, axis=1)
     return gff3_df
 
 
-def crb_to_gff3_df(crb_df, tag, database=''):
+def crb_to_gff3_df(crb_df, tag='', database=''):
 
     gff3_df = pd.DataFrame()
     gff3_df['seqid'] = crb_df['query']
-    gff3_df['source'] = ['crb-blast'] * len(crb_df)
+    source = '{0}.crb-blast'.format(tag) if tag else 'crb-blast'
+    gff3_df['source'] = [source] * len(crb_df)
     gff3_df['type'] = ['translated_nucleotide_match'] * len(crb_df)
     gff3_df['start'] = crb_df['qstart'] + 1
     gff3_df['end'] = crb_df['qend']
@@ -106,7 +74,7 @@ def crb_to_gff3_df(crb_df, tag, database=''):
     def build_attr(row):
         data = []
         data.append('ID=homology:{0}'.format(next(ID_GEN)))
-        data.append('Name={0}:{1}'.format(row.subject, tag))
+        data.append('Name={0}'.format(row.subject))
         data.append('Target={0} {1} {2} {3}'.format(row.subject, row.sstart,
                                                     row.send, row.sstrand))
 
@@ -119,11 +87,12 @@ def build_attr(row):
     return gff3_df
 
 
-def hmmscan_to_gff3_df(hmmscan_df, tag, database=''):
-    
+def hmmscan_to_gff3_df(hmmscan_df, tag='', database=''):
+
     gff3_df = pd.DataFrame()
     gff3_df['seqid'] = hmmscan_df['query_name']
-    gff3_df['source'] = ['HMMER'] * len(hmmscan_df)
+    source = '{0}.HMMER'.format(tag) if tag else 'HMMER'
+    gff3_df['source'] = [source] * len(hmmscan_df)
     gff3_df['type'] = ['protein_hmm_match'] * len(hmmscan_df)
 
     gff3_df['start'] = hmmscan_df['env_coord_from']
@@ -133,11 +102,11 @@ def hmmscan_to_gff3_df(hmmscan_df, tag, database=''):
     gff3_df['score'] = hmmscan_df['domain_i_evalue']
     gff3_df['strand'] = ['.'] * len(hmmscan_df)
     gff3_df['phase'] = ['.'] * len(hmmscan_df)
-    
+
     def build_attr(row):
         data = []
         data.append('ID=homology:{0}'.format(next(ID_GEN)))
-        data.append('Name={0}:{1}'.format(row.target_name, tag))
+        data.append('Name={0}'.format(row.target_name))
         data.append('Target={0} {1} {2} +'.format(row.target_name,
                                                     row.hmm_coord_from,
                                                     row.hmm_coord_to))
@@ -153,11 +122,12 @@ def build_attr(row):
     return gff3_df
 
 
-def cmscan_to_gff3_df(cmscan_df, tag, database=''):
-    
+def cmscan_to_gff3_df(cmscan_df, tag='', database=''):
+
     gff3_df = pd.DataFrame()
     gff3_df['seqid'] = cmscan_df['query_name']
-    gff3_df['source'] = ['Infernal'] * len(cmscan_df)
+    source = '{0}.Infernal'.format(tag) if tag else 'Infernal'
+    gff3_df['source'] = [source] * len(cmscan_df)
 
     # For now, using:
     #  http://www.sequenceontology.org/browser/current_svn/term/SO:0000122
@@ -174,7 +144,7 @@ def cmscan_to_gff3_df(cmscan_df, tag, database=''):
     def build_attr(row):
         data = []
         data.append('ID=homology:{0}'.format(next(ID_GEN)))
-        data.append('Name={0}:{1}'.format(row.target_name, tag))
+        data.append('Name={0}'.format(row.target_name))
         data.append('Target={0} {1} {2} +'.format(row.target_name,
                                                     row.mdl_from,
                                                     row.mdl_to))
@@ -190,4 +160,3 @@ def build_attr(row):
     gff3_df['attributes'] = cmscan_df.apply(build_attr, axis=1)
 
     return gff3_df
-
diff --git a/dammit/parsers.py b/dammit/parsers.py
index cc0f75b7..bdfacbe3 100644
--- a/dammit/parsers.py
+++ b/dammit/parsers.py
@@ -6,41 +6,41 @@
 
 from blast import remap_blast_coords_df as remap_blast
 
-blast_cols = [('qseqid', str), 
-              ('sseqid', str), 
-              ('pident', float), 
-              ('length', int), 
-              ('mismatch', int), 
+blast_cols = [('qseqid', str),
+              ('sseqid', str),
+              ('pident', float),
+              ('length', int),
+              ('mismatch', int),
               ('gapopen', int),
-              ('qstart', int), 
-              ('qend', int), 
-              ('sstart', int), 
-              ('send', int), 
-              ('evalue', float), 
+              ('qstart', int),
+              ('qend', int),
+              ('sstart', int),
+              ('send', int),
+              ('evalue', float),
               ('bitscore', float)]
 
-hmmscan_cols = [('target_name', str), 
-                ('target_accession', str), 
+hmmscan_cols = [('target_name', str),
+                ('target_accession', str),
                 ('tlen', int),
-                ('query_name', str), 
-                ('query_accession', str), 
+                ('query_name', str),
+                ('query_accession', str),
                 ('query_len', int),
-                ('full_evalue', float), 
-                ('full_score', float), 
-                ('full_bias', float), 
-                ('domain_num', int), 
-                ('domain_total', int), 
-                ('domain_c_evalue', float), 
+                ('full_evalue', float),
+                ('full_score', float),
+                ('full_bias', float),
+                ('domain_num', int),
+                ('domain_total', int),
+                ('domain_c_evalue', float),
                 ('domain_i_evalue', float),
-                ('domain_score', float), 
-                ('domain_bias', float), 
-                ('hmm_coord_from', int), 
-                ('hmm_coord_to', int), 
-                ('ali_coord_from', int), 
-                ('ali_coord_to', int), 
-                ('env_coord_from', int), 
-                ('env_coord_to', int), 
-                ('accuracy', float), 
+                ('domain_score', float),
+                ('domain_bias', float),
+                ('hmm_coord_from', int),
+                ('hmm_coord_to', int),
+                ('ali_coord_from', int),
+                ('ali_coord_to', int),
+                ('env_coord_from', int),
+                ('env_coord_to', int),
+                ('accuracy', float),
                 ('description', str)]
 
 cmscan_cols = [('target_name', str),
@@ -52,8 +52,8 @@
                ('mdl_to', int),
                ('seq_from', int),
                ('seq_to', int),
-               ('strand', str), 
-               ('trunc', str), 
+               ('strand', str),
+               ('trunc', str),
                ('pass', str),
                ('gc', float),
                ('bias', float),
@@ -62,10 +62,10 @@
                ('inc', str),
                ('description', str)]
 
-gff3_transdecoder_cols = [('seqid', str), 
-                          ('feature_type', str), 
-                          ('start', int), 
-                          ('end', int), 
+gff3_transdecoder_cols = [('seqid', str),
+                          ('feature_type', str),
+                          ('start', int),
+                          ('end', int),
                           ('strand', str)]
 
 gff_cols = [('seqid', str),
@@ -214,7 +214,7 @@ def attr_col_func(col):
 
 
     # Read everything into a DataFrame
-    for group in  pd.read_table(fn, delimiter='\t', comment='#', 
+    for group in  pd.read_table(fn, delimiter='\t', comment='#',
                                 names=[k for k,_ in gff_cols], na_values='.',
                                 converters={'attributes': attr_col_func},
                                 chunksize=chunksize, header=None,
@@ -225,7 +225,7 @@ def attr_col_func(col):
                           pd.DataFrame(list(group.attributes)),
                           left_index=True, right_index=True)
         del gtf_df['attributes']
-    
+
         # Switch from [start, end] to [start, end)
         gtf_df.end = gtf_df.end + 1
         #convert_dtypes(gtf_df, dict(gff_cols))
@@ -264,37 +264,6 @@ def crb_to_df_iter(fn, chunksize=10000, remap=False):
         yield group
 
 
-def parse_busco(fn):
-    '''Parse a single BUSCO summary file to a dictionary.
-
-    Args:
-        fn (str): The results file.
-    Returns:
-        dict: The parsed results.
-    '''
-
-    res = {}
-    with open(fn) as fp:
-        for ln in fp:
-            if ln.strip().startswith('C:'):
-                tokens = ln.split(',')
-                for token in tokens:
-                    key, _, val = token.partition(':')
-                    key = key.strip()
-                    val = val.strip().strip('%')
-                    if key == 'C':
-                        valc, _, vald = val.partition('%')
-                        valc = valc.strip()
-                        vald = vald.strip('D:][%')
-                        res['C(%)'] = valc
-                        res['D(%)'] = vald
-                    else:
-                        if key != 'n':
-                           key += '(%)'
-                        res[key] = val.strip().strip('%')
-    return res
-
-
 def busco_to_df(fn_list, dbs=['metazoa', 'vertebrata']):
     ''' Given a list of BUSCO results from different databases, produce
     an appropriately multi-indexed DataFrame of the results.
@@ -407,7 +376,7 @@ def build_df(data):
         df = pd.DataFrame(data, columns=[k for k, _ in gff3_transdecoder_cols])
         convert_dtype(df, dict(gff3_transdecoder_cols))
         return df
-    
+
     data = []
     with open(fn) as fp:
         for ln in fp:
@@ -426,86 +395,3 @@ def build_df(data):
 
     if data:
         yield build_df(data)
-
-
-def maf_to_df_iter(fn, chunksize=10000):
-    '''Iterator yielding DataFrames of length chunksize holding MAF alignments.
-
-    An extra column is added for bitscore, using the equation described here:
-        http://last.cbrc.jp/doc/last-evalues.html
-
-    Args:
-        fn (str): Path to the MAF alignment file.
-        chunksize (int): Alignments to parse per iteration.
-    Yields:
-        DataFrame: Pandas DataFrame with the alignments.
-    '''
-
-    def fix_sname(name):
-        new, _, _ = name.partition(',')
-        return new
-
-    def build_df(data, LAMBDA, K):
-        df = pd.DataFrame(data)
-        df['s_name'] = df['s_name'].apply(fix_sname)
-        setattr(df, 'LAMBDA', LAMBDA)
-        setattr(df, 'K', K)
-        df['bitscore'] = (LAMBDA * df['score'] - np.log(K)) / np.log(2)
-        return df
-
-    data = []
-    LAMBDA = None
-    K = None
-    with open(fn) as fp:
-        while (True):
-            try:
-                line = fp.next().strip()
-            except StopIteration:
-                break
-            if not line:
-                continue
-            if line.startswith('#'):
-                if 'lambda' in line:
-                    meta = line.strip(' #').split()
-                    meta = {k:v for k, _, v in map(lambda x: x.partition('='), meta)}
-                    LAMBDA = float(meta['lambda'])
-                    K = float(meta['K'])
-                else:
-                    continue
-            if line.startswith('a'):
-                cur_aln = {}
-
-                # Alignment info
-                tokens = line.split()
-                for token in tokens[1:]:
-                    key, _, val = token.strip().partition('=')
-                    cur_aln[key] = float(val)
-                
-                # First sequence info
-                line = fp.next()
-                tokens = line.split()
-                cur_aln['s_name'] = tokens[1]
-                cur_aln['s_start'] = int(tokens[2])
-                cur_aln['s_aln_len'] = int(tokens[3])
-                cur_aln['s_strand'] = tokens[4]
-                cur_aln['s_len'] = int(tokens[5])
-                
-                # First sequence info
-                line = fp.next()
-                tokens = line.split()
-                cur_aln['q_name'] = tokens[1]
-                cur_aln['q_start'] = int(tokens[2])
-                cur_aln['q_aln_len'] = int(tokens[3])
-                cur_aln['q_strand'] = tokens[4]
-                cur_aln['q_len'] = int(tokens[5])
-
-                data.append(cur_aln)
-                if len(data) >= chunksize:
-                    if LAMBDA is None:
-                        raise Exception("old version of lastal; please update")
-                    yield build_df(data, LAMBDA, K)
-                    data = []
-
-    if data:
-        yield build_df(data, LAMBDA, K)
-    
diff --git a/dammit/report.py b/dammit/report.py
index 24a37d14..c3559b19 100644
--- a/dammit/report.py
+++ b/dammit/report.py
@@ -18,7 +18,6 @@ def get_report_tasks(transcriptome, annotator, databases, n_threads=1):
     tasks = []
     outputs = []
 
-
     orthodb_best_hits = annotator.orthodb_fn + '.best.csv'
     orthodb_gff3 = annotator.orthodb_fn + '.gff3'
     tasks.append(
@@ -44,7 +43,7 @@ def get_report_tasks(transcriptome, annotator, databases, n_threads=1):
     pfam_gff3 = annotator.pfam_fn + '.gff3'
     tasks.append(
         get_hmmscan_gff3_task(annotator.pfam_fn,
-                              pfam_gff3, 
+                              pfam_gff3,
                               'Pfam')
     )
     outputs.append(pfam_gff3)
@@ -52,7 +51,7 @@ def get_report_tasks(transcriptome, annotator, databases, n_threads=1):
     rfam_gff3 = annotator.rfam_fn + '.gff3'
     tasks.append(
         get_cmscan_gff3_task(annotator.rfam_fn,
-                             rfam_gff3, 
+                             rfam_gff3,
                              'Rfam')
     )
     outputs.append(rfam_gff3)
@@ -66,18 +65,13 @@ def get_report_tasks(transcriptome, annotator, databases, n_threads=1):
 
     outputs.append(annotator.transdecoder_gff3_fn)
 
-    merged_gff3 = transcriptome + '.dammit.gff3'
     tasks.append(
-        get_gff3_merge_task(outputs, merged_gff3)
+        get_gff3_merge_task(outputs, annotator.final_gff3_fn)
     )
-    outputs.append(merged_gff3)
 
-    renamed_transcriptome = transcriptome + '.dammit.fasta'
     tasks.append(
-        get_annotate_fasta_task(transcriptome, merged_gff3,
-                                renamed_transcriptome)
+        get_annotate_fasta_task(transcriptome, annotator.final_gff3_fn,
+                                annotator.final_fasta_fn)
     )
-    outputs.append(renamed_transcriptome)
-
-    return outputs, tasks
 
+    return tasks
diff --git a/dammit/tasks.py b/dammit/tasks.py
index fa404897..0da1c433 100644
--- a/dammit/tasks.py
+++ b/dammit/tasks.py
@@ -71,10 +71,10 @@ def get_group_task(group_name, tasks):
 
 
 @create_task_object
-def get_download_task(url, target_fn, label='default'):
+def get_download_task(url, target_fn):
 
     cmd = 'curl -o {target_fn} {url}'.format(**locals())
-    name = '_'.join(['download_gunzip', target_fn, label])
+    name = 'download_' + os.path.basename(target_fn)
 
     return {'title': title_with_actions,
             'name': name,
@@ -150,7 +150,7 @@ def fix():
 
 
 @create_task_object
-def get_rename_transcriptome_task(transcriptome_fn, output_fn, names_fn, 
+def get_rename_transcriptome_task(transcriptome_fn, output_fn, names_fn,
                                   transcript_basename, split_regex=None):
 
     import re
@@ -184,7 +184,7 @@ def fix():
             'actions': [fix],
             'targets': [output_fn, names_fn],
             'file_dep': [transcriptome_fn],
-            'clean': [clean_targets]} 
+            'clean': [clean_targets]}
 
 
 @create_task_object
@@ -242,7 +242,7 @@ def get_lastdb_task(db_fn, db_out_prefix, lastdb_cfg, prot=True):
     Returns:
         dict: A pydoit task.
     '''
-    
+
     exc = which('lastdb')
     params = lastdb_cfg['params']
     if prot:
@@ -299,10 +299,11 @@ def get_lastal_task(query, db, out_fn, translate, cutoff, n_threads, lastal_cfg)
 def get_maf_best_hits_task(maf_fn, output_fn):
 
     hits_mgr = BestHits()
+    from .fileio import maf
 
     def cmd():
         df = pd.concat([group for group in
-                        parsers.maf_to_df_iter(maf_fn)])
+                        maf.MafParser(maf_fn)])
         df = hits_mgr.best_hits(df)
         df.to_csv(output_fn, index=False)
 
@@ -347,13 +348,15 @@ def get_cat_task(file_list, target_fn):
 @create_task_object
 def get_busco_task(input_filename, output_name, busco_db_dir, input_type,
                    n_threads, busco_cfg):
-    
+
     name = 'busco:' + os.path.basename(input_filename) + '-' + os.path.basename(busco_db_dir)
 
     assert input_type in ['genome', 'OGS', 'trans']
     exc = which('BUSCO_v1.1b1.py')
     # BUSCO chokes on file paths as output names
     output_name = os.path.basename(output_name)
+    summary_fn = os.path.join('run_{0}'.format(output_name),
+                              'short_summary_{0}'.format(output_name))
 
     cmd = 'python3 {exc} -in {input_filename} -f -o {output_name} -l {busco_db_dir} '\
             '-m {input_type} -c {n_threads}'.format(**locals())
@@ -361,6 +364,7 @@ def get_busco_task(input_filename, output_name, busco_db_dir, input_type,
     return {'name': name,
             'title': title_with_actions,
             'actions': [cmd],
+            'targets': [summary_fn],
             'file_dep': [input_filename],
             'uptodate': [run_once],
             'clean': [(clean_folder, ['run_' + output_name])]}
@@ -381,12 +385,12 @@ def get_cmpress_task(db_filename, infernal_cfg):
 
 
 @create_task_object
-def get_cmscan_task(input_filename, output_filename, db_filename, 
+def get_cmscan_task(input_filename, output_filename, db_filename,
                     cutoff, n_threads, infernal_cfg):
-    
+
     name = 'cmscan:' + os.path.basename(input_filename) + '.x.' + \
            os.path.basename(db_filename)
-    
+
     exc = which('cmscan')
     cmd = '{exc} --cpu {n_threads} --rfam --nohmmonly -E {cutoff}'\
           ' --tblout {output_filename} {db_filename} {input_filename}'\
@@ -402,7 +406,7 @@ def get_cmscan_task(input_filename, output_filename, db_filename,
 
 @create_task_object
 def get_hmmpress_task(db_filename, hmmer_cfg):
-    
+
     name = 'hmmpress:' + os.path.basename(db_filename)
     exc = which('hmmpress')
     cmd = '{exc} {db_filename}'.format(**locals())
@@ -416,12 +420,12 @@ def get_hmmpress_task(db_filename, hmmer_cfg):
 
 
 @create_task_object
-def get_hmmscan_task(input_filename, output_filename, db_filename, 
+def get_hmmscan_task(input_filename, output_filename, db_filename,
                      cutoff, n_threads, hmmer_cfg):
 
     name = 'hmmscan:' + os.path.basename(input_filename) + '.x.' + \
                 os.path.basename(db_filename)
-    
+
     exc = which('hmmscan')
     stat = output_filename + '.out'
     cmd = '{exc} --cpu {n_threads} --domtblout {output_filename} -E {cutoff}'\
@@ -491,34 +495,34 @@ def get_transdecoder_predict_task(input_filename, db_filename, transdecoder_cfg)
     exc = which('TransDecoder.Predict')
     cmd = '{exc} -t {input_filename} --retain_pfam_hits {db_filename} \
             --retain_long_orfs {orf_cutoff}'.format(**locals())
-    
+
     return {'name': name,
             'title': title_with_actions,
             'actions': [cmd],
-            'file_dep': [input_filename, 
+            'file_dep': [input_filename,
                          input_filename + '.transdecoder_dir/longest_orfs.pep',
                          db_filename],
             'targets': [input_filename + '.transdecoder' + ext \
                         for ext in ['.bed', '.cds', '.pep', '.gff3', '.mRNA']],
-            'clean': [clean_targets, 
+            'clean': [clean_targets,
                      (clean_folder, [input_filename + '.transdecoder_dir'])]}
 
 
 @create_task_object
 def get_maf_gff3_task(input_filename, output_filename, database):
 
+    from .fileio import maf
     name = 'maf-gff3:' + os.path.basename(output_filename)
 
     def cmd():
         if input_filename.endswith('.csv') or input_filename.endswith('.tsv'):
             it = pd.read_csv(input_filename, chunksize=10000)
         else:
-            it = parsers.maf_to_df_iter(input_filename)
+            it = maf.MafParser(input_filename).__iter__()
 
         with open(output_filename, 'a') as fp:
             for group in it:
-                gff_group = gff.maf_to_gff3_df(group, 'dammit.last', 
-                                               database)
+                gff_group = gff.maf_to_gff3_df(group, database=database)
                 gff.write_gff3_df(gff_group, fp)
 
     return {'name': name,
@@ -539,7 +543,7 @@ def cmd():
         with open(output_filename, 'a') as fp:
             for group in parsers.crb_to_df_iter(input_filename,
                                                 remap=True):
-                gff_group = gff.crb_to_gff3_df(group, 'dammit.crbb', database)
+                gff_group = gff.crb_to_gff3_df(group, database=database)
                 gff.write_gff3_df(gff_group, fp)
 
     return {'name': name,
@@ -559,8 +563,7 @@ def get_hmmscan_gff3_task(input_filename, output_filename, database):
     def cmd():
         with open(output_filename, 'a') as fp:
             for group in pd.read_csv(input_filename, chunksize=10000):
-                gff_group = gff.hmmscan_to_gff3_df(group, 'dammit.hmmscan',
-                                                   database)
+                gff_group = gff.hmmscan_to_gff3_df(group, database=database)
                 gff.write_gff3_df(gff_group, fp)
 
     return {'name': name,
@@ -580,8 +583,7 @@ def get_cmscan_gff3_task(input_filename, output_filename, database):
     def cmd():
         with open(output_filename, 'a') as fp:
             for group in parsers.cmscan_to_df_iter(input_filename):
-                gff_group = gff.cmscan_to_gff3_df(group, 'dammit.cmscan',
-                                                  database)
+                gff_group = gff.cmscan_to_gff3_df(group, database=database)
                 gff.write_gff3_df(gff_group, fp)
 
     return {'name': name,
@@ -609,16 +611,33 @@ def get_gff3_merge_task(gff3_filenames, output_filename):
             'targets': [output_filename],
             'clean': [clean_targets]}
 
+'''
+@create_task_object
+def get_json_task(gff3_fn, fasta_fn, output_fn):
+
+    import json
+
+    def create_json():
+        annotations = pd.concat(parsers.parse_gff3(gff3_fn))
+
+        with open(output_fn, 'wb') as fp:
+            fp.write('{\n')
+            for record in ReadParser(fasta_fn):
+                short_name, _, _ = record.name.split()[0]
+                annots = annotations.query('seqid == "{0}"'.format(short_name))
+'''
+
 
 @create_task_object
 def get_annotate_fasta_task(transcriptome_fn, gff3_fn, output_fn):
-    
+
     name = 'fasta-annotate:{0}'.format(output_fn)
 
     def annotate_fasta():
         annotations = pd.concat([g for g in \
                                  parsers.parse_gff3(gff3_fn)])
         with open(output_fn, 'wb') as fp:
+
             for n, record in enumerate(ReadParser(transcriptome_fn)):
                 df = annotations.query('seqid == "{0}"'.format(record.name))
                 annots = ['len={0}'.format(len(record.sequence))]
@@ -630,8 +649,8 @@ def annotate_fasta():
                                         'protein_hmm_match',
                                         'RNA_sequence_secondary_structure']:
 
-                        collapsed = ','.join(['{}:{}-{}'.format(row.Name.split(':dammit')[0], 
-                                                                 int(row.start), 
+                        collapsed = ','.join(['{}:{}-{}'.format(row.Name.split(':dammit')[0],
+                                                                 int(row.start),
                                                                  int(row.end)) \
                                         for _, row in fgroup.iterrows()])
                         if feature_type == 'translated_nucleotide_match':
@@ -643,9 +662,9 @@ def annotate_fasta():
                         annots.append('{0}={1}'.format(key, collapsed))
 
                     elif feature_type in ['exon', 'CDS', 'gene',
-                                          'five_prime_UTR', 'three_prime_UTR', 
+                                          'five_prime_UTR', 'three_prime_UTR',
                                           'mRNA']:
-                        
+
                         collapsed = ','.join(['{}-{}'.format(int(row.start),
                                                              int(row.end)) \
                                         for _, row in fgroup.iterrows()])
@@ -664,29 +683,33 @@ def annotate_fasta():
 
 
 @create_task_object
-def get_transcriptome_stats_task(transcriptome, output_fn):
+def get_summary_task(transcriptome, name_map_fn, work_dir, final_gff3_fn,
+                     busco_summary_fn, output_fn, transcript_info_fn):
 
-    name = 'transcriptome_stats:' + os.path.basename(transcriptome)
+    name = 'json_summary:' + os.path.basename(transcriptome)
     K = 25
-    
+
     def parse(fn):
         hll = HLLCounter(.01, K)
         lens = []
         names = []
+        annots = []
         gc_len = 0
         for contig in ReadParser(fn):
             lens.append(len(contig.sequence))
-            names.append(contig.name)
+            name, _, annot = contig.name.partition(' ')
+            names.append(name)
+            annots.append(annot)
             hll.consume_string(contig.sequence)
             gc_len += contig.sequence.count('C')
             gc_len += contig.sequence.count('G')
-        S = pd.Series(lens, index=names)
+        df = pd.DataFrame({'length': lens, 'annotations': annots}, index=names)
         try:
-            S.sort_values()
+            df.sort_values('length', inplace=True)
         except AttributeError:
-            S.sort()
-        gc_perc = float(gc_len) / S.sum()
-        return S, hll.estimate_cardinality(), gc_perc
+            df.sort('length', inplace=True)
+        gc_perc = float(gc_len) / df['length'].sum()
+        return df, hll.estimate_cardinality(), gc_perc
 
     def calc_NX(lens, X):
         N = lens.sum()
@@ -703,34 +726,93 @@ def calc_NX(lens, X):
                 break
         return NXlen, NXpos
 
-    def cmd():
-        lens, uniq_kmers, gc_perc = parse(transcriptome)
-        
-        exp_kmers = (lens - (K+1)).sum()
+    def stats():
+        len_df, uniq_kmers, gc_perc = parse(transcriptome)
+
+        exp_kmers = (len_df['length'] - (K+1)).sum()
         redundancy = float(exp_kmers - uniq_kmers) / exp_kmers
         if redundancy < 0:
             redundancy = 0.0
 
-        N50len, N50pos = calc_NX(lens, 50)
-        stats = {'N': len(lens),
-                 'sum': lens.sum(),
-                 'min': lens.min(),
-                 'max': lens.max(),
-                 'med': lens.median(),
-                 'mean': lens.mean(),
+        N50len, N50pos = calc_NX(len_df['length'], 50)
+        data = {'N': len(len_df),
+                 'sum': len_df['length'].sum(),
+                 'min': len_df['length'].min(),
+                 'max': len_df['length'].max(),
+                 'med': len_df['length'].median(),
+                 'mean': len_df['length'].mean(),
                  'N50len': N50len,
                  'N50pos': N50pos,
                  '25_mers': exp_kmers,
                  '25_mers_unique': uniq_kmers,
                  'redundancy': redundancy,
                  'GCperc': gc_perc}
-        
+        return len_df, data
+
+    def cmd():
+        len_df, stats_summary = stats()
+        name_map_df = pd.read_csv(name_map_fn)
+        busco_summary = parsers.parse_busco_summary(busco_summary_fn)
+        transcript_df = pd.merge(name_map_df, len_df,
+                                 left_on='renamed',
+                                 right_index=True).rename(columns={'renamed': 'seqid'})
+
+
+        run_summary = {'work_dir': work_dir,
+                       'fasta': transcriptome,
+                       'gff3': final_gff3_fn,
+                       'busco': busco_summary,
+                       'stats': stats_summary}
+        #
+        transcript_df.to_csv(transcript_info_fn)
+
         with open(output_fn, 'wb') as fp:
-            json.dump(stats, fp, indent=4)
+            json.dump(run_summary, fp, indent=4)
 
     return {'name': name,
             'title': title_with_actions,
             'actions': [(cmd, [])],
-            'file_dep': [transcriptome],
-            'targets': [output_fn],
+            'file_dep': [transcriptome,
+                         name_map_fn,
+                         final_gff3_fn,
+                         busco_summary_fn],
+            'targets': [output_fn, transcript_info_fn],
+            'clean': [clean_targets]}
+
+
+@create_task_object
+def get_create_zodb_task(gff3_fn, transcript_info_fn, database_fn):
+    from ZODB import FileStorage, DB
+    from flask.ext.zodb import Dict as zdict
+    import transaction
+
+    name = 'create-zodb:' + os.path.basename(database_fn)
+
+    def cmd():
+        db = DB(FileStorage.FileStorage(database_fn))
+        con = db.open()
+        root = con.root()
+
+        root['transcripts'] =  zdict()
+
+        def func(row):
+            root['transcripts'][row.seqid] = zdict()
+            root['transcripts'][row.seqid]['length'] = row.length
+            root['transcripts'][row.seqid]['short_annot'] = row.annotations
+            transaction.commit()
+        transcript_df = pd.read_csv(transcript_info_fn).apply(func, axis=1)
+
+        gff3_df = pd.concat(parsers.parse_gff3(gff3_fn))
+        for transcript, group in gff3_df.groupby('seqid'):
+            root['transcripts'][transcript]['annotations'] = group
+            transaction.commit()
+
+        con.close()
+
+    return {'name': name,
+            'title': title_with_actions,
+            'actions': ['rm -f {0}'.format(database_fn),
+                        cmd],
+            'file_dep': [gff3_fn, transcript_info_fn],
+            'targets': [database_fn],
             'clean': [clean_targets]}
diff --git a/dammit/tests/test_main.py b/dammit/tests/test_main.py
index 0da5c50a..610534e3 100644
--- a/dammit/tests/test_main.py
+++ b/dammit/tests/test_main.py
@@ -80,7 +80,7 @@ def test_dammit_databases_check_fail(self):
         '''
 
         with TemporaryDirectory() as td:
-            
+
             args = ['databases', '--database-dir', td]
             status, out, err = run(args, fail_ok=True)
             self.assertIn('prep incomplete', err)
@@ -143,7 +143,7 @@ def test_annotate_evalue(self):
 
             self.assertEquals(open(gff3_fn).read(), open(exp_gff3).read())
             self.assertEquals(open(fasta_fn).read(), open(exp_fasta).read())
-  
+
 
     def test_annotate_outdir(self):
         '''Test that the --output-dir argument works.
@@ -177,9 +177,12 @@ def test_annotate_dbdir(self):
         with TemporaryDirectory() as td,\
              TestData('pom.single.fa', td) as transcripts:
 
-            db_dir = os.environ['DAMMIT_DB_DIR']
-            args = ['annotate', transcripts, '--database-dir', db_dir]
-            status, out, err = run(args, in_directory=td)
+            try:
+                db_dir = os.environ['DAMMIT_DB_DIR']
+                args = ['annotate', transcripts, '--database-dir', db_dir]
+                status, out, err = run(args, in_directory=td)
+            except KeyError:
+                pass
 
     def test_annotate_user_databases(self):
         '''Test that a user database works.
@@ -252,7 +255,7 @@ def test_check_system_path_alldeps(self):
                 self.assertIn(name, names)
                 if name != 'LAST':
                     self.assertTrue(stat, msg=name + ' ' + msg)
-    
+
     def test_handle_nodeps(self):
         os.environ['PATH'] = ''
         handler = dependencies.DependencyHandler()
@@ -273,6 +276,3 @@ class TestDatabases(TestCase):
     @classmethod
     def setup_class(cls):
         cls.db_dir = 'test_db_dir'
-
-
-            
diff --git a/dammit/viewer/__init__.py b/dammit/viewer/__init__.py
new file mode 100644
index 00000000..d9801610
--- /dev/null
+++ b/dammit/viewer/__init__.py
@@ -0,0 +1,5 @@
+import os
+from .. import common
+
+static_folder = os.path.join(common.rel_path, 'viewer', 'static')
+template_folder = os.path.join(common.rel_path, 'viewer', 'templates')
diff --git a/dammit/viewer/database.py b/dammit/viewer/database.py
new file mode 100644
index 00000000..e7e2e9b0
--- /dev/null
+++ b/dammit/viewer/database.py
@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+from flask import g, current_app
+from flask.ext.zodb import ZODB
+
+db = ZODB()
diff --git a/dammit/viewer/genomed3plot.py b/dammit/viewer/genomed3plot.py
new file mode 100644
index 00000000..cf500290
--- /dev/null
+++ b/dammit/viewer/genomed3plot.py
@@ -0,0 +1,46 @@
+import pandas as pd
+
+sources = ['HMMER',
+           'LAST',
+           'transdecoder',
+           'crb-blast',
+           'Infernal']
+
+def create_tracks(transcript, transcript_df, track_start=100, track_width=40, track_sep=10):
+    tracks = []
+    for source in sources:
+        if source in transcript_df.source.values:
+            source_df = transcript_df.query('source == "{0}"'.format(source))
+            track = {}
+            track['trackName'] = source
+            track['trackType'] = "track"
+            track['trackFeatures'] = "complex"
+            track['visible'] = True
+            track['min_slice'] = True
+            track['showTooltip'] = True
+
+            track['inner_radius'] = track_start
+            track['outer_radius'] = track_start + track_width
+
+            items = []
+            id_count = 0
+            for _, row in source_df.iterrows():
+
+                if row.notnull().Note:
+                    name = row.Note
+                elif row.notnull().Name:
+                    name = row.Name
+                else:
+                    name = row.ID
+
+                items.append({'id': id_count,
+                              'start': int(row.start),
+                              'end': int(row.end),
+                              'name': name
+                              })
+                id_count += 1
+            track['items'] = items
+            tracks.append(track)
+        track_start += track_width + track_sep
+
+    return tracks
diff --git a/dammit/viewer/static/FileSaver.js b/dammit/viewer/static/FileSaver.js
new file mode 100644
index 00000000..378a9dcc
--- /dev/null
+++ b/dammit/viewer/static/FileSaver.js
@@ -0,0 +1,232 @@
+/* FileSaver.js
+ * A saveAs() FileSaver implementation.
+ * 2013-10-21
+ *
+ * By Eli Grey, http://eligrey.com
+ * License: X11/MIT
+ *   See LICENSE.md
+ */
+
+/*global self */
+/*jslint bitwise: true, regexp: true, confusion: true, es5: true, vars: true, white: true,
+  plusplus: true */
+
+/*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */
+
+var saveAs = saveAs
+  || (typeof navigator !== 'undefined' && navigator.msSaveOrOpenBlob && navigator.msSaveOrOpenBlob.bind(navigator))
+  || (function(view) {
+	"use strict";
+	var
+		  doc = view.document
+		  // only get URL when necessary in case BlobBuilder.js hasn't overridden it yet
+		, get_URL = function() {
+			return view.URL || view.webkitURL || view;
+		}
+		, URL = view.URL || view.webkitURL || view
+		, save_link = doc.createElementNS("http://www.w3.org/1999/xhtml", "a")
+		, can_use_save_link =  !view.externalHost && "download" in save_link
+		, click = function(node) {
+			var event = doc.createEvent("MouseEvents");
+			event.initMouseEvent(
+				"click", true, false, view, 0, 0, 0, 0, 0
+				, false, false, false, false, 0, null
+			);
+			node.dispatchEvent(event);
+		}
+		, webkit_req_fs = view.webkitRequestFileSystem
+		, req_fs = view.requestFileSystem || webkit_req_fs || view.mozRequestFileSystem
+		, throw_outside = function (ex) {
+			(view.setImmediate || view.setTimeout)(function() {
+				throw ex;
+			}, 0);
+		}
+		, force_saveable_type = "application/octet-stream"
+		, fs_min_size = 0
+		, deletion_queue = []
+		, process_deletion_queue = function() {
+			var i = deletion_queue.length;
+			while (i--) {
+				var file = deletion_queue[i];
+				if (typeof file === "string") { // file is an object URL
+					URL.revokeObjectURL(file);
+				} else { // file is a File
+					file.remove();
+				}
+			}
+			deletion_queue.length = 0; // clear queue
+		}
+		, dispatch = function(filesaver, event_types, event) {
+			event_types = [].concat(event_types);
+			var i = event_types.length;
+			while (i--) {
+				var listener = filesaver["on" + event_types[i]];
+				if (typeof listener === "function") {
+					try {
+						listener.call(filesaver, event || filesaver);
+					} catch (ex) {
+						throw_outside(ex);
+					}
+				}
+			}
+		}
+		, FileSaver = function(blob, name) {
+			// First try a.download, then web filesystem, then object URLs
+			var
+				  filesaver = this
+				, type = blob.type
+				, blob_changed = false
+				, object_url
+				, target_view
+				, get_object_url = function() {
+					var object_url = get_URL().createObjectURL(blob);
+					deletion_queue.push(object_url);
+					return object_url;
+				}
+				, dispatch_all = function() {
+					dispatch(filesaver, "writestart progress write writeend".split(" "));
+				}
+				// on any filesys errors revert to saving with object URLs
+				, fs_error = function() {
+					// don't create more object URLs than needed
+					if (blob_changed || !object_url) {
+						object_url = get_object_url(blob);
+					}
+					if (target_view) {
+						target_view.location.href = object_url;
+					} else {
+                        window.open(object_url, "_blank");
+                    }
+					filesaver.readyState = filesaver.DONE;
+					dispatch_all();
+				}
+				, abortable = function(func) {
+					return function() {
+						if (filesaver.readyState !== filesaver.DONE) {
+							return func.apply(this, arguments);
+						}
+					};
+				}
+				, create_if_not_found = {create: true, exclusive: false}
+				, slice
+			;
+			filesaver.readyState = filesaver.INIT;
+			if (!name) {
+				name = "download";
+			}
+			if (can_use_save_link) {
+				object_url = get_object_url(blob);
+				// FF for Android has a nasty garbage collection mechanism
+				// that turns all objects that are not pure javascript into 'deadObject'
+				// this means `doc` and `save_link` are unusable and need to be recreated
+				// `view` is usable though:
+				doc = view.document;
+				save_link = doc.createElementNS("http://www.w3.org/1999/xhtml", "a");
+				save_link.href = object_url;
+				save_link.download = name;
+				var event = doc.createEvent("MouseEvents");
+				event.initMouseEvent(
+					"click", true, false, view, 0, 0, 0, 0, 0
+					, false, false, false, false, 0, null
+				);
+				save_link.dispatchEvent(event);
+				filesaver.readyState = filesaver.DONE;
+				dispatch_all();
+				return;
+			}
+			// Object and web filesystem URLs have a problem saving in Google Chrome when
+			// viewed in a tab, so I force save with application/octet-stream
+			// http://code.google.com/p/chromium/issues/detail?id=91158
+			if (view.chrome && type && type !== force_saveable_type) {
+				slice = blob.slice || blob.webkitSlice;
+				blob = slice.call(blob, 0, blob.size, force_saveable_type);
+				blob_changed = true;
+			}
+			// Since I can't be sure that the guessed media type will trigger a download
+			// in WebKit, I append .download to the filename.
+			// https://bugs.webkit.org/show_bug.cgi?id=65440
+			if (webkit_req_fs && name !== "download") {
+				name += ".download";
+			}
+			if (type === force_saveable_type || webkit_req_fs) {
+				target_view = view;
+			}
+			if (!req_fs) {
+				fs_error();
+				return;
+			}
+			fs_min_size += blob.size;
+			req_fs(view.TEMPORARY, fs_min_size, abortable(function(fs) {
+				fs.root.getDirectory("saved", create_if_not_found, abortable(function(dir) {
+					var save = function() {
+						dir.getFile(name, create_if_not_found, abortable(function(file) {
+							file.createWriter(abortable(function(writer) {
+								writer.onwriteend = function(event) {
+									target_view.location.href = file.toURL();
+									deletion_queue.push(file);
+									filesaver.readyState = filesaver.DONE;
+									dispatch(filesaver, "writeend", event);
+								};
+								writer.onerror = function() {
+									var error = writer.error;
+									if (error.code !== error.ABORT_ERR) {
+										fs_error();
+									}
+								};
+								"writestart progress write abort".split(" ").forEach(function(event) {
+									writer["on" + event] = filesaver["on" + event];
+								});
+								writer.write(blob);
+								filesaver.abort = function() {
+									writer.abort();
+									filesaver.readyState = filesaver.DONE;
+								};
+								filesaver.readyState = filesaver.WRITING;
+							}), fs_error);
+						}), fs_error);
+					};
+					dir.getFile(name, {create: false}, abortable(function(file) {
+						// delete file if it already exists
+						file.remove();
+						save();
+					}), abortable(function(ex) {
+						if (ex.code === ex.NOT_FOUND_ERR) {
+							save();
+						} else {
+							fs_error();
+						}
+					}));
+				}), fs_error);
+			}), fs_error);
+		}
+		, FS_proto = FileSaver.prototype
+		, saveAs = function(blob, name) {
+			return new FileSaver(blob, name);
+		}
+	;
+	FS_proto.abort = function() {
+		var filesaver = this;
+		filesaver.readyState = filesaver.DONE;
+		dispatch(filesaver, "abort");
+	};
+	FS_proto.readyState = FS_proto.INIT = 0;
+	FS_proto.WRITING = 1;
+	FS_proto.DONE = 2;
+
+	FS_proto.error =
+	FS_proto.onwritestart =
+	FS_proto.onprogress =
+	FS_proto.onwrite =
+	FS_proto.onabort =
+	FS_proto.onerror =
+	FS_proto.onwriteend =
+		null;
+
+	view.addEventListener("unload", process_deletion_queue, false);
+	return saveAs;
+}(this.self || this.window || this.content));
+// `self` is undefined in Firefox for Android content script context
+// while `this` is nsIContentFrameMessageManager
+// with an attribute `content` that corresponds to the window
+
+if (typeof module !== 'undefined') module.exports = saveAs;
diff --git a/dammit/viewer/static/StackBlur.js b/dammit/viewer/static/StackBlur.js
new file mode 100644
index 00000000..7dea6d04
--- /dev/null
+++ b/dammit/viewer/static/StackBlur.js
@@ -0,0 +1,611 @@
+/*
+
+StackBlur - a fast almost Gaussian Blur For Canvas
+
+Version: 	0.5
+Author:		Mario Klingemann
+Contact: 	mario@quasimondo.com
+Website:	http://www.quasimondo.com/StackBlurForCanvas
+Twitter:	@quasimondo
+
+In case you find this class useful - especially in commercial projects -
+I am not totally unhappy for a small donation to my PayPal account
+mario@quasimondo.de
+
+Or support me on flattr: 
+https://flattr.com/thing/72791/StackBlur-a-fast-almost-Gaussian-Blur-Effect-for-CanvasJavascript
+
+Copyright (c) 2010 Mario Klingemann
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+var mul_table = [
+        512,512,456,512,328,456,335,512,405,328,271,456,388,335,292,512,
+        454,405,364,328,298,271,496,456,420,388,360,335,312,292,273,512,
+        482,454,428,405,383,364,345,328,312,298,284,271,259,496,475,456,
+        437,420,404,388,374,360,347,335,323,312,302,292,282,273,265,512,
+        497,482,468,454,441,428,417,405,394,383,373,364,354,345,337,328,
+        320,312,305,298,291,284,278,271,265,259,507,496,485,475,465,456,
+        446,437,428,420,412,404,396,388,381,374,367,360,354,347,341,335,
+        329,323,318,312,307,302,297,292,287,282,278,273,269,265,261,512,
+        505,497,489,482,475,468,461,454,447,441,435,428,422,417,411,405,
+        399,394,389,383,378,373,368,364,359,354,350,345,341,337,332,328,
+        324,320,316,312,309,305,301,298,294,291,287,284,281,278,274,271,
+        268,265,262,259,257,507,501,496,491,485,480,475,470,465,460,456,
+        451,446,442,437,433,428,424,420,416,412,408,404,400,396,392,388,
+        385,381,377,374,370,367,363,360,357,354,350,347,344,341,338,335,
+        332,329,326,323,320,318,315,312,310,307,304,302,299,297,294,292,
+        289,287,285,282,280,278,275,273,271,269,267,265,263,261,259];
+        
+   
+var shg_table = [
+	     9, 11, 12, 13, 13, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 17, 
+		17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 19, 
+		19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20,
+		20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21,
+		21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+		21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 
+		22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22,
+		22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 
+		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
+		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
+		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 
+		23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 
+		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24 ];
+
+function stackBlurImage( imageID, canvasID, radius, blurAlphaChannel )
+{
+			
+ 	var img = document.getElementById( imageID );
+	var w = img.naturalWidth;
+    var h = img.naturalHeight;
+       
+	var canvas = document.getElementById( canvasID );
+      
+    canvas.style.width  = w + "px";
+    canvas.style.height = h + "px";
+    canvas.width = w;
+    canvas.height = h;
+    
+    var context = canvas.getContext("2d");
+    context.clearRect( 0, 0, w, h );
+    context.drawImage( img, 0, 0 );
+
+	if ( isNaN(radius) || radius < 1 ) return;
+	
+	if ( blurAlphaChannel )
+		stackBlurCanvasRGBA( canvasID, 0, 0, w, h, radius );
+	else 
+		stackBlurCanvasRGB( canvasID, 0, 0, w, h, radius );
+}
+
+
+function stackBlurCanvasRGBA( id, top_x, top_y, width, height, radius )
+{
+	if ( isNaN(radius) || radius < 1 ) return;
+	radius |= 0;
+	
+	var canvas  = document.getElementById( id );
+	var context = canvas.getContext("2d");
+	var imageData;
+	
+	try {
+	  try {
+		imageData = context.getImageData( top_x, top_y, width, height );
+	  } catch(e) {
+	  
+		// NOTE: this part is supposedly only needed if you want to work with local files
+		// so it might be okay to remove the whole try/catch block and just use
+		// imageData = context.getImageData( top_x, top_y, width, height );
+		try {
+			netscape.security.PrivilegeManager.enablePrivilege("UniversalBrowserRead");
+			imageData = context.getImageData( top_x, top_y, width, height );
+		} catch(e) {
+			alert("Cannot access local image");
+			throw new Error("unable to access local image data: " + e);
+			return;
+		}
+	  }
+	} catch(e) {
+	  alert("Cannot access image");
+	  throw new Error("unable to access image data: " + e);
+	}
+			
+	var pixels = imageData.data;
+			
+	var x, y, i, p, yp, yi, yw, r_sum, g_sum, b_sum, a_sum, 
+	r_out_sum, g_out_sum, b_out_sum, a_out_sum,
+	r_in_sum, g_in_sum, b_in_sum, a_in_sum, 
+	pr, pg, pb, pa, rbs;
+			
+	var div = radius + radius + 1;
+	var w4 = width << 2;
+	var widthMinus1  = width - 1;
+	var heightMinus1 = height - 1;
+	var radiusPlus1  = radius + 1;
+	var sumFactor = radiusPlus1 * ( radiusPlus1 + 1 ) / 2;
+	
+	var stackStart = new BlurStack();
+	var stack = stackStart;
+	for ( i = 1; i < div; i++ )
+	{
+		stack = stack.next = new BlurStack();
+		if ( i == radiusPlus1 ) var stackEnd = stack;
+	}
+	stack.next = stackStart;
+	var stackIn = null;
+	var stackOut = null;
+	
+	yw = yi = 0;
+	
+	var mul_sum = mul_table[radius];
+	var shg_sum = shg_table[radius];
+	
+	for ( y = 0; y < height; y++ )
+	{
+		r_in_sum = g_in_sum = b_in_sum = a_in_sum = r_sum = g_sum = b_sum = a_sum = 0;
+		
+		r_out_sum = radiusPlus1 * ( pr = pixels[yi] );
+		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1] );
+		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2] );
+		a_out_sum = radiusPlus1 * ( pa = pixels[yi+3] );
+		
+		r_sum += sumFactor * pr;
+		g_sum += sumFactor * pg;
+		b_sum += sumFactor * pb;
+		a_sum += sumFactor * pa;
+		
+		stack = stackStart;
+		
+		for( i = 0; i < radiusPlus1; i++ )
+		{
+			stack.r = pr;
+			stack.g = pg;
+			stack.b = pb;
+			stack.a = pa;
+			stack = stack.next;
+		}
+		
+		for( i = 1; i < radiusPlus1; i++ )
+		{
+			p = yi + (( widthMinus1 < i ? widthMinus1 : i ) << 2 );
+			r_sum += ( stack.r = ( pr = pixels[p])) * ( rbs = radiusPlus1 - i );
+			g_sum += ( stack.g = ( pg = pixels[p+1])) * rbs;
+			b_sum += ( stack.b = ( pb = pixels[p+2])) * rbs;
+			a_sum += ( stack.a = ( pa = pixels[p+3])) * rbs;
+			
+			r_in_sum += pr;
+			g_in_sum += pg;
+			b_in_sum += pb;
+			a_in_sum += pa;
+			
+			stack = stack.next;
+		}
+		
+		
+		stackIn = stackStart;
+		stackOut = stackEnd;
+		for ( x = 0; x < width; x++ )
+		{
+			pixels[yi+3] = pa = (a_sum * mul_sum) >> shg_sum;
+			if ( pa != 0 )
+			{
+				pa = 255 / pa;
+				pixels[yi]   = ((r_sum * mul_sum) >> shg_sum) * pa;
+				pixels[yi+1] = ((g_sum * mul_sum) >> shg_sum) * pa;
+				pixels[yi+2] = ((b_sum * mul_sum) >> shg_sum) * pa;
+			} else {
+				pixels[yi] = pixels[yi+1] = pixels[yi+2] = 0;
+			}
+			
+			r_sum -= r_out_sum;
+			g_sum -= g_out_sum;
+			b_sum -= b_out_sum;
+			a_sum -= a_out_sum;
+			
+			r_out_sum -= stackIn.r;
+			g_out_sum -= stackIn.g;
+			b_out_sum -= stackIn.b;
+			a_out_sum -= stackIn.a;
+			
+			p =  ( yw + ( ( p = x + radius + 1 ) < widthMinus1 ? p : widthMinus1 ) ) << 2;
+			
+			r_in_sum += ( stackIn.r = pixels[p]);
+			g_in_sum += ( stackIn.g = pixels[p+1]);
+			b_in_sum += ( stackIn.b = pixels[p+2]);
+			a_in_sum += ( stackIn.a = pixels[p+3]);
+			
+			r_sum += r_in_sum;
+			g_sum += g_in_sum;
+			b_sum += b_in_sum;
+			a_sum += a_in_sum;
+			
+			stackIn = stackIn.next;
+			
+			r_out_sum += ( pr = stackOut.r );
+			g_out_sum += ( pg = stackOut.g );
+			b_out_sum += ( pb = stackOut.b );
+			a_out_sum += ( pa = stackOut.a );
+			
+			r_in_sum -= pr;
+			g_in_sum -= pg;
+			b_in_sum -= pb;
+			a_in_sum -= pa;
+			
+			stackOut = stackOut.next;
+
+			yi += 4;
+		}
+		yw += width;
+	}
+
+	
+	for ( x = 0; x < width; x++ )
+	{
+		g_in_sum = b_in_sum = a_in_sum = r_in_sum = g_sum = b_sum = a_sum = r_sum = 0;
+		
+		yi = x << 2;
+		r_out_sum = radiusPlus1 * ( pr = pixels[yi]);
+		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1]);
+		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2]);
+		a_out_sum = radiusPlus1 * ( pa = pixels[yi+3]);
+		
+		r_sum += sumFactor * pr;
+		g_sum += sumFactor * pg;
+		b_sum += sumFactor * pb;
+		a_sum += sumFactor * pa;
+		
+		stack = stackStart;
+		
+		for( i = 0; i < radiusPlus1; i++ )
+		{
+			stack.r = pr;
+			stack.g = pg;
+			stack.b = pb;
+			stack.a = pa;
+			stack = stack.next;
+		}
+		
+		yp = width;
+		
+		for( i = 1; i <= radius; i++ )
+		{
+			yi = ( yp + x ) << 2;
+			
+			r_sum += ( stack.r = ( pr = pixels[yi])) * ( rbs = radiusPlus1 - i );
+			g_sum += ( stack.g = ( pg = pixels[yi+1])) * rbs;
+			b_sum += ( stack.b = ( pb = pixels[yi+2])) * rbs;
+			a_sum += ( stack.a = ( pa = pixels[yi+3])) * rbs;
+		   
+			r_in_sum += pr;
+			g_in_sum += pg;
+			b_in_sum += pb;
+			a_in_sum += pa;
+			
+			stack = stack.next;
+		
+			if( i < heightMinus1 )
+			{
+				yp += width;
+			}
+		}
+		
+		yi = x;
+		stackIn = stackStart;
+		stackOut = stackEnd;
+		for ( y = 0; y < height; y++ )
+		{
+			p = yi << 2;
+			pixels[p+3] = pa = (a_sum * mul_sum) >> shg_sum;
+			if ( pa > 0 )
+			{
+				pa = 255 / pa;
+				pixels[p]   = ((r_sum * mul_sum) >> shg_sum ) * pa;
+				pixels[p+1] = ((g_sum * mul_sum) >> shg_sum ) * pa;
+				pixels[p+2] = ((b_sum * mul_sum) >> shg_sum ) * pa;
+			} else {
+				pixels[p] = pixels[p+1] = pixels[p+2] = 0;
+			}
+			
+			r_sum -= r_out_sum;
+			g_sum -= g_out_sum;
+			b_sum -= b_out_sum;
+			a_sum -= a_out_sum;
+		   
+			r_out_sum -= stackIn.r;
+			g_out_sum -= stackIn.g;
+			b_out_sum -= stackIn.b;
+			a_out_sum -= stackIn.a;
+			
+			p = ( x + (( ( p = y + radiusPlus1) < heightMinus1 ? p : heightMinus1 ) * width )) << 2;
+			
+			r_sum += ( r_in_sum += ( stackIn.r = pixels[p]));
+			g_sum += ( g_in_sum += ( stackIn.g = pixels[p+1]));
+			b_sum += ( b_in_sum += ( stackIn.b = pixels[p+2]));
+			a_sum += ( a_in_sum += ( stackIn.a = pixels[p+3]));
+		   
+			stackIn = stackIn.next;
+			
+			r_out_sum += ( pr = stackOut.r );
+			g_out_sum += ( pg = stackOut.g );
+			b_out_sum += ( pb = stackOut.b );
+			a_out_sum += ( pa = stackOut.a );
+			
+			r_in_sum -= pr;
+			g_in_sum -= pg;
+			b_in_sum -= pb;
+			a_in_sum -= pa;
+			
+			stackOut = stackOut.next;
+			
+			yi += width;
+		}
+	}
+	
+	context.putImageData( imageData, top_x, top_y );
+	
+}
+
+
+function stackBlurCanvasRGB( id, top_x, top_y, width, height, radius )
+{
+	if ( isNaN(radius) || radius < 1 ) return;
+	radius |= 0;
+	
+	var canvas  = document.getElementById( id );
+	var context = canvas.getContext("2d");
+	var imageData;
+	
+	try {
+	  try {
+		imageData = context.getImageData( top_x, top_y, width, height );
+	  } catch(e) {
+	  
+		// NOTE: this part is supposedly only needed if you want to work with local files
+		// so it might be okay to remove the whole try/catch block and just use
+		// imageData = context.getImageData( top_x, top_y, width, height );
+		try {
+			netscape.security.PrivilegeManager.enablePrivilege("UniversalBrowserRead");
+			imageData = context.getImageData( top_x, top_y, width, height );
+		} catch(e) {
+			alert("Cannot access local image");
+			throw new Error("unable to access local image data: " + e);
+			return;
+		}
+	  }
+	} catch(e) {
+	  alert("Cannot access image");
+	  throw new Error("unable to access image data: " + e);
+	}
+			
+	var pixels = imageData.data;
+			
+	var x, y, i, p, yp, yi, yw, r_sum, g_sum, b_sum,
+	r_out_sum, g_out_sum, b_out_sum,
+	r_in_sum, g_in_sum, b_in_sum,
+	pr, pg, pb, rbs;
+			
+	var div = radius + radius + 1;
+	var w4 = width << 2;
+	var widthMinus1  = width - 1;
+	var heightMinus1 = height - 1;
+	var radiusPlus1  = radius + 1;
+	var sumFactor = radiusPlus1 * ( radiusPlus1 + 1 ) / 2;
+	
+	var stackStart = new BlurStack();
+	var stack = stackStart;
+	for ( i = 1; i < div; i++ )
+	{
+		stack = stack.next = new BlurStack();
+		if ( i == radiusPlus1 ) var stackEnd = stack;
+	}
+	stack.next = stackStart;
+	var stackIn = null;
+	var stackOut = null;
+	
+	yw = yi = 0;
+	
+	var mul_sum = mul_table[radius];
+	var shg_sum = shg_table[radius];
+	
+	for ( y = 0; y < height; y++ )
+	{
+		r_in_sum = g_in_sum = b_in_sum = r_sum = g_sum = b_sum = 0;
+		
+		r_out_sum = radiusPlus1 * ( pr = pixels[yi] );
+		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1] );
+		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2] );
+		
+		r_sum += sumFactor * pr;
+		g_sum += sumFactor * pg;
+		b_sum += sumFactor * pb;
+		
+		stack = stackStart;
+		
+		for( i = 0; i < radiusPlus1; i++ )
+		{
+			stack.r = pr;
+			stack.g = pg;
+			stack.b = pb;
+			stack = stack.next;
+		}
+		
+		for( i = 1; i < radiusPlus1; i++ )
+		{
+			p = yi + (( widthMinus1 < i ? widthMinus1 : i ) << 2 );
+			r_sum += ( stack.r = ( pr = pixels[p])) * ( rbs = radiusPlus1 - i );
+			g_sum += ( stack.g = ( pg = pixels[p+1])) * rbs;
+			b_sum += ( stack.b = ( pb = pixels[p+2])) * rbs;
+			
+			r_in_sum += pr;
+			g_in_sum += pg;
+			b_in_sum += pb;
+			
+			stack = stack.next;
+		}
+		
+		
+		stackIn = stackStart;
+		stackOut = stackEnd;
+		for ( x = 0; x < width; x++ )
+		{
+			pixels[yi]   = (r_sum * mul_sum) >> shg_sum;
+			pixels[yi+1] = (g_sum * mul_sum) >> shg_sum;
+			pixels[yi+2] = (b_sum * mul_sum) >> shg_sum;
+			
+			r_sum -= r_out_sum;
+			g_sum -= g_out_sum;
+			b_sum -= b_out_sum;
+			
+			r_out_sum -= stackIn.r;
+			g_out_sum -= stackIn.g;
+			b_out_sum -= stackIn.b;
+			
+			p =  ( yw + ( ( p = x + radius + 1 ) < widthMinus1 ? p : widthMinus1 ) ) << 2;
+			
+			r_in_sum += ( stackIn.r = pixels[p]);
+			g_in_sum += ( stackIn.g = pixels[p+1]);
+			b_in_sum += ( stackIn.b = pixels[p+2]);
+			
+			r_sum += r_in_sum;
+			g_sum += g_in_sum;
+			b_sum += b_in_sum;
+			
+			stackIn = stackIn.next;
+			
+			r_out_sum += ( pr = stackOut.r );
+			g_out_sum += ( pg = stackOut.g );
+			b_out_sum += ( pb = stackOut.b );
+			
+			r_in_sum -= pr;
+			g_in_sum -= pg;
+			b_in_sum -= pb;
+			
+			stackOut = stackOut.next;
+
+			yi += 4;
+		}
+		yw += width;
+	}
+
+	
+	for ( x = 0; x < width; x++ )
+	{
+		g_in_sum = b_in_sum = r_in_sum = g_sum = b_sum = r_sum = 0;
+		
+		yi = x << 2;
+		r_out_sum = radiusPlus1 * ( pr = pixels[yi]);
+		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1]);
+		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2]);
+		
+		r_sum += sumFactor * pr;
+		g_sum += sumFactor * pg;
+		b_sum += sumFactor * pb;
+		
+		stack = stackStart;
+		
+		for( i = 0; i < radiusPlus1; i++ )
+		{
+			stack.r = pr;
+			stack.g = pg;
+			stack.b = pb;
+			stack = stack.next;
+		}
+		
+		yp = width;
+		
+		for( i = 1; i <= radius; i++ )
+		{
+			yi = ( yp + x ) << 2;
+			
+			r_sum += ( stack.r = ( pr = pixels[yi])) * ( rbs = radiusPlus1 - i );
+			g_sum += ( stack.g = ( pg = pixels[yi+1])) * rbs;
+			b_sum += ( stack.b = ( pb = pixels[yi+2])) * rbs;
+			
+			r_in_sum += pr;
+			g_in_sum += pg;
+			b_in_sum += pb;
+			
+			stack = stack.next;
+		
+			if( i < heightMinus1 )
+			{
+				yp += width;
+			}
+		}
+		
+		yi = x;
+		stackIn = stackStart;
+		stackOut = stackEnd;
+		for ( y = 0; y < height; y++ )
+		{
+			p = yi << 2;
+			pixels[p]   = (r_sum * mul_sum) >> shg_sum;
+			pixels[p+1] = (g_sum * mul_sum) >> shg_sum;
+			pixels[p+2] = (b_sum * mul_sum) >> shg_sum;
+			
+			r_sum -= r_out_sum;
+			g_sum -= g_out_sum;
+			b_sum -= b_out_sum;
+			
+			r_out_sum -= stackIn.r;
+			g_out_sum -= stackIn.g;
+			b_out_sum -= stackIn.b;
+			
+			p = ( x + (( ( p = y + radiusPlus1) < heightMinus1 ? p : heightMinus1 ) * width )) << 2;
+			
+			r_sum += ( r_in_sum += ( stackIn.r = pixels[p]));
+			g_sum += ( g_in_sum += ( stackIn.g = pixels[p+1]));
+			b_sum += ( b_in_sum += ( stackIn.b = pixels[p+2]));
+			
+			stackIn = stackIn.next;
+			
+			r_out_sum += ( pr = stackOut.r );
+			g_out_sum += ( pg = stackOut.g );
+			b_out_sum += ( pb = stackOut.b );
+			
+			r_in_sum -= pr;
+			g_in_sum -= pg;
+			b_in_sum -= pb;
+			
+			stackOut = stackOut.next;
+			
+			yi += width;
+		}
+	}
+	
+	context.putImageData( imageData, top_x, top_y );
+	
+}
+
+function BlurStack()
+{
+	this.r = 0;
+	this.g = 0;
+	this.b = 0;
+	this.a = 0;
+	this.next = null;
+}
\ No newline at end of file
diff --git a/dammit/viewer/static/canvg.js b/dammit/viewer/static/canvg.js
new file mode 100644
index 00000000..7e98e475
--- /dev/null
+++ b/dammit/viewer/static/canvg.js
@@ -0,0 +1,2841 @@
+/*
+ * canvg.js - Javascript SVG parser and renderer on Canvas
+ * MIT Licensed 
+ * Gabe Lerner (gabelerner@gmail.com)
+ * http://code.google.com/p/canvg/
+ *
+ * Requires: rgbcolor.js - http://www.phpied.com/rgb-color-parser-in-javascript/
+ */
+(function(){
+	// canvg(target, s)
+	// empty parameters: replace all 'svg' elements on page with 'canvas' elements
+	// target: canvas element or the id of a canvas element
+	// s: svg string, url to svg file, or xml document
+	// opts: optional hash of options
+	//		 ignoreMouse: true => ignore mouse events
+	//		 ignoreAnimation: true => ignore animations
+	//		 ignoreDimensions: true => does not try to resize canvas
+	//		 ignoreClear: true => does not clear canvas
+	//		 offsetX: int => draws at a x offset
+	//		 offsetY: int => draws at a y offset
+	//		 scaleWidth: int => scales horizontally to width
+	//		 scaleHeight: int => scales vertically to height
+	//		 renderCallback: function => will call the function after the first render is completed
+	//		 forceRedraw: function => will call the function on every frame, if it returns true, will redraw
+	this.canvg = function (target, s, opts) {
+		// no parameters
+		if (target == null && s == null && opts == null) {
+			var svgTags = document.getElementsByTagName('svg');
+			for (var i=0; i<svgTags.length; i++) {
+				var svgTag = svgTags[i];
+				var c = document.createElement('canvas');
+				c.width = svgTag.clientWidth;
+				c.height = svgTag.clientHeight;
+				svgTag.parentNode.insertBefore(c, svgTag);
+				svgTag.parentNode.removeChild(svgTag);
+				var div = document.createElement('div');
+				div.appendChild(svgTag);
+				canvg(c, div.innerHTML);
+			}
+			return;
+		}	
+		opts = opts || {};
+	
+		if (typeof target == 'string') {
+			target = document.getElementById(target);
+		}
+		
+		// store class on canvas
+		if (target.svg != null) target.svg.stop();
+		var svg = build();
+		// on i.e. 8 for flash canvas, we can't assign the property so check for it
+		if (!(target.childNodes.length == 1 && target.childNodes[0].nodeName == 'OBJECT')) target.svg = svg;
+		svg.opts = opts;
+		
+		var ctx = target.getContext('2d');
+		if (typeof(s.documentElement) != 'undefined') {
+			// load from xml doc
+			svg.loadXmlDoc(ctx, s);
+		}
+		else if (s.substr(0,1) == '<') {
+			// load from xml string
+			svg.loadXml(ctx, s);
+		}
+		else {
+			// load from url
+			svg.load(ctx, s);
+		}
+	}
+
+	function build() {
+		var svg = { };
+		
+		svg.FRAMERATE = 30;
+		svg.MAX_VIRTUAL_PIXELS = 30000;
+		
+		// globals
+		svg.init = function(ctx) {
+			var uniqueId = 0;
+			svg.UniqueId = function () { uniqueId++; return 'canvg' + uniqueId;	};
+			svg.Definitions = {};
+			svg.Styles = {};
+			svg.Animations = [];
+			svg.Images = [];
+			svg.ctx = ctx;
+			svg.ViewPort = new (function () {
+				this.viewPorts = [];
+				this.Clear = function() { this.viewPorts = []; }
+				this.SetCurrent = function(width, height) { this.viewPorts.push({ width: width, height: height }); }
+				this.RemoveCurrent = function() { this.viewPorts.pop(); }
+				this.Current = function() { return this.viewPorts[this.viewPorts.length - 1]; }
+				this.width = function() { return this.Current().width; }
+				this.height = function() { return this.Current().height; }
+				this.ComputeSize = function(d) {
+					if (d != null && typeof(d) == 'number') return d;
+					if (d == 'x') return this.width();
+					if (d == 'y') return this.height();
+					return Math.sqrt(Math.pow(this.width(), 2) + Math.pow(this.height(), 2)) / Math.sqrt(2);			
+				}
+			});
+		}
+		svg.init();
+		
+		// images loaded
+		svg.ImagesLoaded = function() { 
+			for (var i=0; i<svg.Images.length; i++) {
+				if (!svg.Images[i].loaded) return false;
+			}
+			return true;
+		}
+
+		// trim
+		svg.trim = function(s) { return s.replace(/^\s+|\s+$/g, ''); }
+		
+		// compress spaces
+		svg.compressSpaces = function(s) { return s.replace(/[\s\r\t\n]+/gm,' '); }
+		
+		// ajax
+		svg.ajax = function(url) {
+			var AJAX;
+			if(window.XMLHttpRequest){AJAX=new XMLHttpRequest();}
+			else{AJAX=new ActiveXObject('Microsoft.XMLHTTP');}
+			if(AJAX){
+			   AJAX.open('GET',url,false);
+			   AJAX.send(null);
+			   return AJAX.responseText;
+			}
+			return null;
+		} 
+		
+		// parse xml
+		svg.parseXml = function(xml) {
+			if (window.DOMParser)
+			{
+				var parser = new DOMParser();
+				return parser.parseFromString(xml, 'text/xml');
+			}
+			else 
+			{
+				xml = xml.replace(/<!DOCTYPE svg[^>]*>/, '');
+				var xmlDoc = new ActiveXObject('Microsoft.XMLDOM');
+				xmlDoc.async = 'false';
+				xmlDoc.loadXML(xml); 
+				return xmlDoc;
+			}		
+		}
+		
+		svg.Property = function(name, value) {
+			this.name = name;
+			this.value = value;
+		}	
+			svg.Property.prototype.getValue = function() {
+				return this.value;
+			}
+		
+			svg.Property.prototype.hasValue = function() {
+				return (this.value != null && this.value !== '');
+			}
+							
+			// return the numerical value of the property
+			svg.Property.prototype.numValue = function() {
+				if (!this.hasValue()) return 0;
+				
+				var n = parseFloat(this.value);
+				if ((this.value + '').match(/%$/)) {
+					n = n / 100.0;
+				}
+				return n;
+			}
+			
+			svg.Property.prototype.valueOrDefault = function(def) {
+				if (this.hasValue()) return this.value;
+				return def;
+			}
+			
+			svg.Property.prototype.numValueOrDefault = function(def) {
+				if (this.hasValue()) return this.numValue();
+				return def;
+			}
+			
+			// color extensions
+				// augment the current color value with the opacity
+				svg.Property.prototype.addOpacity = function(opacity) {
+					var newValue = this.value;
+					if (opacity != null && opacity != '' && typeof(this.value)=='string') { // can only add opacity to colors, not patterns
+						var color = new RGBColor(this.value);
+						if (color.ok) {
+							newValue = 'rgba(' + color.r + ', ' + color.g + ', ' + color.b + ', ' + opacity + ')';
+						}
+					}
+					return new svg.Property(this.name, newValue);
+				}
+			
+			// definition extensions
+				// get the definition from the definitions table
+				svg.Property.prototype.getDefinition = function() {
+					var name = this.value.match(/#([^\)'"]+)/);
+					if (name) { name = name[1]; }
+					if (!name) { name = this.value; }
+					return svg.Definitions[name];
+				}
+				
+				svg.Property.prototype.isUrlDefinition = function() {
+					return this.value.indexOf('url(') == 0
+				}
+				
+				svg.Property.prototype.getFillStyleDefinition = function(e, opacityProp) {
+					var def = this.getDefinition();
+					
+					// gradient
+					if (def != null && def.createGradient) {
+						return def.createGradient(svg.ctx, e, opacityProp);
+					}
+					
+					// pattern
+					if (def != null && def.createPattern) {
+						if (def.getHrefAttribute().hasValue()) {
+							var pt = def.attribute('patternTransform');
+							def = def.getHrefAttribute().getDefinition();
+							if (pt.hasValue()) { def.attribute('patternTransform', true).value = pt.value; }
+						}
+						return def.createPattern(svg.ctx, e);
+					}
+					
+					return null;
+				}
+			
+			// length extensions
+				svg.Property.prototype.getDPI = function(viewPort) {
+					return 96.0; // TODO: compute?
+				}
+				
+				svg.Property.prototype.getEM = function(viewPort) {
+					var em = 12;
+					
+					var fontSize = new svg.Property('fontSize', svg.Font.Parse(svg.ctx.font).fontSize);
+					if (fontSize.hasValue()) em = fontSize.toPixels(viewPort);
+					
+					return em;
+				}
+				
+				svg.Property.prototype.getUnits = function() {
+					var s = this.value+'';
+					return s.replace(/[0-9\.\-]/g,'');
+				}
+			
+				// get the length as pixels
+				svg.Property.prototype.toPixels = function(viewPort, processPercent) {
+					if (!this.hasValue()) return 0;
+					var s = this.value+'';
+					if (s.match(/em$/)) return this.numValue() * this.getEM(viewPort);
+					if (s.match(/ex$/)) return this.numValue() * this.getEM(viewPort) / 2.0;
+					if (s.match(/px$/)) return this.numValue();
+					if (s.match(/pt$/)) return this.numValue() * this.getDPI(viewPort) * (1.0 / 72.0);
+					if (s.match(/pc$/)) return this.numValue() * 15;
+					if (s.match(/cm$/)) return this.numValue() * this.getDPI(viewPort) / 2.54;
+					if (s.match(/mm$/)) return this.numValue() * this.getDPI(viewPort) / 25.4;
+					if (s.match(/in$/)) return this.numValue() * this.getDPI(viewPort);
+					if (s.match(/%$/)) return this.numValue() * svg.ViewPort.ComputeSize(viewPort);
+					var n = this.numValue();
+					if (processPercent && n < 1.0) return n * svg.ViewPort.ComputeSize(viewPort);
+					return n;
+				}
+
+			// time extensions
+				// get the time as milliseconds
+				svg.Property.prototype.toMilliseconds = function() {
+					if (!this.hasValue()) return 0;
+					var s = this.value+'';
+					if (s.match(/s$/)) return this.numValue() * 1000;
+					if (s.match(/ms$/)) return this.numValue();
+					return this.numValue();
+				}
+			
+			// angle extensions
+				// get the angle as radians
+				svg.Property.prototype.toRadians = function() {
+					if (!this.hasValue()) return 0;
+					var s = this.value+'';
+					if (s.match(/deg$/)) return this.numValue() * (Math.PI / 180.0);
+					if (s.match(/grad$/)) return this.numValue() * (Math.PI / 200.0);
+					if (s.match(/rad$/)) return this.numValue();
+					return this.numValue() * (Math.PI / 180.0);
+				}
+		
+		// fonts
+		svg.Font = new (function() {
+			this.Styles = 'normal|italic|oblique|inherit';
+			this.Variants = 'normal|small-caps|inherit';
+			this.Weights = 'normal|bold|bolder|lighter|100|200|300|400|500|600|700|800|900|inherit';
+			
+			this.CreateFont = function(fontStyle, fontVariant, fontWeight, fontSize, fontFamily, inherit) { 
+				var f = inherit != null ? this.Parse(inherit) : this.CreateFont('', '', '', '', '', svg.ctx.font);
+				return { 
+					fontFamily: fontFamily || f.fontFamily, 
+					fontSize: fontSize || f.fontSize, 
+					fontStyle: fontStyle || f.fontStyle, 
+					fontWeight: fontWeight || f.fontWeight, 
+					fontVariant: fontVariant || f.fontVariant,
+					toString: function () { return [this.fontStyle, this.fontVariant, this.fontWeight, this.fontSize, this.fontFamily].join(' ') } 
+				} 
+			}
+			
+			var that = this;
+			this.Parse = function(s) {
+				var f = {};
+				var d = svg.trim(svg.compressSpaces(s || '')).split(' ');
+				var set = { fontSize: false, fontStyle: false, fontWeight: false, fontVariant: false }
+				var ff = '';
+				for (var i=0; i<d.length; i++) {
+					if (!set.fontStyle && that.Styles.indexOf(d[i]) != -1) { if (d[i] != 'inherit') f.fontStyle = d[i]; set.fontStyle = true; }
+					else if (!set.fontVariant && that.Variants.indexOf(d[i]) != -1) { if (d[i] != 'inherit') f.fontVariant = d[i]; set.fontStyle = set.fontVariant = true;	}
+					else if (!set.fontWeight && that.Weights.indexOf(d[i]) != -1) {	if (d[i] != 'inherit') f.fontWeight = d[i]; set.fontStyle = set.fontVariant = set.fontWeight = true; }
+					else if (!set.fontSize) { if (d[i] != 'inherit') f.fontSize = d[i].split('/')[0]; set.fontStyle = set.fontVariant = set.fontWeight = set.fontSize = true; }
+					else { if (d[i] != 'inherit') ff += d[i]; }
+				} if (ff != '') f.fontFamily = ff;
+				return f;
+			}
+		});
+		
+		// points and paths
+		svg.ToNumberArray = function(s) {
+			var a = svg.trim(svg.compressSpaces((s || '').replace(/,/g, ' '))).split(' ');
+			for (var i=0; i<a.length; i++) {
+				a[i] = parseFloat(a[i]);
+			}
+			return a;
+		}		
+		svg.Point = function(x, y) {
+			this.x = x;
+			this.y = y;
+		}	
+			svg.Point.prototype.angleTo = function(p) {
+				return Math.atan2(p.y - this.y, p.x - this.x);
+			}
+			
+			svg.Point.prototype.applyTransform = function(v) {
+				var xp = this.x * v[0] + this.y * v[2] + v[4];
+				var yp = this.x * v[1] + this.y * v[3] + v[5];
+				this.x = xp;
+				this.y = yp;
+			}
+
+		svg.CreatePoint = function(s) {
+			var a = svg.ToNumberArray(s);
+			return new svg.Point(a[0], a[1]);
+		}
+		svg.CreatePath = function(s) {
+			var a = svg.ToNumberArray(s);
+			var path = [];
+			for (var i=0; i<a.length; i+=2) {
+				path.push(new svg.Point(a[i], a[i+1]));
+			}
+			return path;
+		}
+		
+		// bounding box
+		svg.BoundingBox = function(x1, y1, x2, y2) { // pass in initial points if you want
+			this.x1 = Number.NaN;
+			this.y1 = Number.NaN;
+			this.x2 = Number.NaN;
+			this.y2 = Number.NaN;
+			
+			this.x = function() { return this.x1; }
+			this.y = function() { return this.y1; }
+			this.width = function() { return this.x2 - this.x1; }
+			this.height = function() { return this.y2 - this.y1; }
+			
+			this.addPoint = function(x, y) {	
+				if (x != null) {
+					if (isNaN(this.x1) || isNaN(this.x2)) {
+						this.x1 = x;
+						this.x2 = x;
+					}
+					if (x < this.x1) this.x1 = x;
+					if (x > this.x2) this.x2 = x;
+				}
+			
+				if (y != null) {
+					if (isNaN(this.y1) || isNaN(this.y2)) {
+						this.y1 = y;
+						this.y2 = y;
+					}
+					if (y < this.y1) this.y1 = y;
+					if (y > this.y2) this.y2 = y;
+				}
+			}			
+			this.addX = function(x) { this.addPoint(x, null); }
+			this.addY = function(y) { this.addPoint(null, y); }
+			
+			this.addBoundingBox = function(bb) {
+				this.addPoint(bb.x1, bb.y1);
+				this.addPoint(bb.x2, bb.y2);
+			}
+			
+			this.addQuadraticCurve = function(p0x, p0y, p1x, p1y, p2x, p2y) {
+				var cp1x = p0x + 2/3 * (p1x - p0x); // CP1 = QP0 + 2/3 *(QP1-QP0)
+				var cp1y = p0y + 2/3 * (p1y - p0y); // CP1 = QP0 + 2/3 *(QP1-QP0)
+				var cp2x = cp1x + 1/3 * (p2x - p0x); // CP2 = CP1 + 1/3 *(QP2-QP0)
+				var cp2y = cp1y + 1/3 * (p2y - p0y); // CP2 = CP1 + 1/3 *(QP2-QP0)
+				this.addBezierCurve(p0x, p0y, cp1x, cp2x, cp1y,	cp2y, p2x, p2y);
+			}
+			
+			this.addBezierCurve = function(p0x, p0y, p1x, p1y, p2x, p2y, p3x, p3y) {
+				// from http://blog.hackers-cafe.net/2009/06/how-to-calculate-bezier-curves-bounding.html
+				var p0 = [p0x, p0y], p1 = [p1x, p1y], p2 = [p2x, p2y], p3 = [p3x, p3y];
+				this.addPoint(p0[0], p0[1]);
+				this.addPoint(p3[0], p3[1]);
+				
+				for (i=0; i<=1; i++) {
+					var f = function(t) { 
+						return Math.pow(1-t, 3) * p0[i]
+						+ 3 * Math.pow(1-t, 2) * t * p1[i]
+						+ 3 * (1-t) * Math.pow(t, 2) * p2[i]
+						+ Math.pow(t, 3) * p3[i];
+					}
+					
+					var b = 6 * p0[i] - 12 * p1[i] + 6 * p2[i];
+					var a = -3 * p0[i] + 9 * p1[i] - 9 * p2[i] + 3 * p3[i];
+					var c = 3 * p1[i] - 3 * p0[i];
+					
+					if (a == 0) {
+						if (b == 0) continue;
+						var t = -c / b;
+						if (0 < t && t < 1) {
+							if (i == 0) this.addX(f(t));
+							if (i == 1) this.addY(f(t));
+						}
+						continue;
+					}
+					
+					var b2ac = Math.pow(b, 2) - 4 * c * a;
+					if (b2ac < 0) continue;
+					var t1 = (-b + Math.sqrt(b2ac)) / (2 * a);
+					if (0 < t1 && t1 < 1) {
+						if (i == 0) this.addX(f(t1));
+						if (i == 1) this.addY(f(t1));
+					}
+					var t2 = (-b - Math.sqrt(b2ac)) / (2 * a);
+					if (0 < t2 && t2 < 1) {
+						if (i == 0) this.addX(f(t2));
+						if (i == 1) this.addY(f(t2));
+					}
+				}
+			}
+			
+			this.isPointInBox = function(x, y) {
+				return (this.x1 <= x && x <= this.x2 && this.y1 <= y && y <= this.y2);
+			}
+			
+			this.addPoint(x1, y1);
+			this.addPoint(x2, y2);
+		}
+		
+		// transforms
+		svg.Transform = function(v) {	
+			var that = this;
+			this.Type = {}
+		
+			// translate
+			this.Type.translate = function(s) {
+				this.p = svg.CreatePoint(s);			
+				this.apply = function(ctx) {
+					ctx.translate(this.p.x || 0.0, this.p.y || 0.0);
+				}
+				this.unapply = function(ctx) {
+					ctx.translate(-1.0 * this.p.x || 0.0, -1.0 * this.p.y || 0.0);
+				}
+				this.applyToPoint = function(p) {
+					p.applyTransform([1, 0, 0, 1, this.p.x || 0.0, this.p.y || 0.0]);
+				}
+			}
+			
+			// rotate
+			this.Type.rotate = function(s) {
+				var a = svg.ToNumberArray(s);
+				this.angle = new svg.Property('angle', a[0]);
+				this.cx = a[1] || 0;
+				this.cy = a[2] || 0;
+				this.apply = function(ctx) {
+					ctx.translate(this.cx, this.cy);
+					ctx.rotate(this.angle.toRadians());
+					ctx.translate(-this.cx, -this.cy);
+				}
+				this.unapply = function(ctx) {
+					ctx.translate(this.cx, this.cy);
+					ctx.rotate(-1.0 * this.angle.toRadians());
+					ctx.translate(-this.cx, -this.cy);
+				}
+				this.applyToPoint = function(p) {
+					var a = this.angle.toRadians();
+					p.applyTransform([1, 0, 0, 1, this.p.x || 0.0, this.p.y || 0.0]);
+					p.applyTransform([Math.cos(a), Math.sin(a), -Math.sin(a), Math.cos(a), 0, 0]);
+					p.applyTransform([1, 0, 0, 1, -this.p.x || 0.0, -this.p.y || 0.0]);
+				}			
+			}
+			
+			this.Type.scale = function(s) {
+				this.p = svg.CreatePoint(s);
+				this.apply = function(ctx) {
+					ctx.scale(this.p.x || 1.0, this.p.y || this.p.x || 1.0);
+				}
+				this.unapply = function(ctx) {
+					ctx.scale(1.0 / this.p.x || 1.0, 1.0 / this.p.y || this.p.x || 1.0);
+				}
+				this.applyToPoint = function(p) {
+					p.applyTransform([this.p.x || 0.0, 0, 0, this.p.y || 0.0, 0, 0]);
+				}				
+			}
+			
+			this.Type.matrix = function(s) {
+				this.m = svg.ToNumberArray(s);
+				this.apply = function(ctx) {
+					ctx.transform(this.m[0], this.m[1], this.m[2], this.m[3], this.m[4], this.m[5]);
+				}
+				this.applyToPoint = function(p) {
+					p.applyTransform(this.m);
+				}					
+			}
+			
+			this.Type.SkewBase = function(s) {
+				this.base = that.Type.matrix;
+				this.base(s);
+				this.angle = new svg.Property('angle', s);
+			}
+			this.Type.SkewBase.prototype = new this.Type.matrix;
+			
+			this.Type.skewX = function(s) {
+				this.base = that.Type.SkewBase;
+				this.base(s);
+				this.m = [1, 0, Math.tan(this.angle.toRadians()), 1, 0, 0];
+			}
+			this.Type.skewX.prototype = new this.Type.SkewBase;
+			
+			this.Type.skewY = function(s) {
+				this.base = that.Type.SkewBase;
+				this.base(s);
+				this.m = [1, Math.tan(this.angle.toRadians()), 0, 1, 0, 0];
+			}
+			this.Type.skewY.prototype = new this.Type.SkewBase;
+		
+			this.transforms = [];
+			
+			this.apply = function(ctx) {
+				for (var i=0; i<this.transforms.length; i++) {
+					this.transforms[i].apply(ctx);
+				}
+			}
+			
+			this.unapply = function(ctx) {
+				for (var i=this.transforms.length-1; i>=0; i--) {
+					this.transforms[i].unapply(ctx);
+				}
+			}
+			
+			this.applyToPoint = function(p) {
+				for (var i=0; i<this.transforms.length; i++) {
+					this.transforms[i].applyToPoint(p);
+				}
+			}
+			
+			var data = svg.trim(svg.compressSpaces(v)).replace(/\)(\s?,\s?)/g,') ').split(/\s(?=[a-z])/);
+			for (var i=0; i<data.length; i++) {
+				var type = svg.trim(data[i].split('(')[0]);
+				var s = data[i].split('(')[1].replace(')','');
+				var transform = new this.Type[type](s);
+				transform.type = type;
+				this.transforms.push(transform);
+			}
+		}
+		
+		// aspect ratio
+		svg.AspectRatio = function(ctx, aspectRatio, width, desiredWidth, height, desiredHeight, minX, minY, refX, refY) {
+			// aspect ratio - http://www.w3.org/TR/SVG/coords.html#PreserveAspectRatioAttribute
+			aspectRatio = svg.compressSpaces(aspectRatio);
+			aspectRatio = aspectRatio.replace(/^defer\s/,''); // ignore defer
+			var align = aspectRatio.split(' ')[0] || 'xMidYMid';
+			var meetOrSlice = aspectRatio.split(' ')[1] || 'meet';					
+	
+			// calculate scale
+			var scaleX = width / desiredWidth;
+			var scaleY = height / desiredHeight;
+			var scaleMin = Math.min(scaleX, scaleY);
+			var scaleMax = Math.max(scaleX, scaleY);
+			if (meetOrSlice == 'meet') { desiredWidth *= scaleMin; desiredHeight *= scaleMin; }
+			if (meetOrSlice == 'slice') { desiredWidth *= scaleMax; desiredHeight *= scaleMax; }	
+			
+			refX = new svg.Property('refX', refX);
+			refY = new svg.Property('refY', refY);
+			if (refX.hasValue() && refY.hasValue()) {				
+				ctx.translate(-scaleMin * refX.toPixels('x'), -scaleMin * refY.toPixels('y'));
+			} 
+			else {					
+				// align
+				if (align.match(/^xMid/) && ((meetOrSlice == 'meet' && scaleMin == scaleY) || (meetOrSlice == 'slice' && scaleMax == scaleY))) ctx.translate(width / 2.0 - desiredWidth / 2.0, 0); 
+				if (align.match(/YMid$/) && ((meetOrSlice == 'meet' && scaleMin == scaleX) || (meetOrSlice == 'slice' && scaleMax == scaleX))) ctx.translate(0, height / 2.0 - desiredHeight / 2.0); 
+				if (align.match(/^xMax/) && ((meetOrSlice == 'meet' && scaleMin == scaleY) || (meetOrSlice == 'slice' && scaleMax == scaleY))) ctx.translate(width - desiredWidth, 0); 
+				if (align.match(/YMax$/) && ((meetOrSlice == 'meet' && scaleMin == scaleX) || (meetOrSlice == 'slice' && scaleMax == scaleX))) ctx.translate(0, height - desiredHeight); 
+			}
+			
+			// scale
+			if (align == 'none') ctx.scale(scaleX, scaleY);
+			else if (meetOrSlice == 'meet') ctx.scale(scaleMin, scaleMin); 
+			else if (meetOrSlice == 'slice') ctx.scale(scaleMax, scaleMax); 	
+			
+			// translate
+			ctx.translate(minX == null ? 0 : -minX, minY == null ? 0 : -minY);			
+		}
+		
+		// elements
+		svg.Element = {}
+		
+		svg.EmptyProperty = new svg.Property('EMPTY', '');
+		
+		svg.Element.ElementBase = function(node) {	
+			this.attributes = {};
+			this.styles = {};
+			this.children = [];
+			
+			// get or create attribute
+			this.attribute = function(name, createIfNotExists) {
+				var a = this.attributes[name];
+				if (a != null) return a;
+							
+				if (createIfNotExists == true) { a = new svg.Property(name, ''); this.attributes[name] = a; }
+				return a || svg.EmptyProperty;
+			}
+			
+			this.getHrefAttribute = function() {
+				for (var a in this.attributes) { 
+					if (a.match(/:href$/)) { 
+						return this.attributes[a]; 
+					} 
+				}
+				return svg.EmptyProperty;
+			}
+			
+			// get or create style, crawls up node tree
+			this.style = function(name, createIfNotExists) {
+				var s = this.styles[name];
+				if (s != null) return s;
+				
+				var a = this.attribute(name);
+				if (a != null && a.hasValue()) {
+					this.styles[name] = a; // move up to me to cache
+					return a;
+				}
+				
+				var p = this.parent;
+				if (p != null) {
+					var ps = p.style(name);
+					if (ps != null && ps.hasValue()) {
+						return ps;
+					}
+				}
+					
+				if (createIfNotExists == true) { s = new svg.Property(name, ''); this.styles[name] = s; }
+				return s || svg.EmptyProperty;
+			}
+			
+			// base render
+			this.render = function(ctx) {
+				// don't render display=none
+				if (this.style('display').value == 'none') return;
+				
+				// don't render visibility=hidden
+				if (this.attribute('visibility').value == 'hidden') return;
+			
+				ctx.save();
+				if (this.attribute('mask').hasValue()) { // mask
+					var mask = this.attribute('mask').getDefinition();
+					if (mask != null) mask.apply(ctx, this);
+				}
+				else if (this.style('filter').hasValue()) { // filter
+					var filter = this.style('filter').getDefinition();
+					if (filter != null) filter.apply(ctx, this);
+				}
+				else {	
+					this.setContext(ctx);
+					this.renderChildren(ctx);	
+					this.clearContext(ctx);							
+				}
+				ctx.restore();
+			}
+			
+			// base set context
+			this.setContext = function(ctx) {
+				// OVERRIDE ME!
+			}
+			
+			// base clear context
+			this.clearContext = function(ctx) {
+				// OVERRIDE ME!
+			}			
+			
+			// base render children
+			this.renderChildren = function(ctx) {
+				for (var i=0; i<this.children.length; i++) {
+					this.children[i].render(ctx);
+				}
+			}
+			
+			this.addChild = function(childNode, create) {
+				var child = childNode;
+				if (create) child = svg.CreateElement(childNode);
+				child.parent = this;
+				this.children.push(child);			
+			}
+				
+			if (node != null && node.nodeType == 1) { //ELEMENT_NODE
+				// add children
+				for (var i=0; i<node.childNodes.length; i++) {
+					var childNode = node.childNodes[i];
+					if (childNode.nodeType == 1) this.addChild(childNode, true); //ELEMENT_NODE
+					if (this.captureTextNodes && childNode.nodeType == 3) {
+						var text = childNode.nodeValue || childNode.text || '';
+						if (svg.trim(svg.compressSpaces(text)) != '') {
+							this.addChild(new svg.Element.tspan(childNode), false); // TEXT_NODE
+						}
+					}
+				}
+				
+				// add attributes
+				for (var i=0; i<node.attributes.length; i++) {
+					var attribute = node.attributes[i];
+					this.attributes[attribute.nodeName] = new svg.Property(attribute.nodeName, attribute.nodeValue);
+				}
+										
+				// add tag styles
+				var styles = svg.Styles[node.nodeName];
+				if (styles != null) {
+					for (var name in styles) {
+						this.styles[name] = styles[name];
+					}
+				}					
+				
+				// add class styles
+				if (this.attribute('class').hasValue()) {
+					var classes = svg.compressSpaces(this.attribute('class').value).split(' ');
+					for (var j=0; j<classes.length; j++) {
+						styles = svg.Styles['.'+classes[j]];
+						if (styles != null) {
+							for (var name in styles) {
+								this.styles[name] = styles[name];
+							}
+						}
+						styles = svg.Styles[node.nodeName+'.'+classes[j]];
+						if (styles != null) {
+							for (var name in styles) {
+								this.styles[name] = styles[name];
+							}
+						}
+					}
+				}
+				
+				// add id styles
+				if (this.attribute('id').hasValue()) {
+					var styles = svg.Styles['#' + this.attribute('id').value];
+					if (styles != null) {
+						for (var name in styles) {
+							this.styles[name] = styles[name];
+						}
+					}
+				}
+				
+				// add inline styles
+				if (this.attribute('style').hasValue()) {
+					var styles = this.attribute('style').value.split(';');
+					for (var i=0; i<styles.length; i++) {
+						if (svg.trim(styles[i]) != '') {
+							var style = styles[i].split(':');
+							var name = svg.trim(style[0]);
+							var value = svg.trim(style[1]);
+							this.styles[name] = new svg.Property(name, value);
+						}
+					}
+				}	
+
+				// add id
+				if (this.attribute('id').hasValue()) {
+					if (svg.Definitions[this.attribute('id').value] == null) {
+						svg.Definitions[this.attribute('id').value] = this;
+					}
+				}
+			}
+		}
+		
+		svg.Element.RenderedElementBase = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			this.setContext = function(ctx) {
+				// fill
+				if (this.style('fill').isUrlDefinition()) {
+					var fs = this.style('fill').getFillStyleDefinition(this, this.style('fill-opacity'));
+					if (fs != null) ctx.fillStyle = fs;
+				}
+				else if (this.style('fill').hasValue()) {
+					var fillStyle = this.style('fill');
+					if (fillStyle.value == 'currentColor') fillStyle.value = this.style('color').value;
+					ctx.fillStyle = (fillStyle.value == 'none' ? 'rgba(0,0,0,0)' : fillStyle.value);
+				}
+				if (this.style('fill-opacity').hasValue()) {
+					var fillStyle = new svg.Property('fill', ctx.fillStyle);
+					fillStyle = fillStyle.addOpacity(this.style('fill-opacity').value);
+					ctx.fillStyle = fillStyle.value;
+				}
+									
+				// stroke
+				if (this.style('stroke').isUrlDefinition()) {
+					var fs = this.style('stroke').getFillStyleDefinition(this, this.style('stroke-opacity'));
+					if (fs != null) ctx.strokeStyle = fs;
+				}
+				else if (this.style('stroke').hasValue()) {
+					var strokeStyle = this.style('stroke');
+					if (strokeStyle.value == 'currentColor') strokeStyle.value = this.style('color').value;
+					ctx.strokeStyle = (strokeStyle.value == 'none' ? 'rgba(0,0,0,0)' : strokeStyle.value);
+				}
+				if (this.style('stroke-opacity').hasValue()) {
+					var strokeStyle = new svg.Property('stroke', ctx.strokeStyle);
+					strokeStyle = strokeStyle.addOpacity(this.style('stroke-opacity').value);
+					ctx.strokeStyle = strokeStyle.value;
+				}
+				if (this.style('stroke-width').hasValue()) {
+					var newLineWidth = this.style('stroke-width').toPixels();
+					ctx.lineWidth = newLineWidth == 0 ? 0.001 : newLineWidth; // browsers don't respect 0
+			    }
+				if (this.style('stroke-linecap').hasValue()) ctx.lineCap = this.style('stroke-linecap').value;
+				if (this.style('stroke-linejoin').hasValue()) ctx.lineJoin = this.style('stroke-linejoin').value;
+				if (this.style('stroke-miterlimit').hasValue()) ctx.miterLimit = this.style('stroke-miterlimit').value;
+				if (this.style('stroke-dasharray').hasValue()) {
+					var gaps = svg.ToNumberArray(this.style('stroke-dasharray').value);
+					if (typeof(ctx.setLineDash) != 'undefined') { ctx.setLineDash(gaps); }
+					else if (typeof(ctx.webkitLineDash) != 'undefined') { ctx.webkitLineDash = gaps; }
+					else if (typeof(ctx.mozDash ) != 'undefined') { ctx.mozDash  = gaps; }
+					
+					var offset = this.style('stroke-dashoffset').numValueOrDefault(1);
+					if (typeof(ctx.lineDashOffset) != 'undefined') { ctx.lineDashOffset = offset; }
+					else if (typeof(ctx.webkitLineDashOffset) != 'undefined') { ctx.webkitLineDashOffset = offset; }
+					else if (typeof(ctx.mozDashOffset) != 'undefined') { ctx.mozDashOffset = offset; }
+				}
+
+				// font
+				if (typeof(ctx.font) != 'undefined') {
+					ctx.font = svg.Font.CreateFont( 
+						this.style('font-style').value, 
+						this.style('font-variant').value, 
+						this.style('font-weight').value, 
+						this.style('font-size').hasValue() ? this.style('font-size').toPixels() + 'px' : '', 
+						this.style('font-family').value).toString();
+				}
+				
+				// transform
+				if (this.attribute('transform').hasValue()) { 
+					var transform = new svg.Transform(this.attribute('transform').value);
+					transform.apply(ctx);
+				}
+				
+				// clip
+				if (this.style('clip-path').hasValue()) {
+					var clip = this.style('clip-path').getDefinition();
+					if (clip != null) clip.apply(ctx);
+				}
+				
+				// opacity
+				if (this.style('opacity').hasValue()) {
+					ctx.globalAlpha = this.style('opacity').numValue();
+				}
+			}		
+		}
+		svg.Element.RenderedElementBase.prototype = new svg.Element.ElementBase;
+		
+		svg.Element.PathElementBase = function(node) {
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			this.path = function(ctx) {
+				if (ctx != null) ctx.beginPath();
+				return new svg.BoundingBox();
+			}
+			
+			this.renderChildren = function(ctx) {
+				this.path(ctx);
+				svg.Mouse.checkPath(this, ctx);
+				if (ctx.fillStyle != '') {
+					if (this.attribute('fill-rule').hasValue()) { ctx.fill(this.attribute('fill-rule').value); }
+					else { ctx.fill(); }
+				}
+				if (ctx.strokeStyle != '') ctx.stroke();
+				
+				var markers = this.getMarkers();
+				if (markers != null) {
+					if (this.style('marker-start').isUrlDefinition()) {
+						var marker = this.style('marker-start').getDefinition();
+						marker.render(ctx, markers[0][0], markers[0][1]);
+					}
+					if (this.style('marker-mid').isUrlDefinition()) {
+						var marker = this.style('marker-mid').getDefinition();
+						for (var i=1;i<markers.length-1;i++) {
+							marker.render(ctx, markers[i][0], markers[i][1]);
+						}
+					}
+					if (this.style('marker-end').isUrlDefinition()) {
+						var marker = this.style('marker-end').getDefinition();
+						marker.render(ctx, markers[markers.length-1][0], markers[markers.length-1][1]);
+					}
+				}					
+			}
+			
+			this.getBoundingBox = function() {
+				return this.path();
+			}
+			
+			this.getMarkers = function() {
+				return null;
+			}
+		}
+		svg.Element.PathElementBase.prototype = new svg.Element.RenderedElementBase;
+		
+		// svg element
+		svg.Element.svg = function(node) {
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			this.baseClearContext = this.clearContext;
+			this.clearContext = function(ctx) {
+				this.baseClearContext(ctx);
+				svg.ViewPort.RemoveCurrent();
+			}
+			
+			this.baseSetContext = this.setContext;
+			this.setContext = function(ctx) {
+				// initial values
+				ctx.strokeStyle = 'rgba(0,0,0,0)';
+				ctx.lineCap = 'butt';
+				ctx.lineJoin = 'miter';
+				ctx.miterLimit = 4;			
+			
+				this.baseSetContext(ctx);
+				
+				// create new view port
+				if (!this.attribute('x').hasValue()) this.attribute('x', true).value = 0;
+				if (!this.attribute('y').hasValue()) this.attribute('y', true).value = 0;
+				ctx.translate(this.attribute('x').toPixels('x'), this.attribute('y').toPixels('y'));
+				
+				var width = svg.ViewPort.width();
+				var height = svg.ViewPort.height();
+				
+				if (!this.attribute('width').hasValue()) this.attribute('width', true).value = '100%';
+				if (!this.attribute('height').hasValue()) this.attribute('height', true).value = '100%';
+				if (typeof(this.root) == 'undefined') {
+					width = this.attribute('width').toPixels('x');
+					height = this.attribute('height').toPixels('y');
+					
+					var x = 0;
+					var y = 0;
+					if (this.attribute('refX').hasValue() && this.attribute('refY').hasValue()) {
+						x = -this.attribute('refX').toPixels('x');
+						y = -this.attribute('refY').toPixels('y');
+					}
+					
+					ctx.beginPath();
+					ctx.moveTo(x, y);
+					ctx.lineTo(width, y);
+					ctx.lineTo(width, height);
+					ctx.lineTo(x, height);
+					ctx.closePath();
+					ctx.clip();
+				}
+				svg.ViewPort.SetCurrent(width, height);	
+						
+				// viewbox
+				if (this.attribute('viewBox').hasValue()) {				
+					var viewBox = svg.ToNumberArray(this.attribute('viewBox').value);
+					var minX = viewBox[0];
+					var minY = viewBox[1];
+					width = viewBox[2];
+					height = viewBox[3];
+					
+					svg.AspectRatio(ctx,
+									this.attribute('preserveAspectRatio').value, 
+									svg.ViewPort.width(), 
+									width,
+									svg.ViewPort.height(),
+									height,
+									minX,
+									minY,
+									this.attribute('refX').value,
+									this.attribute('refY').value);
+										
+					svg.ViewPort.RemoveCurrent();	
+					svg.ViewPort.SetCurrent(viewBox[2], viewBox[3]);						
+				}				
+			}
+		}
+		svg.Element.svg.prototype = new svg.Element.RenderedElementBase;
+
+		// rect element
+		svg.Element.rect = function(node) {
+			this.base = svg.Element.PathElementBase;
+			this.base(node);
+			
+			this.path = function(ctx) {
+				var x = this.attribute('x').toPixels('x');
+				var y = this.attribute('y').toPixels('y');
+				var width = this.attribute('width').toPixels('x');
+				var height = this.attribute('height').toPixels('y');
+				var rx = this.attribute('rx').toPixels('x');
+				var ry = this.attribute('ry').toPixels('y');
+				if (this.attribute('rx').hasValue() && !this.attribute('ry').hasValue()) ry = rx;
+				if (this.attribute('ry').hasValue() && !this.attribute('rx').hasValue()) rx = ry;
+				rx = Math.min(rx, width / 2.0);
+				ry = Math.min(ry, height / 2.0);
+				if (ctx != null) {
+					ctx.beginPath();
+					ctx.moveTo(x + rx, y);
+					ctx.lineTo(x + width - rx, y);
+					ctx.quadraticCurveTo(x + width, y, x + width, y + ry)
+					ctx.lineTo(x + width, y + height - ry);
+					ctx.quadraticCurveTo(x + width, y + height, x + width - rx, y + height)
+					ctx.lineTo(x + rx, y + height);
+					ctx.quadraticCurveTo(x, y + height, x, y + height - ry)
+					ctx.lineTo(x, y + ry);
+					ctx.quadraticCurveTo(x, y, x + rx, y)
+					ctx.closePath();
+				}
+				
+				return new svg.BoundingBox(x, y, x + width, y + height);
+			}
+		}
+		svg.Element.rect.prototype = new svg.Element.PathElementBase;
+		
+		// circle element
+		svg.Element.circle = function(node) {
+			this.base = svg.Element.PathElementBase;
+			this.base(node);
+			
+			this.path = function(ctx) {
+				var cx = this.attribute('cx').toPixels('x');
+				var cy = this.attribute('cy').toPixels('y');
+				var r = this.attribute('r').toPixels();
+			
+				if (ctx != null) {
+					ctx.beginPath();
+					ctx.arc(cx, cy, r, 0, Math.PI * 2, true); 
+					ctx.closePath();
+				}
+				
+				return new svg.BoundingBox(cx - r, cy - r, cx + r, cy + r);
+			}
+		}
+		svg.Element.circle.prototype = new svg.Element.PathElementBase;	
+
+		// ellipse element
+		svg.Element.ellipse = function(node) {
+			this.base = svg.Element.PathElementBase;
+			this.base(node);
+			
+			this.path = function(ctx) {
+				var KAPPA = 4 * ((Math.sqrt(2) - 1) / 3);
+				var rx = this.attribute('rx').toPixels('x');
+				var ry = this.attribute('ry').toPixels('y');
+				var cx = this.attribute('cx').toPixels('x');
+				var cy = this.attribute('cy').toPixels('y');
+				
+				if (ctx != null) {
+					ctx.beginPath();
+					ctx.moveTo(cx, cy - ry);
+					ctx.bezierCurveTo(cx + (KAPPA * rx), cy - ry,  cx + rx, cy - (KAPPA * ry), cx + rx, cy);
+					ctx.bezierCurveTo(cx + rx, cy + (KAPPA * ry), cx + (KAPPA * rx), cy + ry, cx, cy + ry);
+					ctx.bezierCurveTo(cx - (KAPPA * rx), cy + ry, cx - rx, cy + (KAPPA * ry), cx - rx, cy);
+					ctx.bezierCurveTo(cx - rx, cy - (KAPPA * ry), cx - (KAPPA * rx), cy - ry, cx, cy - ry);
+					ctx.closePath();
+				}
+				
+				return new svg.BoundingBox(cx - rx, cy - ry, cx + rx, cy + ry);
+			}
+		}
+		svg.Element.ellipse.prototype = new svg.Element.PathElementBase;			
+		
+		// line element
+		svg.Element.line = function(node) {
+			this.base = svg.Element.PathElementBase;
+			this.base(node);
+			
+			this.getPoints = function() {
+				return [
+					new svg.Point(this.attribute('x1').toPixels('x'), this.attribute('y1').toPixels('y')),
+					new svg.Point(this.attribute('x2').toPixels('x'), this.attribute('y2').toPixels('y'))];
+			}
+								
+			this.path = function(ctx) {
+				var points = this.getPoints();
+				
+				if (ctx != null) {
+					ctx.beginPath();
+					ctx.moveTo(points[0].x, points[0].y);
+					ctx.lineTo(points[1].x, points[1].y);
+				}
+				
+				return new svg.BoundingBox(points[0].x, points[0].y, points[1].x, points[1].y);
+			}
+			
+			this.getMarkers = function() {
+				var points = this.getPoints();	
+				var a = points[0].angleTo(points[1]);
+				return [[points[0], a], [points[1], a]];
+			}
+		}
+		svg.Element.line.prototype = new svg.Element.PathElementBase;		
+				
+		// polyline element
+		svg.Element.polyline = function(node) {
+			this.base = svg.Element.PathElementBase;
+			this.base(node);
+			
+			this.points = svg.CreatePath(this.attribute('points').value);
+			this.path = function(ctx) {
+				var bb = new svg.BoundingBox(this.points[0].x, this.points[0].y);
+				if (ctx != null) {
+					ctx.beginPath();
+					ctx.moveTo(this.points[0].x, this.points[0].y);
+				}
+				for (var i=1; i<this.points.length; i++) {
+					bb.addPoint(this.points[i].x, this.points[i].y);
+					if (ctx != null) ctx.lineTo(this.points[i].x, this.points[i].y);
+				}
+				return bb;
+			}
+			
+			this.getMarkers = function() {
+				var markers = [];
+				for (var i=0; i<this.points.length - 1; i++) {
+					markers.push([this.points[i], this.points[i].angleTo(this.points[i+1])]);
+				}
+				markers.push([this.points[this.points.length-1], markers[markers.length-1][1]]);
+				return markers;
+			}			
+		}
+		svg.Element.polyline.prototype = new svg.Element.PathElementBase;				
+				
+		// polygon element
+		svg.Element.polygon = function(node) {
+			this.base = svg.Element.polyline;
+			this.base(node);
+			
+			this.basePath = this.path;
+			this.path = function(ctx) {
+				var bb = this.basePath(ctx);
+				if (ctx != null) {
+					ctx.lineTo(this.points[0].x, this.points[0].y);
+					ctx.closePath();
+				}
+				return bb;
+			}
+		}
+		svg.Element.polygon.prototype = new svg.Element.polyline;
+
+		// path element
+		svg.Element.path = function(node) {
+			this.base = svg.Element.PathElementBase;
+			this.base(node);
+					
+			var d = this.attribute('d').value;
+			// TODO: convert to real lexer based on http://www.w3.org/TR/SVG11/paths.html#PathDataBNF
+			d = d.replace(/,/gm,' '); // get rid of all commas
+			d = d.replace(/([MmZzLlHhVvCcSsQqTtAa])([MmZzLlHhVvCcSsQqTtAa])/gm,'$1 $2'); // separate commands from commands
+			d = d.replace(/([MmZzLlHhVvCcSsQqTtAa])([MmZzLlHhVvCcSsQqTtAa])/gm,'$1 $2'); // separate commands from commands
+			d = d.replace(/([MmZzLlHhVvCcSsQqTtAa])([^\s])/gm,'$1 $2'); // separate commands from points
+			d = d.replace(/([^\s])([MmZzLlHhVvCcSsQqTtAa])/gm,'$1 $2'); // separate commands from points
+			d = d.replace(/([0-9])([+\-])/gm,'$1 $2'); // separate digits when no comma
+			d = d.replace(/(\.[0-9]*)(\.)/gm,'$1 $2'); // separate digits when no comma
+			d = d.replace(/([Aa](\s+[0-9]+){3})\s+([01])\s*([01])/gm,'$1 $3 $4 '); // shorthand elliptical arc path syntax
+			d = svg.compressSpaces(d); // compress multiple spaces
+			d = svg.trim(d);
+			this.PathParser = new (function(d) {
+				this.tokens = d.split(' ');
+				
+				this.reset = function() {
+					this.i = -1;
+					this.command = '';
+					this.previousCommand = '';
+					this.start = new svg.Point(0, 0);
+					this.control = new svg.Point(0, 0);
+					this.current = new svg.Point(0, 0);
+					this.points = [];
+					this.angles = [];
+				}
+								
+				this.isEnd = function() {
+					return this.i >= this.tokens.length - 1;
+				}
+				
+				this.isCommandOrEnd = function() {
+					if (this.isEnd()) return true;
+					return this.tokens[this.i + 1].match(/^[A-Za-z]$/) != null;
+				}
+				
+				this.isRelativeCommand = function() {
+					switch(this.command)
+					{
+						case 'm':
+						case 'l':
+						case 'h':
+						case 'v':
+						case 'c':
+						case 's':
+						case 'q':
+						case 't':
+						case 'a':
+						case 'z':
+							return true;
+							break;
+					}
+					return false;
+				}
+							
+				this.getToken = function() {
+					this.i++;
+					return this.tokens[this.i];
+				}
+				
+				this.getScalar = function() {
+					return parseFloat(this.getToken());
+				}
+				
+				this.nextCommand = function() {
+					this.previousCommand = this.command;
+					this.command = this.getToken();
+				}				
+				
+				this.getPoint = function() {
+					var p = new svg.Point(this.getScalar(), this.getScalar());
+					return this.makeAbsolute(p);
+				}
+				
+				this.getAsControlPoint = function() {
+					var p = this.getPoint();
+					this.control = p;
+					return p;
+				}
+				
+				this.getAsCurrentPoint = function() {
+					var p = this.getPoint();
+					this.current = p;
+					return p;	
+				}
+				
+				this.getReflectedControlPoint = function() {
+					if (this.previousCommand.toLowerCase() != 'c' && 
+					    this.previousCommand.toLowerCase() != 's' &&
+						this.previousCommand.toLowerCase() != 'q' && 
+						this.previousCommand.toLowerCase() != 't' ){
+						return this.current;
+					}
+					
+					// reflect point
+					var p = new svg.Point(2 * this.current.x - this.control.x, 2 * this.current.y - this.control.y);					
+					return p;
+				}
+				
+				this.makeAbsolute = function(p) {
+					if (this.isRelativeCommand()) {
+						p.x += this.current.x;
+						p.y += this.current.y;
+					}
+					return p;
+				}
+				
+				this.addMarker = function(p, from, priorTo) {
+					// if the last angle isn't filled in because we didn't have this point yet ...
+					if (priorTo != null && this.angles.length > 0 && this.angles[this.angles.length-1] == null) {
+						this.angles[this.angles.length-1] = this.points[this.points.length-1].angleTo(priorTo);
+					}
+					this.addMarkerAngle(p, from == null ? null : from.angleTo(p));
+				}
+				
+				this.addMarkerAngle = function(p, a) {
+					this.points.push(p);
+					this.angles.push(a);
+				}				
+				
+				this.getMarkerPoints = function() { return this.points; }
+				this.getMarkerAngles = function() {
+					for (var i=0; i<this.angles.length; i++) {
+						if (this.angles[i] == null) {
+							for (var j=i+1; j<this.angles.length; j++) {
+								if (this.angles[j] != null) {
+									this.angles[i] = this.angles[j];
+									break;
+								}
+							}
+						}
+					}
+					return this.angles;
+				}
+			})(d);
+
+			this.path = function(ctx) {
+				var pp = this.PathParser;
+				pp.reset();
+
+				var bb = new svg.BoundingBox();
+				if (ctx != null) ctx.beginPath();
+				while (!pp.isEnd()) {
+					pp.nextCommand();
+					switch (pp.command) {
+					case 'M':
+					case 'm':
+						var p = pp.getAsCurrentPoint();
+						pp.addMarker(p);
+						bb.addPoint(p.x, p.y);
+						if (ctx != null) ctx.moveTo(p.x, p.y);
+						pp.start = pp.current;
+						while (!pp.isCommandOrEnd()) {
+							var p = pp.getAsCurrentPoint();
+							pp.addMarker(p, pp.start);
+							bb.addPoint(p.x, p.y);
+							if (ctx != null) ctx.lineTo(p.x, p.y);
+						}
+						break;
+					case 'L':
+					case 'l':
+						while (!pp.isCommandOrEnd()) {
+							var c = pp.current;
+							var p = pp.getAsCurrentPoint();
+							pp.addMarker(p, c);
+							bb.addPoint(p.x, p.y);
+							if (ctx != null) ctx.lineTo(p.x, p.y);
+						}
+						break;
+					case 'H':
+					case 'h':
+						while (!pp.isCommandOrEnd()) {
+							var newP = new svg.Point((pp.isRelativeCommand() ? pp.current.x : 0) + pp.getScalar(), pp.current.y);
+							pp.addMarker(newP, pp.current);
+							pp.current = newP;
+							bb.addPoint(pp.current.x, pp.current.y);
+							if (ctx != null) ctx.lineTo(pp.current.x, pp.current.y);
+						}
+						break;
+					case 'V':
+					case 'v':
+						while (!pp.isCommandOrEnd()) {
+							var newP = new svg.Point(pp.current.x, (pp.isRelativeCommand() ? pp.current.y : 0) + pp.getScalar());
+							pp.addMarker(newP, pp.current);
+							pp.current = newP;
+							bb.addPoint(pp.current.x, pp.current.y);
+							if (ctx != null) ctx.lineTo(pp.current.x, pp.current.y);
+						}
+						break;
+					case 'C':
+					case 'c':
+						while (!pp.isCommandOrEnd()) {
+							var curr = pp.current;
+							var p1 = pp.getPoint();
+							var cntrl = pp.getAsControlPoint();
+							var cp = pp.getAsCurrentPoint();
+							pp.addMarker(cp, cntrl, p1);
+							bb.addBezierCurve(curr.x, curr.y, p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
+							if (ctx != null) ctx.bezierCurveTo(p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
+						}
+						break;
+					case 'S':
+					case 's':
+						while (!pp.isCommandOrEnd()) {
+							var curr = pp.current;
+							var p1 = pp.getReflectedControlPoint();
+							var cntrl = pp.getAsControlPoint();
+							var cp = pp.getAsCurrentPoint();
+							pp.addMarker(cp, cntrl, p1);
+							bb.addBezierCurve(curr.x, curr.y, p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
+							if (ctx != null) ctx.bezierCurveTo(p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
+						}
+						break;
+					case 'Q':
+					case 'q':
+						while (!pp.isCommandOrEnd()) {
+							var curr = pp.current;
+							var cntrl = pp.getAsControlPoint();
+							var cp = pp.getAsCurrentPoint();
+							pp.addMarker(cp, cntrl, cntrl);
+							bb.addQuadraticCurve(curr.x, curr.y, cntrl.x, cntrl.y, cp.x, cp.y);
+							if (ctx != null) ctx.quadraticCurveTo(cntrl.x, cntrl.y, cp.x, cp.y);
+						}
+						break;
+					case 'T':
+					case 't':
+						while (!pp.isCommandOrEnd()) {
+							var curr = pp.current;
+							var cntrl = pp.getReflectedControlPoint();
+							pp.control = cntrl;
+							var cp = pp.getAsCurrentPoint();
+							pp.addMarker(cp, cntrl, cntrl);
+							bb.addQuadraticCurve(curr.x, curr.y, cntrl.x, cntrl.y, cp.x, cp.y);
+							if (ctx != null) ctx.quadraticCurveTo(cntrl.x, cntrl.y, cp.x, cp.y);
+						}
+						break;
+					case 'A':
+					case 'a':
+						while (!pp.isCommandOrEnd()) {
+						    var curr = pp.current;
+							var rx = pp.getScalar();
+							var ry = pp.getScalar();
+							var xAxisRotation = pp.getScalar() * (Math.PI / 180.0);
+							var largeArcFlag = pp.getScalar();
+							var sweepFlag = pp.getScalar();
+							var cp = pp.getAsCurrentPoint();
+
+							// Conversion from endpoint to center parameterization
+							// http://www.w3.org/TR/SVG11/implnote.html#ArcImplementationNotes
+							// x1', y1'
+							var currp = new svg.Point(
+								Math.cos(xAxisRotation) * (curr.x - cp.x) / 2.0 + Math.sin(xAxisRotation) * (curr.y - cp.y) / 2.0,
+								-Math.sin(xAxisRotation) * (curr.x - cp.x) / 2.0 + Math.cos(xAxisRotation) * (curr.y - cp.y) / 2.0
+							);
+							// adjust radii
+							var l = Math.pow(currp.x,2)/Math.pow(rx,2)+Math.pow(currp.y,2)/Math.pow(ry,2);
+							if (l > 1) {
+								rx *= Math.sqrt(l);
+								ry *= Math.sqrt(l);
+							}
+							// cx', cy'
+							var s = (largeArcFlag == sweepFlag ? -1 : 1) * Math.sqrt(
+								((Math.pow(rx,2)*Math.pow(ry,2))-(Math.pow(rx,2)*Math.pow(currp.y,2))-(Math.pow(ry,2)*Math.pow(currp.x,2))) /
+								(Math.pow(rx,2)*Math.pow(currp.y,2)+Math.pow(ry,2)*Math.pow(currp.x,2))
+							);
+							if (isNaN(s)) s = 0;
+							var cpp = new svg.Point(s * rx * currp.y / ry, s * -ry * currp.x / rx);
+							// cx, cy
+							var centp = new svg.Point(
+								(curr.x + cp.x) / 2.0 + Math.cos(xAxisRotation) * cpp.x - Math.sin(xAxisRotation) * cpp.y,
+								(curr.y + cp.y) / 2.0 + Math.sin(xAxisRotation) * cpp.x + Math.cos(xAxisRotation) * cpp.y
+							);
+							// vector magnitude
+							var m = function(v) { return Math.sqrt(Math.pow(v[0],2) + Math.pow(v[1],2)); }
+							// ratio between two vectors
+							var r = function(u, v) { return (u[0]*v[0]+u[1]*v[1]) / (m(u)*m(v)) }
+							// angle between two vectors
+							var a = function(u, v) { return (u[0]*v[1] < u[1]*v[0] ? -1 : 1) * Math.acos(r(u,v)); }
+							// initial angle
+							var a1 = a([1,0], [(currp.x-cpp.x)/rx,(currp.y-cpp.y)/ry]);
+							// angle delta
+							var u = [(currp.x-cpp.x)/rx,(currp.y-cpp.y)/ry];
+							var v = [(-currp.x-cpp.x)/rx,(-currp.y-cpp.y)/ry];
+							var ad = a(u, v);
+							if (r(u,v) <= -1) ad = Math.PI;
+							if (r(u,v) >= 1) ad = 0;
+
+							// for markers
+							var dir = 1 - sweepFlag ? 1.0 : -1.0;
+							var ah = a1 + dir * (ad / 2.0);
+							var halfWay = new svg.Point(
+								centp.x + rx * Math.cos(ah),
+								centp.y + ry * Math.sin(ah)
+							);
+							pp.addMarkerAngle(halfWay, ah - dir * Math.PI / 2);
+							pp.addMarkerAngle(cp, ah - dir * Math.PI);
+
+							bb.addPoint(cp.x, cp.y); // TODO: this is too naive, make it better
+							if (ctx != null) {
+								var r = rx > ry ? rx : ry;
+								var sx = rx > ry ? 1 : rx / ry;
+								var sy = rx > ry ? ry / rx : 1;
+
+								ctx.translate(centp.x, centp.y);
+								ctx.rotate(xAxisRotation);
+								ctx.scale(sx, sy);
+								ctx.arc(0, 0, r, a1, a1 + ad, 1 - sweepFlag);
+								ctx.scale(1/sx, 1/sy);
+								ctx.rotate(-xAxisRotation);
+								ctx.translate(-centp.x, -centp.y);
+							}
+						}
+						break;
+					case 'Z':
+					case 'z':
+						if (ctx != null) ctx.closePath();
+						pp.current = pp.start;
+					}
+				}
+
+				return bb;
+			}
+
+			this.getMarkers = function() {
+				var points = this.PathParser.getMarkerPoints();
+				var angles = this.PathParser.getMarkerAngles();
+				
+				var markers = [];
+				for (var i=0; i<points.length; i++) {
+					markers.push([points[i], angles[i]]);
+				}
+				return markers;
+			}
+		}
+		svg.Element.path.prototype = new svg.Element.PathElementBase;
+		
+		// pattern element
+		svg.Element.pattern = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			this.createPattern = function(ctx, element) {
+				var width = this.attribute('width').toPixels('x', true);
+				var height = this.attribute('height').toPixels('y', true);
+			
+				// render me using a temporary svg element
+				var tempSvg = new svg.Element.svg();
+				tempSvg.attributes['viewBox'] = new svg.Property('viewBox', this.attribute('viewBox').value);
+				tempSvg.attributes['width'] = new svg.Property('width', width + 'px');
+				tempSvg.attributes['height'] = new svg.Property('height', height + 'px');
+				tempSvg.attributes['transform'] = new svg.Property('transform', this.attribute('patternTransform').value);
+				tempSvg.children = this.children;
+				
+				var c = document.createElement('canvas');
+				c.width = width;
+				c.height = height;
+				var cctx = c.getContext('2d');
+				if (this.attribute('x').hasValue() && this.attribute('y').hasValue()) {
+					cctx.translate(this.attribute('x').toPixels('x', true), this.attribute('y').toPixels('y', true));
+				}
+				// render 3x3 grid so when we transform there's no white space on edges
+				for (var x=-1; x<=1; x++) {
+					for (var y=-1; y<=1; y++) {
+						cctx.save();
+						cctx.translate(x * c.width, y * c.height);
+						tempSvg.render(cctx);
+						cctx.restore();
+					}
+				}
+				var pattern = ctx.createPattern(c, 'repeat');
+				return pattern;
+			}
+		}
+		svg.Element.pattern.prototype = new svg.Element.ElementBase;
+		
+		// marker element
+		svg.Element.marker = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			this.baseRender = this.render;
+			this.render = function(ctx, point, angle) {
+				ctx.translate(point.x, point.y);
+				if (this.attribute('orient').valueOrDefault('auto') == 'auto') ctx.rotate(angle);
+				if (this.attribute('markerUnits').valueOrDefault('strokeWidth') == 'strokeWidth') ctx.scale(ctx.lineWidth, ctx.lineWidth);
+				ctx.save();
+							
+				// render me using a temporary svg element
+				var tempSvg = new svg.Element.svg();
+				tempSvg.attributes['viewBox'] = new svg.Property('viewBox', this.attribute('viewBox').value);
+				tempSvg.attributes['refX'] = new svg.Property('refX', this.attribute('refX').value);
+				tempSvg.attributes['refY'] = new svg.Property('refY', this.attribute('refY').value);
+				tempSvg.attributes['width'] = new svg.Property('width', this.attribute('markerWidth').value);
+				tempSvg.attributes['height'] = new svg.Property('height', this.attribute('markerHeight').value);
+				tempSvg.attributes['fill'] = new svg.Property('fill', this.attribute('fill').valueOrDefault('black'));
+				tempSvg.attributes['stroke'] = new svg.Property('stroke', this.attribute('stroke').valueOrDefault('none'));
+				tempSvg.children = this.children;
+				tempSvg.render(ctx);
+				
+				ctx.restore();
+				if (this.attribute('markerUnits').valueOrDefault('strokeWidth') == 'strokeWidth') ctx.scale(1/ctx.lineWidth, 1/ctx.lineWidth);
+				if (this.attribute('orient').valueOrDefault('auto') == 'auto') ctx.rotate(-angle);
+				ctx.translate(-point.x, -point.y);
+			}
+		}
+		svg.Element.marker.prototype = new svg.Element.ElementBase;
+		
+		// definitions element
+		svg.Element.defs = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);	
+			
+			this.render = function(ctx) {
+				// NOOP
+			}
+		}
+		svg.Element.defs.prototype = new svg.Element.ElementBase;
+		
+		// base for gradients
+		svg.Element.GradientBase = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			this.gradientUnits = this.attribute('gradientUnits').valueOrDefault('objectBoundingBox');
+			
+			this.stops = [];			
+			for (var i=0; i<this.children.length; i++) {
+				var child = this.children[i];
+				if (child.type == 'stop') this.stops.push(child);
+			}	
+			
+			this.getGradient = function() {
+				// OVERRIDE ME!
+			}			
+
+			this.createGradient = function(ctx, element, parentOpacityProp) {
+				var stopsContainer = this;
+				if (this.getHrefAttribute().hasValue()) {
+					stopsContainer = this.getHrefAttribute().getDefinition();
+				}
+				
+				var addParentOpacity = function (color) {
+					if (parentOpacityProp.hasValue()) {
+						var p = new svg.Property('color', color);
+						return p.addOpacity(parentOpacityProp.value).value;
+					}
+					return color;
+				};
+			
+				var g = this.getGradient(ctx, element);
+				if (g == null) return addParentOpacity(stopsContainer.stops[stopsContainer.stops.length - 1].color);
+				for (var i=0; i<stopsContainer.stops.length; i++) {
+					g.addColorStop(stopsContainer.stops[i].offset, addParentOpacity(stopsContainer.stops[i].color));
+				}
+				
+				if (this.attribute('gradientTransform').hasValue()) {
+					// render as transformed pattern on temporary canvas
+					var rootView = svg.ViewPort.viewPorts[0];
+					
+					var rect = new svg.Element.rect();
+					rect.attributes['x'] = new svg.Property('x', -svg.MAX_VIRTUAL_PIXELS/3.0);
+					rect.attributes['y'] = new svg.Property('y', -svg.MAX_VIRTUAL_PIXELS/3.0);
+					rect.attributes['width'] = new svg.Property('width', svg.MAX_VIRTUAL_PIXELS);
+					rect.attributes['height'] = new svg.Property('height', svg.MAX_VIRTUAL_PIXELS);
+					
+					var group = new svg.Element.g();
+					group.attributes['transform'] = new svg.Property('transform', this.attribute('gradientTransform').value);
+					group.children = [ rect ];
+					
+					var tempSvg = new svg.Element.svg();
+					tempSvg.attributes['x'] = new svg.Property('x', 0);
+					tempSvg.attributes['y'] = new svg.Property('y', 0);
+					tempSvg.attributes['width'] = new svg.Property('width', rootView.width);
+					tempSvg.attributes['height'] = new svg.Property('height', rootView.height);
+					tempSvg.children = [ group ];
+					
+					var c = document.createElement('canvas');
+					c.width = rootView.width;
+					c.height = rootView.height;
+					var tempCtx = c.getContext('2d');
+					tempCtx.fillStyle = g;
+					tempSvg.render(tempCtx);		
+					return tempCtx.createPattern(c, 'no-repeat');
+				}
+				
+				return g;				
+			}
+		}
+		svg.Element.GradientBase.prototype = new svg.Element.ElementBase;
+		
+		// linear gradient element
+		svg.Element.linearGradient = function(node) {
+			this.base = svg.Element.GradientBase;
+			this.base(node);
+			
+			this.getGradient = function(ctx, element) {
+				var bb = element.getBoundingBox();
+				
+				if (!this.attribute('x1').hasValue()
+				 && !this.attribute('y1').hasValue()
+				 && !this.attribute('x2').hasValue()
+				 && !this.attribute('y2').hasValue()) {
+					this.attribute('x1', true).value = 0;
+					this.attribute('y1', true).value = 0;
+					this.attribute('x2', true).value = 1;
+					this.attribute('y2', true).value = 0;
+				 }
+				
+				var x1 = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.x() + bb.width() * this.attribute('x1').numValue() 
+					: this.attribute('x1').toPixels('x'));
+				var y1 = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.y() + bb.height() * this.attribute('y1').numValue()
+					: this.attribute('y1').toPixels('y'));
+				var x2 = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.x() + bb.width() * this.attribute('x2').numValue()
+					: this.attribute('x2').toPixels('x'));
+				var y2 = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.y() + bb.height() * this.attribute('y2').numValue()
+					: this.attribute('y2').toPixels('y'));
+
+				if (x1 == x2 && y1 == y2) return null;
+				return ctx.createLinearGradient(x1, y1, x2, y2);
+			}
+		}
+		svg.Element.linearGradient.prototype = new svg.Element.GradientBase;
+		
+		// radial gradient element
+		svg.Element.radialGradient = function(node) {
+			this.base = svg.Element.GradientBase;
+			this.base(node);
+			
+			this.getGradient = function(ctx, element) {
+				var bb = element.getBoundingBox();
+				
+				if (!this.attribute('cx').hasValue()) this.attribute('cx', true).value = '50%';
+				if (!this.attribute('cy').hasValue()) this.attribute('cy', true).value = '50%';
+				if (!this.attribute('r').hasValue()) this.attribute('r', true).value = '50%';
+				
+				var cx = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.x() + bb.width() * this.attribute('cx').numValue() 
+					: this.attribute('cx').toPixels('x'));
+				var cy = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.y() + bb.height() * this.attribute('cy').numValue() 
+					: this.attribute('cy').toPixels('y'));
+				
+				var fx = cx;
+				var fy = cy;
+				if (this.attribute('fx').hasValue()) {
+					fx = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.x() + bb.width() * this.attribute('fx').numValue() 
+					: this.attribute('fx').toPixels('x'));
+				}
+				if (this.attribute('fy').hasValue()) {
+					fy = (this.gradientUnits == 'objectBoundingBox' 
+					? bb.y() + bb.height() * this.attribute('fy').numValue() 
+					: this.attribute('fy').toPixels('y'));
+				}
+				
+				var r = (this.gradientUnits == 'objectBoundingBox' 
+					? (bb.width() + bb.height()) / 2.0 * this.attribute('r').numValue()
+					: this.attribute('r').toPixels());
+				
+				return ctx.createRadialGradient(fx, fy, 0, cx, cy, r);
+			}
+		}
+		svg.Element.radialGradient.prototype = new svg.Element.GradientBase;
+		
+		// gradient stop element
+		svg.Element.stop = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			this.offset = this.attribute('offset').numValue();
+			if (this.offset < 0) this.offset = 0;
+			if (this.offset > 1) this.offset = 1;
+			
+			var stopColor = this.style('stop-color');
+			if (this.style('stop-opacity').hasValue()) stopColor = stopColor.addOpacity(this.style('stop-opacity').value);
+			this.color = stopColor.value;
+		}
+		svg.Element.stop.prototype = new svg.Element.ElementBase;
+		
+		// animation base element
+		svg.Element.AnimateBase = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			svg.Animations.push(this);
+			
+			this.duration = 0.0;
+			this.begin = this.attribute('begin').toMilliseconds();
+			this.maxDuration = this.begin + this.attribute('dur').toMilliseconds();
+			
+			this.getProperty = function() {
+				var attributeType = this.attribute('attributeType').value;
+				var attributeName = this.attribute('attributeName').value;
+				
+				if (attributeType == 'CSS') {
+					return this.parent.style(attributeName, true);
+				}
+				return this.parent.attribute(attributeName, true);			
+			};
+			
+			this.initialValue = null;
+			this.initialUnits = '';
+			this.removed = false;			
+
+			this.calcValue = function() {
+				// OVERRIDE ME!
+				return '';
+			}
+					
+			this.update = function(delta) {	
+				// set initial value
+				if (this.initialValue == null) {
+					this.initialValue = this.getProperty().value;
+					this.initialUnits = this.getProperty().getUnits();
+				}
+			
+				// if we're past the end time
+				if (this.duration > this.maxDuration) {
+					// loop for indefinitely repeating animations
+					if (this.attribute('repeatCount').value == 'indefinite'
+					 || this.attribute('repeatDur').value == 'indefinite') {
+						this.duration = 0.0
+					}
+					else if (this.attribute('fill').valueOrDefault('remove') == 'remove' && !this.removed) {
+						this.removed = true;
+						this.getProperty().value = this.initialValue;
+						return true;
+					}
+					else {
+						return false; // no updates made
+					}
+				}			
+				this.duration = this.duration + delta;
+			
+				// if we're past the begin time
+				var updated = false;
+				if (this.begin < this.duration) {
+					var newValue = this.calcValue(); // tween
+					
+					if (this.attribute('type').hasValue()) {
+						// for transform, etc.
+						var type = this.attribute('type').value;
+						newValue = type + '(' + newValue + ')';
+					}
+					
+					this.getProperty().value = newValue;
+					updated = true;
+				}
+				
+				return updated;
+			}
+			
+			this.from = this.attribute('from');
+			this.to = this.attribute('to');
+			this.values = this.attribute('values');
+			if (this.values.hasValue()) this.values.value = this.values.value.split(';');
+			
+			// fraction of duration we've covered
+			this.progress = function() {
+				var ret = { progress: (this.duration - this.begin) / (this.maxDuration - this.begin) };
+				if (this.values.hasValue()) {
+					var p = ret.progress * (this.values.value.length - 1);
+					var lb = Math.floor(p), ub = Math.ceil(p);
+					ret.from = new svg.Property('from', parseFloat(this.values.value[lb]));
+					ret.to = new svg.Property('to', parseFloat(this.values.value[ub]));
+					ret.progress = (p - lb) / (ub - lb);
+				}
+				else {
+					ret.from = this.from;
+					ret.to = this.to;
+				}
+				return ret;
+			}			
+		}
+		svg.Element.AnimateBase.prototype = new svg.Element.ElementBase;
+		
+		// animate element
+		svg.Element.animate = function(node) {
+			this.base = svg.Element.AnimateBase;
+			this.base(node);
+			
+			this.calcValue = function() {
+				var p = this.progress();
+				
+				// tween value linearly
+				var newValue = p.from.numValue() + (p.to.numValue() - p.from.numValue()) * p.progress; 
+				return newValue + this.initialUnits;
+			};
+		}
+		svg.Element.animate.prototype = new svg.Element.AnimateBase;
+			
+		// animate color element
+		svg.Element.animateColor = function(node) {
+			this.base = svg.Element.AnimateBase;
+			this.base(node);
+
+			this.calcValue = function() {
+				var p = this.progress();
+				var from = new RGBColor(p.from.value);
+				var to = new RGBColor(p.to.value);
+				
+				if (from.ok && to.ok) {
+					// tween color linearly
+					var r = from.r + (to.r - from.r) * p.progress;
+					var g = from.g + (to.g - from.g) * p.progress;
+					var b = from.b + (to.b - from.b) * p.progress;
+					return 'rgb('+parseInt(r,10)+','+parseInt(g,10)+','+parseInt(b,10)+')';
+				}
+				return this.attribute('from').value;
+			};
+		}
+		svg.Element.animateColor.prototype = new svg.Element.AnimateBase;
+		
+		// animate transform element
+		svg.Element.animateTransform = function(node) {
+			this.base = svg.Element.AnimateBase;
+			this.base(node);
+			
+			this.calcValue = function() {
+				var p = this.progress();
+				
+				// tween value linearly
+				var from = svg.ToNumberArray(p.from.value);
+				var to = svg.ToNumberArray(p.to.value);
+				var newValue = '';
+				for (var i=0; i<from.length; i++) {
+					newValue += from[i] + (to[i] - from[i]) * p.progress + ' ';
+				}
+				return newValue;
+			};
+		}
+		svg.Element.animateTransform.prototype = new svg.Element.animate;
+		
+		// font element
+		svg.Element.font = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+
+			this.horizAdvX = this.attribute('horiz-adv-x').numValue();			
+			
+			this.isRTL = false;
+			this.isArabic = false;
+			this.fontFace = null;
+			this.missingGlyph = null;
+			this.glyphs = [];			
+			for (var i=0; i<this.children.length; i++) {
+				var child = this.children[i];
+				if (child.type == 'font-face') {
+					this.fontFace = child;
+					if (child.style('font-family').hasValue()) {
+						svg.Definitions[child.style('font-family').value] = this;
+					}
+				}
+				else if (child.type == 'missing-glyph') this.missingGlyph = child;
+				else if (child.type == 'glyph') {
+					if (child.arabicForm != '') {
+						this.isRTL = true;
+						this.isArabic = true;
+						if (typeof(this.glyphs[child.unicode]) == 'undefined') this.glyphs[child.unicode] = [];
+						this.glyphs[child.unicode][child.arabicForm] = child;
+					}
+					else {
+						this.glyphs[child.unicode] = child;
+					}
+				}
+			}	
+		}
+		svg.Element.font.prototype = new svg.Element.ElementBase;
+		
+		// font-face element
+		svg.Element.fontface = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);	
+			
+			this.ascent = this.attribute('ascent').value;
+			this.descent = this.attribute('descent').value;
+			this.unitsPerEm = this.attribute('units-per-em').numValue();				
+		}
+		svg.Element.fontface.prototype = new svg.Element.ElementBase;
+		
+		// missing-glyph element
+		svg.Element.missingglyph = function(node) {
+			this.base = svg.Element.path;
+			this.base(node);	
+			
+			this.horizAdvX = 0;
+		}
+		svg.Element.missingglyph.prototype = new svg.Element.path;
+		
+		// glyph element
+		svg.Element.glyph = function(node) {
+			this.base = svg.Element.path;
+			this.base(node);	
+			
+			this.horizAdvX = this.attribute('horiz-adv-x').numValue();
+			this.unicode = this.attribute('unicode').value;
+			this.arabicForm = this.attribute('arabic-form').value;
+		}
+		svg.Element.glyph.prototype = new svg.Element.path;
+		
+		// text element
+		svg.Element.text = function(node) {
+			this.captureTextNodes = true;
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			this.baseSetContext = this.setContext;
+			this.setContext = function(ctx) {
+				this.baseSetContext(ctx);
+				if (this.style('dominant-baseline').hasValue()) ctx.textBaseline = this.style('dominant-baseline').value;
+				if (this.style('alignment-baseline').hasValue()) ctx.textBaseline = this.style('alignment-baseline').value;
+			}
+			
+			this.getBoundingBox = function () {
+				// TODO: implement
+				return new svg.BoundingBox(this.attribute('x').toPixels('x'), this.attribute('y').toPixels('y'), 0, 0);
+			}
+			
+			this.renderChildren = function(ctx) {
+				this.x = this.attribute('x').toPixels('x');
+				this.y = this.attribute('y').toPixels('y');
+				this.x += this.getAnchorDelta(ctx, this, 0);
+				for (var i=0; i<this.children.length; i++) {
+					this.renderChild(ctx, this, i);
+				}
+			}
+			
+			this.getAnchorDelta = function (ctx, parent, startI) {
+				var textAnchor = this.style('text-anchor').valueOrDefault('start');
+				if (textAnchor != 'start') {
+					var width = 0;
+					for (var i=startI; i<parent.children.length; i++) {
+						var child = parent.children[i];
+						if (i > startI && child.attribute('x').hasValue()) break; // new group
+						width += child.measureTextRecursive(ctx);
+					}
+					return -1 * (textAnchor == 'end' ? width : width / 2.0);
+				}
+				return 0;
+			}
+			
+			this.renderChild = function(ctx, parent, i) {
+				var child = parent.children[i];
+				if (child.attribute('x').hasValue()) {
+					child.x = child.attribute('x').toPixels('x') + this.getAnchorDelta(ctx, parent, i);
+				}
+				else {
+					if (this.attribute('dx').hasValue()) this.x += this.attribute('dx').toPixels('x');
+					if (child.attribute('dx').hasValue()) this.x += child.attribute('dx').toPixels('x');
+					child.x = this.x;
+				}
+				this.x = child.x + child.measureText(ctx);
+				
+				if (child.attribute('y').hasValue()) {
+					child.y = child.attribute('y').toPixels('y');
+				}
+				else {
+					if (this.attribute('dy').hasValue()) this.y += this.attribute('dy').toPixels('y');
+					if (child.attribute('dy').hasValue()) this.y += child.attribute('dy').toPixels('y');
+					child.y = this.y;
+				}
+				this.y = child.y;
+				
+				child.render(ctx);
+				
+				for (var i=0; i<child.children.length; i++) {
+					this.renderChild(ctx, child, i);
+				}
+			}
+		}
+		svg.Element.text.prototype = new svg.Element.RenderedElementBase;
+		
+		// text base
+		svg.Element.TextElementBase = function(node) {
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			this.getGlyph = function(font, text, i) {
+				var c = text[i];
+				var glyph = null;
+				if (font.isArabic) {
+					var arabicForm = 'isolated';
+					if ((i==0 || text[i-1]==' ') && i<text.length-2 && text[i+1]!=' ') arabicForm = 'terminal'; 
+					if (i>0 && text[i-1]!=' ' && i<text.length-2 && text[i+1]!=' ') arabicForm = 'medial';
+					if (i>0 && text[i-1]!=' ' && (i == text.length-1 || text[i+1]==' ')) arabicForm = 'initial';
+					if (typeof(font.glyphs[c]) != 'undefined') {
+						glyph = font.glyphs[c][arabicForm];
+						if (glyph == null && font.glyphs[c].type == 'glyph') glyph = font.glyphs[c];
+					}
+				}
+				else {
+					glyph = font.glyphs[c];
+				}
+				if (glyph == null) glyph = font.missingGlyph;
+				return glyph;
+			}
+			
+			this.renderChildren = function(ctx) {
+				var customFont = this.parent.style('font-family').getDefinition();
+				if (customFont != null) {
+					var fontSize = this.parent.style('font-size').numValueOrDefault(svg.Font.Parse(svg.ctx.font).fontSize);
+					var fontStyle = this.parent.style('font-style').valueOrDefault(svg.Font.Parse(svg.ctx.font).fontStyle);
+					var text = this.getText();
+					if (customFont.isRTL) text = text.split("").reverse().join("");
+					
+					var dx = svg.ToNumberArray(this.parent.attribute('dx').value);
+					for (var i=0; i<text.length; i++) {
+						var glyph = this.getGlyph(customFont, text, i);
+						var scale = fontSize / customFont.fontFace.unitsPerEm;
+						ctx.translate(this.x, this.y);
+						ctx.scale(scale, -scale);
+						var lw = ctx.lineWidth;
+						ctx.lineWidth = ctx.lineWidth * customFont.fontFace.unitsPerEm / fontSize;
+						if (fontStyle == 'italic') ctx.transform(1, 0, .4, 1, 0, 0);
+						glyph.render(ctx);
+						if (fontStyle == 'italic') ctx.transform(1, 0, -.4, 1, 0, 0);
+						ctx.lineWidth = lw;
+						ctx.scale(1/scale, -1/scale);
+						ctx.translate(-this.x, -this.y);	
+						
+						this.x += fontSize * (glyph.horizAdvX || customFont.horizAdvX) / customFont.fontFace.unitsPerEm;
+						if (typeof(dx[i]) != 'undefined' && !isNaN(dx[i])) {
+							this.x += dx[i];
+						}
+					}
+					return;
+				}
+			
+				if (ctx.fillStyle != '') ctx.fillText(svg.compressSpaces(this.getText()), this.x, this.y);
+				if (ctx.strokeStyle != '') ctx.strokeText(svg.compressSpaces(this.getText()), this.x, this.y);
+			}
+			
+			this.getText = function() {
+				// OVERRIDE ME
+			}
+			
+			this.measureTextRecursive = function(ctx) {
+				var width = this.measureText(ctx);
+				for (var i=0; i<this.children.length; i++) {
+					width += this.children[i].measureTextRecursive(ctx);
+				}
+				return width;
+			}
+			
+			this.measureText = function(ctx) {
+				var customFont = this.parent.style('font-family').getDefinition();
+				if (customFont != null) {
+					var fontSize = this.parent.style('font-size').numValueOrDefault(svg.Font.Parse(svg.ctx.font).fontSize);
+					var measure = 0;
+					var text = this.getText();
+					if (customFont.isRTL) text = text.split("").reverse().join("");
+					var dx = svg.ToNumberArray(this.parent.attribute('dx').value);
+					for (var i=0; i<text.length; i++) {
+						var glyph = this.getGlyph(customFont, text, i);
+						measure += (glyph.horizAdvX || customFont.horizAdvX) * fontSize / customFont.fontFace.unitsPerEm;
+						if (typeof(dx[i]) != 'undefined' && !isNaN(dx[i])) {
+							measure += dx[i];
+						}
+					}
+					return measure;
+				}
+			
+				var textToMeasure = svg.compressSpaces(this.getText());
+				if (!ctx.measureText) return textToMeasure.length * 10;
+				
+				ctx.save();
+				this.setContext(ctx);
+				var width = ctx.measureText(textToMeasure).width;
+				ctx.restore();
+				return width;
+			}
+		}
+		svg.Element.TextElementBase.prototype = new svg.Element.RenderedElementBase;
+		
+		// tspan 
+		svg.Element.tspan = function(node) {
+			this.captureTextNodes = true;
+			this.base = svg.Element.TextElementBase;
+			this.base(node);
+			
+			this.text = node.nodeValue || node.text || '';
+			this.getText = function() {
+				return this.text;
+			}
+		}
+		svg.Element.tspan.prototype = new svg.Element.TextElementBase;
+		
+		// tref
+		svg.Element.tref = function(node) {
+			this.base = svg.Element.TextElementBase;
+			this.base(node);
+			
+			this.getText = function() {
+				var element = this.getHrefAttribute().getDefinition();
+				if (element != null) return element.children[0].getText();
+			}
+		}
+		svg.Element.tref.prototype = new svg.Element.TextElementBase;		
+		
+		// a element
+		svg.Element.a = function(node) {
+			this.base = svg.Element.TextElementBase;
+			this.base(node);
+			
+			this.hasText = true;
+			for (var i=0; i<node.childNodes.length; i++) {
+				if (node.childNodes[i].nodeType != 3) this.hasText = false;
+			}
+			
+			// this might contain text
+			this.text = this.hasText ? node.childNodes[0].nodeValue : '';
+			this.getText = function() {
+				return this.text;
+			}		
+
+			this.baseRenderChildren = this.renderChildren;
+			this.renderChildren = function(ctx) {
+				if (this.hasText) {
+					// render as text element
+					this.baseRenderChildren(ctx);
+					var fontSize = new svg.Property('fontSize', svg.Font.Parse(svg.ctx.font).fontSize);
+					svg.Mouse.checkBoundingBox(this, new svg.BoundingBox(this.x, this.y - fontSize.toPixels('y'), this.x + this.measureText(ctx), this.y));					
+				}
+				else {
+					// render as temporary group
+					var g = new svg.Element.g();
+					g.children = this.children;
+					g.parent = this;
+					g.render(ctx);
+				}
+			}
+			
+			this.onclick = function() {
+				window.open(this.getHrefAttribute().value);
+			}
+			
+			this.onmousemove = function() {
+				svg.ctx.canvas.style.cursor = 'pointer';
+			}
+		}
+		svg.Element.a.prototype = new svg.Element.TextElementBase;		
+		
+		// image element
+		svg.Element.image = function(node) {
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			var href = this.getHrefAttribute().value;
+			var isSvg = href.match(/\.svg$/)
+			
+			svg.Images.push(this);
+			this.loaded = false;
+			if (!isSvg) {
+				this.img = document.createElement('img');
+				var self = this;
+				this.img.onload = function() { self.loaded = true; }
+				this.img.onerror = function() { if (typeof(console) != 'undefined') { console.log('ERROR: image "' + href + '" not found'); self.loaded = true; } }
+				this.img.src = href;
+			}
+			else {
+				this.img = svg.ajax(href);
+				this.loaded = true;
+			}
+			
+			this.renderChildren = function(ctx) {
+				var x = this.attribute('x').toPixels('x');
+				var y = this.attribute('y').toPixels('y');
+				
+				var width = this.attribute('width').toPixels('x');
+				var height = this.attribute('height').toPixels('y');			
+				if (width == 0 || height == 0) return;
+			
+				ctx.save();
+				if (isSvg) {
+					ctx.drawSvg(this.img, x, y, width, height);
+				}
+				else {
+					ctx.translate(x, y);
+					svg.AspectRatio(ctx,
+									this.attribute('preserveAspectRatio').value,
+									width,
+									this.img.width,
+									height,
+									this.img.height,
+									0,
+									0);	
+					ctx.drawImage(this.img, 0, 0);		
+				}
+				ctx.restore();
+			}
+			
+			this.getBoundingBox = function() {
+				var x = this.attribute('x').toPixels('x');
+				var y = this.attribute('y').toPixels('y');
+				var width = this.attribute('width').toPixels('x');
+				var height = this.attribute('height').toPixels('y');
+				return new svg.BoundingBox(x, y, x + width, y + height);
+			}
+		}
+		svg.Element.image.prototype = new svg.Element.RenderedElementBase;
+		
+		// group element
+		svg.Element.g = function(node) {
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			this.getBoundingBox = function() {
+				var bb = new svg.BoundingBox();
+				for (var i=0; i<this.children.length; i++) {
+					bb.addBoundingBox(this.children[i].getBoundingBox());
+				}
+				return bb;
+			};
+		}
+		svg.Element.g.prototype = new svg.Element.RenderedElementBase;
+
+		// symbol element
+		svg.Element.symbol = function(node) {
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			this.baseSetContext = this.setContext;
+			this.setContext = function(ctx) {		
+				this.baseSetContext(ctx);
+				
+				// viewbox
+				if (this.attribute('viewBox').hasValue()) {				
+					var viewBox = svg.ToNumberArray(this.attribute('viewBox').value);
+					var minX = viewBox[0];
+					var minY = viewBox[1];
+					width = viewBox[2];
+					height = viewBox[3];
+					
+					svg.AspectRatio(ctx,
+									this.attribute('preserveAspectRatio').value, 
+									this.attribute('width').toPixels('x'),
+									width,
+									this.attribute('height').toPixels('y'),
+									height,
+									minX,
+									minY);
+
+					svg.ViewPort.SetCurrent(viewBox[2], viewBox[3]);						
+				}
+			}			
+		}
+		svg.Element.symbol.prototype = new svg.Element.RenderedElementBase;		
+			
+		// style element
+		svg.Element.style = function(node) { 
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			// text, or spaces then CDATA
+			var css = ''
+			for (var i=0; i<node.childNodes.length; i++) {
+			  css += node.childNodes[i].nodeValue;
+			}
+			css = css.replace(/(\/\*([^*]|[\r\n]|(\*+([^*\/]|[\r\n])))*\*+\/)|(^[\s]*\/\/.*)/gm, ''); // remove comments
+			css = svg.compressSpaces(css); // replace whitespace
+			var cssDefs = css.split('}');
+			for (var i=0; i<cssDefs.length; i++) {
+				if (svg.trim(cssDefs[i]) != '') {
+					var cssDef = cssDefs[i].split('{');
+					var cssClasses = cssDef[0].split(',');
+					var cssProps = cssDef[1].split(';');
+					for (var j=0; j<cssClasses.length; j++) {
+						var cssClass = svg.trim(cssClasses[j]);
+						if (cssClass != '') {
+							var props = {};
+							for (var k=0; k<cssProps.length; k++) {
+								var prop = cssProps[k].indexOf(':');
+								var name = cssProps[k].substr(0, prop);
+								var value = cssProps[k].substr(prop + 1, cssProps[k].length - prop);
+								if (name != null && value != null) {
+									props[svg.trim(name)] = new svg.Property(svg.trim(name), svg.trim(value));
+								}
+							}
+							svg.Styles[cssClass] = props;
+							if (cssClass == '@font-face') {
+								var fontFamily = props['font-family'].value.replace(/"/g,'');
+								var srcs = props['src'].value.split(',');
+								for (var s=0; s<srcs.length; s++) {
+									if (srcs[s].indexOf('format("svg")') > 0) {
+										var urlStart = srcs[s].indexOf('url');
+										var urlEnd = srcs[s].indexOf(')', urlStart);
+										var url = srcs[s].substr(urlStart + 5, urlEnd - urlStart - 6);
+										var doc = svg.parseXml(svg.ajax(url));
+										var fonts = doc.getElementsByTagName('font');
+										for (var f=0; f<fonts.length; f++) {
+											var font = svg.CreateElement(fonts[f]);
+											svg.Definitions[fontFamily] = font;
+										}
+									}
+								}
+							}
+						}
+					}
+				}
+			}
+		}
+		svg.Element.style.prototype = new svg.Element.ElementBase;
+		
+		// use element 
+		svg.Element.use = function(node) {
+			this.base = svg.Element.RenderedElementBase;
+			this.base(node);
+			
+			this.baseSetContext = this.setContext;
+			this.setContext = function(ctx) {
+				this.baseSetContext(ctx);
+				if (this.attribute('x').hasValue()) ctx.translate(this.attribute('x').toPixels('x'), 0);
+				if (this.attribute('y').hasValue()) ctx.translate(0, this.attribute('y').toPixels('y'));
+			}
+			
+			this.getDefinition = function() {
+				var element = this.getHrefAttribute().getDefinition();
+				if (this.attribute('width').hasValue()) element.attribute('width', true).value = this.attribute('width').value;
+				if (this.attribute('height').hasValue()) element.attribute('height', true).value = this.attribute('height').value;
+				return element;
+			}
+			
+			this.path = function(ctx) {
+				var element = this.getDefinition();
+				if (element != null) element.path(ctx);
+			}
+			
+			this.getBoundingBox = function() {
+				var element = this.getDefinition();
+				if (element != null) return element.getBoundingBox();
+			}
+			
+			this.renderChildren = function(ctx) {
+				var element = this.getDefinition();
+				if (element != null) {
+					// temporarily detach from parent and render
+					var oldParent = element.parent;
+					element.parent = null;
+					element.render(ctx);
+					element.parent = oldParent;
+				}
+			}
+		}
+		svg.Element.use.prototype = new svg.Element.RenderedElementBase;
+		
+		// mask element
+		svg.Element.mask = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+						
+			this.apply = function(ctx, element) {
+				// render as temp svg	
+				var x = this.attribute('x').toPixels('x');
+				var y = this.attribute('y').toPixels('y');
+				var width = this.attribute('width').toPixels('x');
+				var height = this.attribute('height').toPixels('y');
+				
+				if (width == 0 && height == 0) {
+					var bb = new svg.BoundingBox();
+					for (var i=0; i<this.children.length; i++) {
+						bb.addBoundingBox(this.children[i].getBoundingBox());
+					}
+					var x = Math.floor(bb.x1);
+					var y = Math.floor(bb.y1);
+					var width = Math.floor(bb.width());
+					var	height = Math.floor(bb.height());
+				}
+				
+				// temporarily remove mask to avoid recursion
+				var mask = element.attribute('mask').value;
+				element.attribute('mask').value = '';
+				
+					var cMask = document.createElement('canvas');
+					cMask.width = x + width;
+					cMask.height = y + height;
+					var maskCtx = cMask.getContext('2d');
+					this.renderChildren(maskCtx);
+				
+					var c = document.createElement('canvas');
+					c.width = x + width;
+					c.height = y + height;
+					var tempCtx = c.getContext('2d');
+					element.render(tempCtx);
+					tempCtx.globalCompositeOperation = 'destination-in';
+					tempCtx.fillStyle = maskCtx.createPattern(cMask, 'no-repeat');
+					tempCtx.fillRect(0, 0, x + width, y + height);
+					
+					ctx.fillStyle = tempCtx.createPattern(c, 'no-repeat');
+					ctx.fillRect(0, 0, x + width, y + height);
+					
+				// reassign mask
+				element.attribute('mask').value = mask;	
+			}
+			
+			this.render = function(ctx) {
+				// NO RENDER
+			}
+		}
+		svg.Element.mask.prototype = new svg.Element.ElementBase;
+		
+		// clip element
+		svg.Element.clipPath = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			this.apply = function(ctx) {
+				for (var i=0; i<this.children.length; i++) {
+					var child = this.children[i];
+					if (typeof(child.path) != 'undefined') {
+						var transform = null;
+						if (child.attribute('transform').hasValue()) { 
+							transform = new svg.Transform(child.attribute('transform').value);
+							transform.apply(ctx);
+						}
+						child.path(ctx);
+						ctx.clip();
+						if (transform) { transform.unapply(ctx); }
+					}
+				}
+			}
+			
+			this.render = function(ctx) {
+				// NO RENDER
+			}
+		}
+		svg.Element.clipPath.prototype = new svg.Element.ElementBase;
+
+		// filters
+		svg.Element.filter = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+						
+			this.apply = function(ctx, element) {
+				// render as temp svg	
+				var bb = element.getBoundingBox();
+				var x = Math.floor(bb.x1);
+				var y = Math.floor(bb.y1);
+				var width = Math.floor(bb.width());
+				var	height = Math.floor(bb.height());
+
+				// temporarily remove filter to avoid recursion
+				var filter = element.style('filter').value;
+				element.style('filter').value = '';
+				
+				var px = 0, py = 0;
+				for (var i=0; i<this.children.length; i++) {
+					var efd = this.children[i].extraFilterDistance || 0;
+					px = Math.max(px, efd);
+					py = Math.max(py, efd);
+				}
+				
+				var c = document.createElement('canvas');
+				c.width = width + 2*px;
+				c.height = height + 2*py;
+				var tempCtx = c.getContext('2d');
+				tempCtx.translate(-x + px, -y + py);
+				element.render(tempCtx);
+			
+				// apply filters
+				for (var i=0; i<this.children.length; i++) {
+					this.children[i].apply(tempCtx, 0, 0, width + 2*px, height + 2*py);
+				}
+				
+				// render on me
+				ctx.drawImage(c, 0, 0, width + 2*px, height + 2*py, x - px, y - py, width + 2*px, height + 2*py);
+				
+				// reassign filter
+				element.style('filter', true).value = filter;	
+			}
+			
+			this.render = function(ctx) {
+				// NO RENDER
+			}		
+		}
+		svg.Element.filter.prototype = new svg.Element.ElementBase;
+		
+		svg.Element.feMorphology = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			this.apply = function(ctx, x, y, width, height) {
+				// TODO: implement
+			}
+		}
+		svg.Element.feMorphology.prototype = new svg.Element.ElementBase;
+		
+		svg.Element.feColorMatrix = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+			
+			function imGet(img, x, y, width, height, rgba) {
+				return img[y*width*4 + x*4 + rgba];
+			}
+			
+			function imSet(img, x, y, width, height, rgba, val) {
+				img[y*width*4 + x*4 + rgba] = val;
+			}
+			
+			this.apply = function(ctx, x, y, width, height) {
+				// only supporting grayscale for now per Issue 195, need to extend to all matrix
+				// assuming x==0 && y==0 for now
+				var srcData = ctx.getImageData(0, 0, width, height);
+				for (var y = 0; y < height; y++) {
+					for (var x = 0; x < width; x++) {
+						var r = imGet(srcData.data, x, y, width, height, 0);
+						var g = imGet(srcData.data, x, y, width, height, 1);
+						var b = imGet(srcData.data, x, y, width, height, 2);
+						var gray = (r + g + b) / 3;
+						imSet(srcData.data, x, y, width, height, 0, gray);
+						imSet(srcData.data, x, y, width, height, 1, gray);
+						imSet(srcData.data, x, y, width, height, 2, gray);
+					}
+				}
+				ctx.clearRect(0, 0, width, height);
+				ctx.putImageData(srcData, 0, 0);
+			}
+		}
+		svg.Element.feColorMatrix.prototype = new svg.Element.ElementBase;
+		
+		svg.Element.feGaussianBlur = function(node) {
+			this.base = svg.Element.ElementBase;
+			this.base(node);
+
+			this.blurRadius = Math.floor(this.attribute('stdDeviation').numValue());
+			this.extraFilterDistance = this.blurRadius;
+			
+			this.apply = function(ctx, x, y, width, height) {
+				if (typeof(stackBlurCanvasRGBA) == 'undefined') {
+					if (typeof(console) != 'undefined') { console.log('ERROR: StackBlur.js must be included for blur to work'); }
+					return;
+				}
+				
+				// StackBlur requires canvas be on document
+				ctx.canvas.id = svg.UniqueId();
+				ctx.canvas.style.display = 'none';
+				document.body.appendChild(ctx.canvas);
+				stackBlurCanvasRGBA(ctx.canvas.id, x, y, width, height, this.blurRadius);
+				document.body.removeChild(ctx.canvas);
+			}
+		}
+		svg.Element.feGaussianBlur.prototype = new svg.Element.ElementBase;
+		
+		// title element, do nothing
+		svg.Element.title = function(node) {
+		}
+		svg.Element.title.prototype = new svg.Element.ElementBase;
+
+		// desc element, do nothing
+		svg.Element.desc = function(node) {
+		}
+		svg.Element.desc.prototype = new svg.Element.ElementBase;		
+		
+		svg.Element.MISSING = function(node) {
+			if (typeof(console) != 'undefined') { console.log('ERROR: Element \'' + node.nodeName + '\' not yet implemented.'); }
+		}
+		svg.Element.MISSING.prototype = new svg.Element.ElementBase;
+		
+		// element factory
+		svg.CreateElement = function(node) {	
+			var className = node.nodeName.replace(/^[^:]+:/,''); // remove namespace
+			className = className.replace(/\-/g,''); // remove dashes
+			var e = null;
+			if (typeof(svg.Element[className]) != 'undefined') {
+				e = new svg.Element[className](node);
+			}
+			else {
+				e = new svg.Element.MISSING(node);
+			}
+
+			e.type = node.nodeName;
+			return e;
+		}
+				
+		// load from url
+		svg.load = function(ctx, url) {
+			svg.loadXml(ctx, svg.ajax(url));
+		}
+		
+		// load from xml
+		svg.loadXml = function(ctx, xml) {
+			svg.loadXmlDoc(ctx, svg.parseXml(xml));
+		}
+		
+		svg.loadXmlDoc = function(ctx, dom) {
+			svg.init(ctx);
+			
+			var mapXY = function(p) {
+				var e = ctx.canvas;
+				while (e) {
+					p.x -= e.offsetLeft;
+					p.y -= e.offsetTop;
+					e = e.offsetParent;
+				}
+				if (window.scrollX) p.x += window.scrollX;
+				if (window.scrollY) p.y += window.scrollY;
+				return p;
+			}
+			
+			// bind mouse
+			if (svg.opts['ignoreMouse'] != true) {
+				ctx.canvas.onclick = function(e) {
+					var p = mapXY(new svg.Point(e != null ? e.clientX : event.clientX, e != null ? e.clientY : event.clientY));
+					svg.Mouse.onclick(p.x, p.y);
+				};
+				ctx.canvas.onmousemove = function(e) {
+					var p = mapXY(new svg.Point(e != null ? e.clientX : event.clientX, e != null ? e.clientY : event.clientY));
+					svg.Mouse.onmousemove(p.x, p.y);
+				};
+			}
+		
+			var e = svg.CreateElement(dom.documentElement);
+			e.root = true;
+					
+			// render loop
+			var isFirstRender = true;
+			var draw = function() {
+				svg.ViewPort.Clear();
+				if (ctx.canvas.parentNode) svg.ViewPort.SetCurrent(ctx.canvas.parentNode.clientWidth, ctx.canvas.parentNode.clientHeight);
+			
+				if (svg.opts['ignoreDimensions'] != true) {
+					// set canvas size
+					if (e.style('width').hasValue()) {
+						ctx.canvas.width = e.style('width').toPixels('x');
+						ctx.canvas.style.width = ctx.canvas.width + 'px';
+					}
+					if (e.style('height').hasValue()) {
+						ctx.canvas.height = e.style('height').toPixels('y');
+						ctx.canvas.style.height = ctx.canvas.height + 'px';
+					}
+				}
+				var cWidth = ctx.canvas.clientWidth || ctx.canvas.width;
+				var cHeight = ctx.canvas.clientHeight || ctx.canvas.height;
+				if (svg.opts['ignoreDimensions'] == true && e.style('width').hasValue() && e.style('height').hasValue()) {
+					cWidth = e.style('width').toPixels('x');
+					cHeight = e.style('height').toPixels('y');
+				}
+				svg.ViewPort.SetCurrent(cWidth, cHeight);		
+				
+				if (svg.opts['offsetX'] != null) e.attribute('x', true).value = svg.opts['offsetX'];
+				if (svg.opts['offsetY'] != null) e.attribute('y', true).value = svg.opts['offsetY'];
+				if (svg.opts['scaleWidth'] != null && svg.opts['scaleHeight'] != null) {
+					var xRatio = 1, yRatio = 1, viewBox = svg.ToNumberArray(e.attribute('viewBox').value);
+					if (e.attribute('width').hasValue()) xRatio = e.attribute('width').toPixels('x') / svg.opts['scaleWidth'];
+					else if (!isNaN(viewBox[2])) xRatio = viewBox[2] / svg.opts['scaleWidth'];
+					if (e.attribute('height').hasValue()) yRatio = e.attribute('height').toPixels('y') / svg.opts['scaleHeight'];
+					else if (!isNaN(viewBox[3])) yRatio = viewBox[3] / svg.opts['scaleHeight'];
+					
+					e.attribute('width', true).value = svg.opts['scaleWidth'];
+					e.attribute('height', true).value = svg.opts['scaleHeight'];			
+					e.attribute('viewBox', true).value = '0 0 ' + (cWidth * xRatio) + ' ' + (cHeight * yRatio);
+					e.attribute('preserveAspectRatio', true).value = 'none';
+				}
+			
+				// clear and render
+				if (svg.opts['ignoreClear'] != true) {
+					ctx.clearRect(0, 0, cWidth, cHeight);
+				}
+				e.render(ctx);
+				if (isFirstRender) {
+					isFirstRender = false;
+					if (typeof(svg.opts['renderCallback']) == 'function') svg.opts['renderCallback'](dom);
+				}			
+			}
+			
+			var waitingForImages = true;
+			if (svg.ImagesLoaded()) {
+				waitingForImages = false;
+				draw();
+			}
+			svg.intervalID = setInterval(function() { 
+				var needUpdate = false;
+				
+				if (waitingForImages && svg.ImagesLoaded()) {
+					waitingForImages = false;
+					needUpdate = true;
+				}
+			
+				// need update from mouse events?
+				if (svg.opts['ignoreMouse'] != true) {
+					needUpdate = needUpdate | svg.Mouse.hasEvents();
+				}
+			
+				// need update from animations?
+				if (svg.opts['ignoreAnimation'] != true) {
+					for (var i=0; i<svg.Animations.length; i++) {
+						needUpdate = needUpdate | svg.Animations[i].update(1000 / svg.FRAMERATE);
+					}
+				}
+				
+				// need update from redraw?
+				if (typeof(svg.opts['forceRedraw']) == 'function') {
+					if (svg.opts['forceRedraw']() == true) needUpdate = true;
+				}
+				
+				// render if needed
+				if (needUpdate) {
+					draw();				
+					svg.Mouse.runEvents(); // run and clear our events
+				}
+			}, 1000 / svg.FRAMERATE);
+		}
+		
+		svg.stop = function() {
+			if (svg.intervalID) {
+				clearInterval(svg.intervalID);
+			}
+		}
+		
+		svg.Mouse = new (function() {
+			this.events = [];
+			this.hasEvents = function() { return this.events.length != 0; }
+		
+			this.onclick = function(x, y) {
+				this.events.push({ type: 'onclick', x: x, y: y, 
+					run: function(e) { if (e.onclick) e.onclick(); }
+				});
+			}
+			
+			this.onmousemove = function(x, y) {
+				this.events.push({ type: 'onmousemove', x: x, y: y,
+					run: function(e) { if (e.onmousemove) e.onmousemove(); }
+				});
+			}			
+			
+			this.eventElements = [];
+			
+			this.checkPath = function(element, ctx) {
+				for (var i=0; i<this.events.length; i++) {
+					var e = this.events[i];
+					if (ctx.isPointInPath && ctx.isPointInPath(e.x, e.y)) this.eventElements[i] = element;
+				}
+			}
+			
+			this.checkBoundingBox = function(element, bb) {
+				for (var i=0; i<this.events.length; i++) {
+					var e = this.events[i];
+					if (bb.isPointInBox(e.x, e.y)) this.eventElements[i] = element;
+				}			
+			}
+			
+			this.runEvents = function() {
+				svg.ctx.canvas.style.cursor = '';
+				
+				for (var i=0; i<this.events.length; i++) {
+					var e = this.events[i];
+					var element = this.eventElements[i];
+					while (element) {
+						e.run(element);
+						element = element.parent;
+					}
+				}		
+			
+				// done running, clear
+				this.events = []; 
+				this.eventElements = [];
+			}
+		});
+		
+		return svg;
+	}
+})();
+
+if (typeof(CanvasRenderingContext2D) != 'undefined') {
+	CanvasRenderingContext2D.prototype.drawSvg = function(s, dx, dy, dw, dh) {
+		canvg(this.canvas, s, { 
+			ignoreMouse: true, 
+			ignoreAnimation: true, 
+			ignoreDimensions: true, 
+			ignoreClear: true, 
+			offsetX: dx, 
+			offsetY: dy, 
+			scaleWidth: dw, 
+			scaleHeight: dh
+		});
+	}
+}
\ No newline at end of file
diff --git a/dammit/viewer/static/circularplot.js b/dammit/viewer/static/circularplot.js
new file mode 100644
index 00000000..673093d4
--- /dev/null
+++ b/dammit/viewer/static/circularplot.js
@@ -0,0 +1,1755 @@
+var circularTrackDefaults = {
+    radius: 5,
+    w: 600,
+    h: 600,
+    factor: 1,
+    factorLegend: .85,
+    TranslateX: 80,
+    TranslateY: 30,
+    ExtraWidthX: 100,
+    ExtraWidthY: 100,
+    radians: 2 * Math.PI,
+    spacing: 100000,
+    legend_spacing: 5,
+    min_radians: .02 * Math.PI,
+    dragresize: true,
+    movecursor: false
+}
+
+function circularTrack(layout,tracks) {
+
+    this.tracks = tracks;
+    this.layout = layout;
+    this.numTracks = tracks.length;
+
+    if('undefined' !== typeof layout) {
+	    // Copy over any defaults not passed in
+	    // by the user
+	    for(var i in circularTrackDefaults) {
+		if('undefined' == typeof layout[i]) {
+		    this.layout[i] = circularTrackDefaults[i];
+		}
+	    }
+	}
+
+    if('undefined' == typeof layout.plotid) {
+	this.layout.plotid = layout.container.slice(1);
+    }
+
+    this.layout.containerid =  layout.container.slice(1);
+
+    // Some constants for later so we don't have to keep recalculating
+    this.layout.w2 = this.layout.w / 2;
+    this.layout.h2 = this.layout.h / 2;
+    this.layout.PI2 = Math.PI/2;
+
+    // Setup some constants we'll need and build the canvas
+    this.layout.radians_pre_bp = this.layout.radians/this.layout.genomesize;
+    this.layout.min_bp_per_slice = this.layout.min_radians / this.layout.radians_pre_bp;
+    this.layout.min_bp_per_slice_half = this.layout.min_bp_per_slice/2;
+    this.layout.radius = this.layout.factor*Math.min(this.layout.w2, this.layout.h2);
+    this.xScale = d3.scale.linear()
+	.range([0,this.layout.radians])
+	.domain([0, layout.genomesize]);
+    var xScale = this.xScale;
+    d3.select(layout.container).select("svg").remove();
+
+    this.container = d3.select(layout.container)
+	.append("svg")	
+	.attr("id", function() { return layout.container.slice(1) + "_svg"; })
+	.attr("width", this.layout.w+this.layout.ExtraWidthX)
+	.attr("height", this.layout.h+this.layout.ExtraWidthY); 
+   
+    this.g = this.container
+	.append("g")
+	.attr("id", function() { return layout.container.slice(1) + "_g"; })
+	.attr("transform", "translate(" + this.layout.TranslateX + "," + this.layout.TranslateY + ")");
+
+    // Add the double click functionality, but we needed to define g first
+    this.container.on("dblclick", function(d,i) {
+	    if('undefined' !== typeof this.layout.dblclick) {
+		var node = this.g.node();
+		var curBP = calcRadBPfromXY((d3.mouse(node)[0] - (this.layout.w2)),
+						  -(d3.mouse(node)[1] - (this.layout.h2)),
+						  xScale)[1];
+		var fn = window[this.layout.dblclick];
+
+		if('object' ==  typeof fn) {
+		    return fn.ondblclick(this.layout.plotid, curBP);
+		} else if('function' == typeof fn) {
+		    return fn(this.layout.plotid, curBP);
+		}
+
+	    } else {
+		null;
+	    }
+	}.bind(this));
+
+    this.defs = this.g.append("defs");
+
+    this.defs.append('svg:marker')
+	.attr('id', 'end-arrow')
+	.attr('viewBox', '0 -5 10 10')
+	.attr('refX', 6)
+	.attr('markerWidth', 7)
+	.attr('markerHeight', 7)
+	.attr('orient', 'auto')
+	.append('svg:path')
+	.attr('d', 'M0,-5L10,0L0,5')
+	.attr('class', "move-cross");
+
+    this.defs.append('svg:marker')
+	.attr('id', 'start-arrow')
+	.attr('viewBox', '0 -5 10 10')
+	.attr('refX', 4)
+	.attr('markerWidth', 7)
+	.attr('markerHeight', 7)
+	.attr('orient', 'auto')
+	.append('svg:path')
+	.attr('d', 'M10,-5L0,0L10,5')
+	.attr('class', "move-cross");
+	//    .attr('fill', '#000');
+
+    // Display the dragging cross if needed
+    if(this.layout.movecursor == true) {
+	this.g.append("rect")
+	    .attr("width", 18)
+	    .attr("height", 18)
+	    .attr("fill-opacity", 0)
+	    .attr("class", "move-shadow move_" + this.layout.containerid);
+
+	this.g.append("line")
+	    .attr("x1", 0)
+	    .attr("x2", 18)
+	    .attr("y1", 9)
+	    .attr("y2", 9)
+	    .style('marker-start', 'url(#start-arrow)')
+	    .style('marker-end', 'url(#end-arrow)')
+	    .attr("class", "move-cross move_" + this.layout.containerid);
+
+	this.g.append("line")
+	    .attr("x1", 9)
+	    .attr("x2", 9)
+	    .attr("y1", 0)
+	    .attr("y2", 18)
+	    .style('marker-start', 'url(#start-arrow)')
+	    .style('marker-end', 'url(#end-arrow)')
+	    .attr("class", "move-cross move_" + this.layout.containerid);
+    }
+
+    // Resize drag shadow
+    if(this.layout.dragresize == true) {
+	this.drag_shadow = this.container.append("rect")
+	    .attr("width", (this.layout.w+this.layout.ExtraWidthX))
+	    .attr("height", (this.layout.h+this.layout.ExtraWidthY))
+	    .attr("class", "dragbar-shadow linear_hidden");
+    }
+
+    // Now we can start drawing the plots, first the basic axis...
+    this.drawAxis();
+
+    this.tip = d3.tip()
+	.attr('class', 'd3-tip')
+	.offset([-10, 0])
+	.html(function(d) {
+		return "<strong>Name:</strong> <span style='color:red'>" + d.name + "</span>";
+	    });
+
+    this.container.call(this.tip);
+
+    // Draw the plots
+    for(var i=0; i < this.tracks.length; i++) {
+
+	if('undefined' !== typeof this.tracks[i].visible) {
+	    if(! this.tracks[i].visible) {
+		continue;
+	    }
+	} else {
+	    // If the user didn't set visible,
+	    // then it's visible.
+	    this.tracks[i].visible = true;
+	}
+
+	// We're going to see what type of tracks we have
+	// and dispatch them appropriately
+
+	switch(this.tracks[i].trackType) {
+	case "plot":
+	    tracks[i].rad_per_elem = tracks[i].bp_per_element*this.layout.radians_pre_bp;
+	    this.drawPlot(i);
+	    break;
+	case "track":
+	    this.drawTrack(i);
+	    break;
+	case "stranded":
+	    this.drawTrack(i);
+	    break;
+	case "gap":
+	    this.drawGap(i);
+	    break;
+	case "glyph":
+	    this.findGlyphTypes(i);
+
+	    if('undefined' !== typeof this.tracks[i].hideTypes) {
+		this.maskGlyphTypes(i, this.tracks[i].hideTypes)
+	    }
+	    //	    this.tracks[i].container = 
+	    //	this.g.append("g")
+	    //	.attr("class", this.tracks[i].trackName + "_glyph_container")
+	    this.drawGlyphTrack(i);
+	    break;
+	default:
+	    // Do nothing for an unknown track type
+	}
+    }
+
+    // Resize dragger
+    if(this.layout.dragresize == true) {
+	var dragright = d3.behavior.drag()
+	.on("dragstart", this.dragresize_start.bind(this))
+	    .on("drag", this.dragresize.bind(this))
+	    .on("dragend", this.dragresize_end.bind(this));
+
+	this.dragbar_y_mid = this.layout.h/2;
+	this.dragbar = this.container.append("g")
+	    .attr("transform", "translate(" + (this.layout.w+this.layout.ExtraWidthX-25) + "," +  (this.layout.h+this.layout.ExtraWidthY-25) + ")")
+	    .attr("width", 25)
+	    .attr("height", 20)
+	    .attr("fill", "lightblue")
+	    .attr("fill-opacity", .2)
+	    .attr("cursor", "ew-resize")
+	    .call(dragright);
+
+	this.dragbar.append("rect")
+	    .attr("width", 25)
+	    .attr("height", 20)
+	    .attr("fill-opacity", 0);
+
+	this.dragbar.append("line")
+	    .attr("x1", 16)
+	    .attr("x2", 16)
+	    .attr("y1", 0)
+	    .attr("y2", 14)
+	    .attr("class", "dragbar-line");
+	this.dragbar.append("line")
+	    .attr("x1", 2)
+	    .attr("x2", 16)
+	    .attr("y1", 14)
+	    .attr("y2", 14)
+	    .attr("class", "dragbar-line");
+	this.dragbar.append("line")
+	    .attr("x1", 19)
+	    .attr("x2", 19)
+	    .attr("y1", 0)
+	    .attr("y2", 17)
+	    .attr("class", "dragbar-line");
+	this.dragbar.append("line")
+	    .attr("x1", 2)
+	    .attr("x2", 19)
+	    .attr("y1", 17)
+	    .attr("y2", 17)
+	    .attr("class", "dragbar-line");
+	this.dragbar.append("line")
+	    .attr("x1", 22)
+	    .attr("x2", 22)
+	    .attr("y1", 0)
+	    .attr("y2", 20)
+	    .attr("class", "dragbar-line");
+	this.dragbar.append("line")
+	    .attr("x1", 2)
+	    .attr("x2", 22)
+	    .attr("y1", 20)
+	    .attr("y2", 20)
+	    .attr("class", "dragbar-line");
+    }
+
+}
+
+circularTrack.prototype.drawAxis = function() {
+    var cfg = this.layout;
+    var g = this.g;
+
+    this.axis_container = this.g
+	.append("g")
+	.attr("id", "axis_container");
+
+    var axis = this.axis_container.selectAll(".axis")
+    .data(d3.range(0,cfg.genomesize, cfg.spacing))
+    .enter()
+    .append("g")
+    .attr("class", "axis");
+
+    axis.append("line")
+    .attr("x1", function(d, i){return cfg.w2 + (20*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
+    .attr("y1", function(d, i){return cfg.h2 + (20*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));})
+    .attr("x2", function(d, i){return cfg.w2 + (cfg.radius*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
+    .attr("y2", function(d, i){return cfg.h2 + (cfg.radius*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));})
+    .attr("class", "line")
+    .style("stroke", "grey")
+    .style("stroke-width", "1px");
+
+    var axis_label = this.axis_container.selectAll(".axislabel")
+    .data(d3.range(0,cfg.genomesize, cfg.spacing*cfg.legend_spacing))
+    .enter()
+    .append("g")
+    .attr("class", "axislabel");
+      
+    axis_label.append("text")
+    .attr("class", "legend")
+    .text(function(d){ var prefix = d3.formatPrefix(d);
+	    return prefix.scale(d) + prefix.symbol;
+	})
+    .style("font-family", "sans-serif")
+    .style("font-size", "11px")
+    .attr("text-anchor", "middle")
+    .attr("dy", "1.5em")
+    .attr("transform", function(d, i){return "translate(0, -10)"})
+    .attr("x", function(d, i){return cfg.w2 + ((cfg.radius+10)*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
+    .attr("y", function(d, i){return cfg.h2 + ((cfg.radius+10)*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));});
+
+    // And draw the pretty outer circle for the axis
+    this.drawCircle("outerAxis", cfg.radius-10, 'grey');
+}
+
+circularTrack.prototype.moveAxis = function() {
+    var cfg = this.layout;
+
+    this.axis_container
+	.selectAll("line")
+	.data(d3.range(0,cfg.genomesize, cfg.spacing))
+        .transition()
+        .duration(1000)
+	.attr("x1", function(d, i){return cfg.w2 + (20*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
+	.attr("y1", function(d, i){return cfg.h2 + (20*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));})
+	.attr("x2", function(d, i){return cfg.w2 + (cfg.radius*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
+	.attr("y2", function(d, i){return cfg.h2 + (cfg.radius*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));});
+
+    this.axis_container
+	.selectAll("text")
+	.data(d3.range(0,cfg.genomesize, cfg.spacing*cfg.legend_spacing))
+        .transition()
+        .duration(1000)
+	.attr("x", function(d, i){return cfg.w2 + ((cfg.radius+10)*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
+	.attr("y", function(d, i){return cfg.h2 + ((cfg.radius+10)*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));});
+
+    // And draw the pretty outer circle for the axis
+    this.moveCircle("outerAxis", cfg.radius-10);
+
+}
+// Helper function for drawing needed circles such
+// as in stranded tracks
+// Can be called standalone in setting up the look
+// of your genome
+
+circularTrack.prototype.drawCircle = function(name, radius, line_stroke, animate) {
+    var g = this.g;
+    var cfg = this.layout;
+
+    g.append("circle")
+    .attr("r", (('undefined' == typeof animate) ? radius : 1 ))
+    .attr("class", name + "_circle")
+    .style("fill", "none")
+    .style("stroke", line_stroke)
+    .attr("cx", cfg.w2)
+    .attr("cy", cfg.h2);
+
+    // An animated entrance
+    if('undefined' !== typeof animate) {
+	this.moveCircle(name, radius);
+    }
+
+}
+
+// Change the radius of an inscribed circle
+
+circularTrack.prototype.moveCircle = function(name, radius) {
+    var g = this.g;
+    var cfg = this.layout;
+
+    g.selectAll("." + name + "_circle")
+    .transition()
+    .duration(1000)
+    .attr("r", radius)
+    .attr("cx", cfg.w2)
+    .attr("cy", cfg.h2);
+
+}
+
+// Remove a drawn circle, in a pretty animated way
+
+circularTrack.prototype.removeCircle = function(name) {
+    var g = this.g;
+
+    g.selectAll("." + name + "_circle")
+    .transition()
+    .duration(1000)
+    .attr("r", 1)
+    .style("opacity", 0)
+    .remove();
+}
+
+/////////////////////////////////////////
+//
+// Plot type tracks (as in line graphs)
+//
+/////////////////////////////////////////
+
+circularTrack.prototype.drawPlot = function(i, animate) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+
+    this.tracks[i].plotRange = d3.scale.linear()
+    .domain([track.plot_min, track.plot_max])
+    .range([track.plot_radius-(track.plot_width/2), track.plot_radius+(track.plot_width/2)]);
+
+    var plotRange = this.tracks[i].plotRange;
+
+    var lineFunction = d3.svg.line()
+    .x(function(d, i) { return cfg.w2 + ((('undefined' == typeof animate) ? plotRange(d) : 1 )*Math.cos((i*track.rad_per_elem)-(cfg.PI2))); })
+    .y(function(d, i) { return cfg.h2 + ((('undefined' == typeof animate) ? plotRange(d) : 1 )*Math.sin((i*track.rad_per_elem)-(cfg.PI2))); })
+    .interpolate("linear");
+
+    g.append("path")
+    .attr("d", lineFunction(track.items))
+    .attr("class", track.trackName)
+    .attr("id", track.trackName)
+    .attr("stroke-width", 1)
+    .attr("fill", "none");
+
+    // Now do the mean circle if we have one
+    if('undefined' !== typeof track.plot_mean) {
+	this.drawCircle(track.trackName,  this.tracks[i].plotRange(track.plot_mean), "grey", animate);
+    }  
+
+    // And if we're doing an animated entrance...
+    if('undefined' !== typeof animate) {
+	this.movePlot(i, track.plot_radius);
+    }
+
+    // Mark the track as visible, if not already
+    this.tracks[i].visible = true;
+}
+
+circularTrack.prototype.movePlot = function(i, radius) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+
+    // Save this in case this is a change of radius
+    // ratherthan an animated entrance
+    if('undefined' !== typeof this.tracks[i].plot_radius) {
+	this.tracks[i].plot_radius = radius;
+    }
+
+    // We needed to save the new radius but if this
+    // track isn't visible, do nothing
+    if(! this.tracks[i].visible) {
+	return;
+    }
+
+    this.tracks[i].plotRange
+	.range([track.plot_radius-(track.plot_width/2), track.plot_radius+(track.plot_width/2)]);
+
+    var plotRange = this.tracks[i].plotRange;
+
+    var lineFunction = d3.svg.line()
+    .x(function(d, i, j) { return cfg.w2 + (plotRange(d)*Math.cos((i*track.rad_per_elem)-(cfg.PI2))); })
+    .y(function(d, i) { return cfg.h2 + (plotRange(d)*Math.sin((i*track.rad_per_elem)-(cfg.PI2))); })
+    .interpolate("linear");
+
+    var plot = g.selectAll("." + track.trackName)
+
+    plot.transition()
+    .duration(1000)
+    .attr("d", function(d,i) { return lineFunction(track.items)});
+
+    // Now move the mean circle if we have one
+    if('undefined' !== typeof track.plot_mean) {
+	this.moveCircle(track.trackName, this.tracks[i].plotRange(track.plot_mean));
+    }  
+}
+
+circularTrack.prototype.removePlot = function(i) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+
+    var plotRange = d3.scale.linear()
+    .domain([track.plot_min, track.plot_max])
+    .range([1-(track.plot_width/2), 1+(track.plot_width/2)]);
+
+    var lineFunction = d3.svg.line()
+    .x(function(d, i) { return cfg.w2 + (plotRange(d)*Math.cos((i*track.rad_per_elem)-(cfg.PI2))); })
+    .y(function(d, i) { return cfg.h2 + (plotRange(d)*Math.sin((i*track.rad_per_elem)-(cfg.PI2))); })
+    .interpolate("linear");
+
+    g.selectAll("." + track.trackName)
+    .transition()
+    .duration(1000)
+    .attr("d", lineFunction(track.items))
+    .style("opacity", 0)
+    .remove();
+
+      if('undefined' !== typeof track.plot_mean) {
+	  this.removeCircle(track.trackName);
+      }
+
+    // Mark the track as not visible
+    this.tracks[i].visible = false;
+}
+
+
+////////////////////////////////////////////////
+//
+// Track type tracks (as blocks without strands)
+//
+////////////////////////////////////////////////
+
+circularTrack.prototype.drawTrack = function(i, animate) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+
+    // Because of how the tooltip library binds to the SVG object we have to turn it
+    // on or off here rather than in the .on() call, we'll redirect the calls to
+    // a dummy do-nothing object if we're not showing tips in this context.
+    var tip = {show: function() {}, hide: function() {} };
+    if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
+	tip = this.tip;
+    }
+
+    // The arc object which will be passed in to each
+    // set of data
+    var arc = d3.svg.arc()
+    .innerRadius(function(d){ return (('undefined' == typeof animate) ? 
+				      calcInnerRadius(track.inner_radius, track.outer_radius, d.strand) 
+				      : 1);})
+    .outerRadius(function(d){ return (('undefined' == typeof animate) ? 
+				      calcOuterRadius(track.inner_radius, track.outer_radius, d.strand)
+				      : 2);})
+    .startAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
+		return (d.start - ((d.end - d.start - cfg.min_bp_per_slice_half) / 2))*cfg.radians_pre_bp;
+	    } else {
+		return cfg.radians_pre_bp*d.start;
+	    }
+	})
+    .endAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
+		return (d.end + ((d.end - d.start - cfg.min_bp_per_slice_half)/2))*cfg.radians_pre_bp;
+	    } else {
+		return cfg.radians_pre_bp*d.end;
+	    }
+	});
+      
+    // Draw the track, putting in elements such as hover colour change
+    // if one exists, click events, etc
+    g.selectAll(".tracks."+track.trackName)
+    .data(track.items)
+    .enter()
+    .append("path")
+    .attr("d", arc)
+    .attr("class", function(d) { return track.trackName + ('undefined' !== typeof d.strand ? '_' + (d.strand == 1 ? 'pos' : 'neg') : '') + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
+    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")
+    .on("click", function(d,i) {
+	    if('undefined' !== typeof track.mouseclick) {
+		var fn = window[track.mouseclick];
+		if('object' ==  typeof fn) {
+//		    console.log(fn);
+		    return fn.onclick(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+
+	    } else {
+		null;
+	    }
+	})
+    .on("mouseover", function(d, i) {
+	    tip.show(d);
+	    if('undefined' !== typeof track.mouseover_callback) {
+		var fn = window[track.mouseover_callback];
+		if('object' ==  typeof fn) {
+		    fn.mouseover(track.trackName, d, cfg.plotid);
+		    return true;
+		} else if('function' == typeof fn) {
+		    return fn(track.trackNamed, cfg.plotid);
+		}
+
+	    } else {
+		return null;
+	    }
+	})
+    .on("mouseout", function(d, i) {
+	    tip.hide(d);
+    	    if('undefined' !== typeof track.mouseout_callback) {
+		var fn = window[track.mouseout_callback];
+		if('object' ==  typeof fn) {
+		    return fn.mouseout(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackNamed, cfg.plotid);
+		}
+
+    	    } else {
+		return null;
+	    }
+    	});
+
+    // If we're doing an animated addition, move the track out to its
+    // new spot
+    if('undefined' !== typeof animate) {
+	this.moveTrack(i, track.inner_radius, track.outer_radius);
+    }
+
+    // And check if we've been asked to do a centre line
+    if('undefined' !== typeof track.centre_line_stroke) {
+	this.drawCircle(track.trackName, (track.inner_radius + track.outer_radius)/2, track.centre_line_stroke, animate);
+      }
+
+    this.tracks[i].visible = true;
+
+}
+
+circularTrack.prototype.moveTrack = function(i, innerRadius, outerRadius) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+
+    // Just record the new radii in case we need them later
+    if('undefined' !== typeof this.tracks[i].inner_radius) {
+	this.tracks[i].inner_radius = innerRadius;
+    }
+    if('undefined' !== typeof this.tracks[i].outer_radius) {
+	this.tracks[i].outer_radius = outerRadius;
+    }
+
+    // We needed to save the new radius but if this
+    // track isn't visible, do nothing
+    if(! this.tracks[i].visible) {
+	return;
+    }
+
+    var arcShrink = d3.svg.arc()
+    .innerRadius(function(d){return calcInnerRadius(innerRadius, outerRadius, d.strand);})
+    .outerRadius(function(d){return calcOuterRadius(innerRadius, outerRadius, d.strand);})
+    .startAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
+		return (d.start - ((d.end - d.start - cfg.min_bp_per_slice_half) / 2))*cfg.radians_pre_bp;
+	    } else {
+		return cfg.radians_pre_bp*d.start;
+	    }
+	})
+    .endAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
+		return (d.end + ((d.end - d.start - cfg.min_bp_per_slice_half)/2))*cfg.radians_pre_bp;
+	    } else {
+		return cfg.radians_pre_bp*d.end;
+	    }
+	});
+ 
+
+    //   .endAngle(function(d){return cfg.radians_pre_bp*d.start;})
+    //    .startAngle(function(d){return cfg.radians_pre_bp*d.end;});
+
+    g.selectAll("." + track.trackName + ", ." + track.trackName + "_pos, ." + track.trackName + "_neg")
+    .transition()
+    .duration(1000)
+    .attr("d", arcShrink)
+    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")
+
+    // And check if we've been asked to do a centre line
+    if('undefined' !== typeof track.centre_line_stroke) {
+	this.moveCircle(track.trackName, (track.inner_radius + track.outer_radius)/2);
+      }
+
+}
+
+circularTrack.prototype.removeTrack = function(i) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+
+    var arcShrink = d3.svg.arc()
+    .innerRadius(1)
+    .outerRadius(2)
+    .endAngle(function(d){return cfg.radians_pre_bp*d.start;})
+    .startAngle(function(d){return cfg.radians_pre_bp*d.end;});
+
+    g.selectAll("." + track.trackName + ", ." + track.trackName + "_pos, ." + track.trackName + "_neg")
+    .transition()
+    .duration(1000)
+    .attr("d", arcShrink)
+    .style("opacity", 0)
+    .remove();
+
+    if('undefined' !== track.centre_line_stroke) {
+	this.removeCircle(track.trackName);
+    }
+
+    this.tracks[i].visible = false;
+
+}
+
+////////////////////////////////////////////////
+//
+// Gap type tracks
+//
+////////////////////////////////////////////////
+
+circularTrack.prototype.drawGap = function(i, animate) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+    var self = this;
+
+    var gap_range = ('undefined' == typeof animate) ? d3.range(track.inner_radius, track.outer_radius, 8) : [1,2];
+
+    // Draw the track, putting in elements such as hover colour change
+    // if one exists, click events, etc
+    var gaps = g.selectAll(".tracks."+track.trackName)
+    .data(track.items)
+    .enter()
+    .append("g")
+    .attr("class", function(d) { return track.trackName + ' ' + track.trackName + '_g ' + track.trackName + '_' + d.name + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
+    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")
+    .each(function(d) {
+	    d3.select(this)
+	    .append("path")
+	    .attr("d", self.jaggedLineGenerator(d.start, gap_range))
+	    .attr("class", function(d2) { return track.trackName + ' ' + track.trackName + '_line' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
+	    .attr("stroke-width", 1)
+	    .attr("fill", "none");
+
+	    d3.select(this)
+	    .append("path")
+	    .attr("d", self.jaggedLineGenerator(d.end, gap_range))
+	    .attr("class", function(d2) { return track.trackName + ' ' + track.trackName + '_line' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
+	    .attr("stroke-width", 1)
+	    .attr("fill", "none");
+	});
+
+    // If we're doing an animated addition, move the track out to its
+    // new spot
+    if('undefined' !== typeof animate) {
+	this.moveGap(i, track.inner_radius, track.outer_radius);
+    }
+
+}
+
+circularTrack.prototype.moveGap = function(i, innerRadius, outerRadius) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+    var self = this;
+
+    // Just record the new radii in case we need them later
+    if('undefined' !== typeof this.tracks[i].inner_radius) {
+	this.tracks[i].inner_radius = innerRadius;
+    }
+    if('undefined' !== typeof this.tracks[i].outer_radius) {
+	this.tracks[i].outer_radius = outerRadius;
+    }
+
+    // We needed to save the new radius but if this
+    // track isn't visible, do nothing
+    if(! this.tracks[i].visible) {
+	return;
+    }
+
+    var gap_range = d3.range(innerRadius, outerRadius, 8);
+
+    g.selectAll("." + track.trackName + '_g') 
+    .transition()
+    .duration(1000)
+    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")
+
+    g.selectAll('.' + track.trackName + '_line')
+    .transition()
+    .duration(1000)
+    .attrTween("d", function(d) { return pathTween(this, self.jaggedLineGenerator(d.start, gap_range), 4) });
+
+    
+}
+
+circularTrack.prototype.removeGap = function(i) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+    var self = this;
+
+    g.selectAll('.' + track.trackName + '_line')
+    .transition()
+    .duration(1000)
+    .attrTween("d", function(d) { return pathTween(this, self.jaggedLineGenerator(d.start, [1,2]), 4) })
+    .remove();
+
+    g.selectAll("." + track.trackName + '_g') 
+    .transition()
+    .duration(1000)
+    .style('opacity', 0)
+    .remove()
+
+    this.tracks[i].visible = false;
+
+}
+
+// Jagged line path generator for the gap track type
+
+circularTrack.prototype.jaggedLineGenerator = function(bp, data) {
+    var cfg = this.layout;
+
+    var generator = d3.svg.line()
+	.x(function(d, i) { var offset = ((i % 2 === 0) ? 0.02 : -0.02); return d * Math.cos((bp*cfg.radians_pre_bp)-cfg.PI2+(i ? offset : 0) ); } )
+	.y(function(d, i) { var offset = ((i % 2 === 0) ? 0.02 : -0.02); return d * Math.sin((bp*cfg.radians_pre_bp)-cfg.PI2+ (i ? offset : 0) ); } )
+	.interpolate("linear");
+
+    return generator(data);
+}
+
+function pathTween(path, d1, precision) {
+    //  return function() {
+      //    var path0 = this,
+    var path0 = path,
+        path1 = path0.cloneNode(),
+        n0 = path0.getTotalLength(),
+        n1 = (path1.setAttribute("d", d1), path1).getTotalLength();
+
+    // Uniform sampling of distance based on specified precision.
+    var distances = [0], i = 0, dt = precision / Math.max(n0, n1);
+    while ((i += dt) < 1) distances.push(i);
+    distances.push(1);
+
+    // Compute point-interpolators at each distance.
+    var points = distances.map(function(t) {
+      var p0 = path0.getPointAtLength(t * n0),
+          p1 = path1.getPointAtLength(t * n1);
+      return d3.interpolate([p0.x, p0.y], [p1.x, p1.y]);
+    });
+
+    return function(t) {
+      return t < 1 ? "M" + points.map(function(p) { return p(t); }).join("L") : d1;
+    };
+    //  };
+}
+
+////////////////////////////////////////////////
+//
+// Glyph type tracks
+//
+////////////////////////////////////////////////
+
+// We will probably need to send a localized
+// version of the data so the update works
+// properly
+
+circularTrack.prototype.drawGlyphTrack = function(i) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+    var stack_count = 0;
+
+    var items = track.items.filter(function(d) { return track.visTypes.contains(d.type) } );
+
+    // Because on update the order of processing changes we need
+    // to recompute the stacking order manually each time
+    for(var i = 0; i < items.length; i++) {
+	if(i < 1) {
+	    items[i].stackCount = 0;
+	    continue;
+	}
+
+	xs = (cfg.h/2 + (track.radius*Math.sin((items[i].bp*cfg.radians_pre_bp)-cfg.PI2))) -
+	(cfg.h/2 + (track.radius*Math.sin((items[i-1].bp*cfg.radians_pre_bp)-cfg.PI2)));
+	ys = (cfg.h/2 + (track.radius*Math.cos((items[i].bp*cfg.radians_pre_bp)-cfg.PI2))) -
+	(cfg.h/2 + (track.radius*Math.cos((items[i-1].bp*cfg.radians_pre_bp)-cfg.PI2)));
+	xs = xs * xs;
+	ys = ys * ys;
+	var dist = Math.sqrt(xs + ys);
+
+	if(dist < track.pixel_spacing) { 
+	    items[i].stackCount = items[i-1].stackCount + 1; 
+	    continue;
+	}
+
+	items[i].stackCount = 0;
+    }
+
+    var x = function(d,i) { return cfg.w2 + (((track.glyph_buffer * d.stackCount) + track.radius)*Math.cos((d.bp*cfg.radians_pre_bp)-cfg.PI2)); };
+    var y = function(d,i) { return cfg.h2 + (((track.glyph_buffer * d.stackCount) + track.radius)*Math.sin((d.bp*cfg.radians_pre_bp)-cfg.PI2)); };
+
+    var trackPath = g.selectAll("." + track.trackName)
+    //    var trackPath = track.container.selectAll("." + track.trackName)
+    .data(items, function(d) { return d.id; });
+
+    trackPath.transition()
+    .duration(1000)
+    .attr("transform", function(d,i) { return "translate(" + x(d,i) + ","
+		+ y(d,i) + ")" })
+    .style("opacity", 1);    
+
+    trackPath.exit()
+    .transition()
+    .duration(1000)
+    .attr("transform", "translate(" + cfg.h2 + "," + cfg.w2 + ")")
+    .style("opacity", 0)
+    .remove();
+
+    trackPath.enter()
+    .append('path')
+    .attr('id', function(d,i) { return track.trackName + "_glyph" + d.id; })
+    .attr('class', function(d) {return track.trackName + '_' + d.type + ' ' + track.trackName})
+    .attr("d", d3.svg.symbol().type(track.glyphType).size(track.glyphSize))
+    .attr("transform", "translate(" + cfg.h2 + "," + cfg.w2 + ")")
+    .style("opacity", 0)
+    .transition()
+    .duration(1000)
+    .attr("transform", function(d,i) { return "translate(" + x(d,i) + ","
+				       + y(d,i) + ")" })
+    .style("opacity", 1);
+
+
+}
+
+circularTrack.prototype.updateGlyphTrack = function(i) {
+    var g = this.g;
+    var cfg = this.layout;
+    var track = this.tracks[i];
+    var stack_count = 0;
+
+    
+}
+
+////////////////////////////////////////////////
+//
+// Brush functionality
+//
+////////////////////////////////////////////////
+
+circularTrack.prototype.attachBrush = function(callbackObj) {
+    if('undefined' !== typeof this.callbackObj) {
+
+	if( Object.prototype.toString.call( callbackObj ) === '[object Array]' ) { 
+	    this.callbackObj.push(callbackObj);
+	} else {
+	    var tmpobj = this.callbackObj;
+	    this.callbackObj = [tmpobj, callbackObj];
+	}
+    } else {
+	this.callbackObj = callbackObj;
+	this.createBrush();
+    }
+
+}
+
+circularTrack.prototype.redrawBrush = function(startRad, endRad) {
+    var cfg = this.layout;
+
+    if('undefined' !== typeof this.brush) {
+
+	this.brushArc
+	    .outerRadius(cfg.radius-10);
+
+	this.brush
+	    .transition()
+	    .duration(1000)
+	    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")");
+
+	this.moveBrush(startRad, endRad);
+
+	d3.select("#brushStart_" + cfg.containerid)		
+	    .transition()
+	    .duration(1000)
+	    .attr("cx", cfg.h/2 + ((cfg.radius-10)*Math.cos(startRad-cfg.PI2)))
+	    .attr("cy", cfg.h/2 + ((cfg.radius-10)*Math.sin(startRad-cfg.PI2)));
+
+	d3.select("#brushEnd_" + cfg.containerid)		
+	    .transition()
+	    .duration(1000)
+	    .attr("cx", cfg.w2 + ((cfg.radius-10)*Math.cos(endRad-cfg.PI2)))
+	    .attr("cy", cfg.h2 + ((cfg.radius-10)*Math.sin(endRad-cfg.PI2)));
+
+    }
+}
+
+circularTrack.prototype.createBrush = function() {
+    var g = this.g;
+    var cfg = this.layout;
+    var xScale = this.xScale;
+    var self = this;
+
+    this.brushStart = 0;
+    this.brushEnd = 0;
+    this.brushStartBP = 0;
+    this.brushEndBP = 0;
+
+    this.brushArc = d3.svg.arc()
+    .innerRadius(20)
+    .outerRadius(cfg.radius-10)
+    .endAngle(function(d){return xScale(0);})
+    .startAngle(function(d){return xScale(0);});
+
+    this.brush = g.insert("path", "defs")
+    .attr("d", this.brushArc)
+    .attr("id", "polarbrush_" + cfg.containerid)
+    .attr("class", "polarbrush circularbrush")
+    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")
+
+    var dragStart = d3.behavior.drag()
+    .on("drag", function(d) {
+	    var mx = d3.mouse(this)[0];
+	    var my = d3.mouse(this)[1];
+
+	    var curRadandBP = calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w2)),
+					      -(d3.mouse(this)[1] - (cfg.h2)),
+					      xScale);
+
+	    // Don't allow the brush to go beyond the other
+	    if(curRadandBP[0] >= self.brushEnd) {
+		return;
+	    }
+
+	    g.select("#brushStart_" + cfg.containerid)		
+	    .attr("cx", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.cos((curRadandBP[0])-cfg.PI2);})
+	    .attr("cy", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.sin((curRadandBP[0])-cfg.PI2); });
+		
+	    self.brushStart = curRadandBP[0];
+	    self.brushStartBP = curRadandBP[1];
+	    self.moveBrush(self.brushStart, self.brushEnd);
+	    if('undefined' !== typeof self.callbackObj) {
+		self.doBrushCallback(self.brushStartBP, self.brushEndBP);
+		//		self.callbackObj.update(self.brushStartBP, self.brushEndBP);
+	    }
+	})
+    .on("dragend", function(d) {
+	    self.doBrushFinishedCallback(self.brushStartBP, self.brushEndBP);
+	});
+
+    var dragEnd = d3.behavior.drag()
+    .on("drag", function(d) {
+	    var mx = d3.mouse(this)[0];
+	    var my = d3.mouse(this)[1];
+
+	    var curRadandBP = calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w2)),
+					      -(d3.mouse(this)[1] - (cfg.h2)),
+					      xScale);
+
+	    // Don't allow the brush to go beyond the other
+	    if(curRadandBP[0] <= self.brushStart) {
+		return;
+	    }
+
+	    g.select("#brushEnd_" + cfg.containerid)		
+	    .attr("cx", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.cos((curRadandBP[0])-cfg.PI2);})
+	    .attr("cy", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.sin((curRadandBP[0])-cfg.PI2); });
+		
+	    self.brushEnd = curRadandBP[0];
+	    self.brushEndBP = curRadandBP[1];
+	    self.moveBrush(self.brushStart, self.brushEnd);
+	    if('undefined' !== typeof self.callbackObj) {
+		self.doBrushCallback(self.brushStartBP, self.brushEndBP);
+		//		self.callbackObj.update(self.brushStartBP, self.brushEndBP);
+	    }
+	})
+    .on("dragend", function(d) {
+	    self.doBrushFinishedCallback(self.brushStartBP, self.brushEndBP);
+	});
+
+    this.endBrushObj = g.append("circle")
+    .attr({
+	    id: 'brushEnd_' + cfg.containerid,
+	    class: 'brushEnd circularbrush',
+		cx: (cfg.w2 + ((cfg.radius-10)*Math.cos((this.xScale(0))-cfg.PI2))),
+		cy: (cfg.h2 + ((cfg.radius-10)*Math.sin((this.xScale(0))-cfg.PI2))),
+		r: 5
+	    })
+            .call(dragEnd);
+
+    this.startBrushObj = g.append("circle")
+    .attr({
+	    id: 'brushStart_' + cfg.containerid,
+	    class: 'brushStart circularbrush',
+		cx: (cfg.w2 + ((cfg.radius-10)*Math.cos((this.xScale(0))-cfg.PI2))),
+		cy: (cfg.h2 + ((cfg.radius-10)*Math.sin((this.xScale(0))-cfg.PI2))),
+		r: 5
+		})
+    .call(dragStart);
+
+    // Create the start and stop pointers
+
+}
+
+circularTrack.prototype.doBrushCallback = function(startBP, endBP) {
+    var cfg = this.layout;
+
+    if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
+	for(var obj in this.callbackObj) {
+	    if(this.callbackObj.hasOwnProperty(obj)) {
+		this.callbackObj[obj].update(startBP, endBP, { plotid: cfg.plotid } );
+	    }
+	}
+    } else {
+	this.callbackObj.update(startBP, endBP, { plotid: cfg.plotid });
+    }
+
+}
+
+circularTrack.prototype.doBrushFinishedCallback = function(startBP, endBP) {
+    var cfg = this.layout;
+
+    if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
+	for(var obj in this.callbackObj) {
+	    if(this.callbackObj.hasOwnProperty(obj)) {
+		this.callbackObj[obj].update_finished(startBP, endBP, { plotid: cfg.plotid });
+	    }
+	}
+    } else {
+	this.callbackObj.update_finished(startBP, endBP, { plotid: cfg.plotid });
+    }
+
+}
+
+circularTrack.prototype.moveBrush = function(startRad, endRad) {
+    var g = this.g;
+    var cfg = this.layout;
+
+    //    console.log("moving brush to " + startRad, endRad);
+
+    this.brushArc
+    .startAngle(startRad)
+    .endAngle(endRad);
+
+    d3.select('#polarbrush_' + cfg.containerid)
+    .attr("d", this.brushArc);
+
+    this.currentStart = startRad;
+    this.currentEnd = endRad;
+    
+}
+
+circularTrack.prototype.moveBrushbyBP = function(startbp, endbp) {
+    var cfg = this.layout;
+
+    var startRad = startbp*this.layout.radians_pre_bp;
+    var endRad = endbp*this.layout.radians_pre_bp;
+    this.moveBrush(startRad,endRad);
+
+    this.brushStart = startRad;
+    this.brushStartBP = startbp;
+    this.currentStart = startRad;
+    this.currentEnd = endRad;
+    d3.select("#brushStart_" + cfg.containerid)		
+    .attr("cx", cfg.h/2 + ((cfg.radius-10)*Math.cos(startRad-cfg.PI2)))
+    .attr("cy", cfg.h/2 + ((cfg.radius-10)*Math.sin(startRad-cfg.PI2)));
+
+    this.brushEnd = endRad;
+    this.brushEndBP = endbp;
+    d3.select("#brushEnd_" + cfg.containerid)		
+    .attr("cx", cfg.w2 + ((cfg.radius-10)*Math.cos(endRad-cfg.PI2)))
+    .attr("cy", cfg.h2 + ((cfg.radius-10)*Math.sin(endRad-cfg.PI2)));
+
+
+}
+
+circularTrack.prototype.hideBrush = function() {
+    var cfg = this.layout;
+
+    d3.select("#brushStart_" + cfg.containerid)
+    .style("visibility", "hidden");
+
+    d3.select("#brushEnd_" + cfg.containerid)
+    .style("visibility", "hidden");
+
+    d3.select('#polarbrush_' + cfg.containerid)
+    .style("visibility", "hidden");
+}
+
+circularTrack.prototype.showBrush = function() {
+    var cfg = this.layout;
+
+    d3.select("#brushStart_" + cfg.containerid)
+    .style("visibility", "visible");
+
+    d3.select("#brushEnd_" + cfg.containerid)
+    .style("visibility", "visible");
+
+    d3.select('#polarbrush_' + cfg.containerid)
+    .style("visibility", "visible");
+}
+
+    circularTrack.prototype.update = function(startBP, endBP, params) {
+    this.moveBrushbyBP(startBP, endBP);
+}
+
+	circularTrack.prototype.update_finished = function(startBP, endBP, params) {
+    //    console.log("Thank you, got: " + startBP, endBP);
+}
+
+////////////////////////////////////////////////
+//
+// Export functionality
+//
+////////////////////////////////////////////////
+
+// Allowed export formats are 'png' and 'svg'
+// The extension will be added, just summply the base
+// filename.
+
+// Saving to raster format is dependent on FileSaver.js
+// and canvg.js (which include rgbcolor.js & StackBlur.js),
+// they must be loaded before circularplot.js
+
+circularTrack.prototype.savePlot = function(scaling, filename, stylesheetfile, format) {
+
+    // First lets get the stylesheet
+    var sheetlength = stylesheetfile.length;
+    var style = document.createElementNS("http://www.w3.org/1999/xhtml", "style");
+	style.textContent += "<![CDATA[\n";
+    for (var i=0;i<document.styleSheets.length; i++) {
+	str = document.styleSheets[i].href;
+	if(null == str) continue;
+
+	if (str.substr(str.length-sheetlength)==stylesheetfile){
+            var rules;
+            if(document.styleSheets[i].cssRules) {
+                rules = document.styleSheets[i].cssRules;
+            } else if (document.styleSheets[i].rules) {
+                rules = document.styleSheets[i].rules;
+            }
+            if(rules) {
+                for (var j=0; j<rules.length;j++){
+                    style.textContent += (rules[j].cssText + "\n");
+                }
+            }
+            break;
+    	}
+    }
+    style.textContent += "]]>";
+
+    // Now we clone the SVG element, resize and scale it up
+    var container = this.layout.container.slice(1);
+    var containertag = document.getElementById(container);
+    var clonedSVG = containertag.cloneNode(true);
+    var svg = clonedSVG.getElementsByTagName("svg")[0];
+
+    // Remove drag-resize shadow element
+    var tags = svg.getElementsByClassName("dragbar-shadow")
+    for(var i=0; i<tags.length; i++) {
+	if(tags[i].getAttributeNS(null, "name") === name) {
+	    tags[i].parentNode.removeChild(tags[i]);
+        }
+    }
+
+    // Remove the brush if it's on the chart
+    var tags = svg.getElementsByClassName("circularbrush")
+    for(var i=tags.length-1; i>=0; i--) {
+//	if(tags[i].getAttributeNS(null, "name") === name) {
+	    tags[i].parentNode.removeChild(tags[i]);
+//        }
+    }
+
+    // Remove the move croshairs if on the chart
+    var tags = svg.getElementsByClassName("move_circularchart")
+    for(var i=tags.length-1; i>=0; i--) {
+//	if(tags[i].getAttributeNS(null, "name") === name) {
+	    tags[i].parentNode.removeChild(tags[i]);
+//        }
+    }
+
+    // We need to resize the svg with the new canvas size
+    svg.removeAttribute('width');
+    svg.removeAttribute('height');
+    svg.setAttribute('width', this.layout.w*scaling +  this.layout.TranslateX*scaling);
+    svg.setAttribute('height', this.layout.h*scaling +  this.layout.TranslateY*scaling);
+
+    // Update first g tag with the scaling
+    g = svg.getElementsByTagName("g")[0];
+    transform = g.getAttribute("transform");
+    g.setAttribute("transform", transform + " scale(" + scaling + ")");
+
+    // Append the stylehsheet to the cloned svg element
+    // so when we export it the style are inline and 
+    // get rendered
+    svg.getElementsByTagName("defs")[0].appendChild(style);
+
+    // Fetch the actual SVG tag and convert it to a canvas
+    // element
+    var content = clonedSVG.innerHTML.trim();
+
+    if(format == 'svg') {
+	var a = document.createElement('a');
+	a.href = "data:application/octet-stream;base64;attachment," + btoa(content);
+	a.download = filename + ".svg";
+	a.click();
+
+    } else if(format == 'png') {
+	var canvas = document.createElement('canvas');
+	canvg(canvas, content);
+
+	// Convert the canvas to a data url (this could
+	// be displayed inline by inserting it in to an 
+	// <img> tag in the src attribute, ie
+	// <img src="'+imgData+'">
+	var theImage = canvas.toDataURL('image/png');
+
+	// Convert to a blob
+	var blob = this.dataURLtoBlob(theImage);
+
+	// Prompt to save
+	saveAs(blob, filename);
+    }
+}
+
+// Saving to raster format is dependent on FileSaver.js
+// and canvg.js (which include rgbcolor.js & StackBlur.js),
+// they must be loaded before circularplot.js
+
+circularTrack.prototype.saveRaster = function(scaling, filename, stylesheetfile) {
+    // First lets get the stylesheet
+    var sheetlength = stylesheetfile.length;
+    var style = document.createElementNS("http://www.w3.org/1999/xhtml", "style");
+	style.textContent += "<![CDATA[\n";
+    for (var i=0;i<document.styleSheets.length; i++) {
+	str = document.styleSheets[i].href;
+	if(null == str) continue;
+
+	if (str.substr(str.length-sheetlength)==stylesheetfile){
+      	    var rules = document.styleSheets[i].rules;
+            for (var j=0; j<rules.length;j++){
+		style.textContent += (rules[j].cssText + "\n");
+            }
+            break;
+    	}
+    }
+    style.textContent += "]]>";
+
+    // Now we clone the SVG element, resize and scale it up
+    var container = this.layout.container.slice(1);
+    var containertag = document.getElementById(container);
+    var clonedSVG = containertag.cloneNode(true);
+    var svg = clonedSVG.getElementsByTagName("svg")[0];
+
+    // We need to resize the svg with the new canvas size
+    svg.removeAttribute('width');
+    svg.removeAttribute('height');
+    svg.setAttribute('width', this.layout.w*scaling +  this.layout.TranslateX*scaling);
+    svg.setAttribute('height', this.layout.h*scaling +  this.layout.TranslateY*scaling);
+
+    // Update first g tag with the scaling
+    g = svg.getElementsByTagName("g")[0];
+    transform = g.getAttribute("transform");
+    g.setAttribute("transform", transform + " scale(" + scaling + ")");
+
+    // Append the stylehsheet to the cloned svg element
+    // so when we export it the style are inline and 
+    // get rendered
+    svg.getElementsByTagName("defs")[0].appendChild(style);
+
+    // Fetch the actual SVG tag and convert it to a canvas
+    // element
+    var content = clonedSVG.innerHTML.trim();
+    var canvas = document.createElement('canvas');
+    canvg(canvas, content);
+
+    // Convert the canvas to a data url (this could
+    // be displayed inline by inserting it in to an 
+    // <img> tag in the src attribute, ie
+    // <img src="'+imgData+'">
+    var theImage = canvas.toDataURL('image/png');
+
+    // Convert to a blob
+    var blob = this.dataURLtoBlob(theImage);
+
+    // Prompt to save
+    saveAs(blob, filename);
+
+}
+
+circularTrack.prototype.dataURLtoBlob = function(dataURL) {
+  // Decode the dataURL    
+  var binary = atob(dataURL.split(',')[1]);
+  // Create 8-bit unsigned array
+  var array = [];
+  for(var i = 0; i < binary.length; i++) {
+      array.push(binary.charCodeAt(i));
+  }
+  // Return our Blob object
+  return new Blob([new Uint8Array(array)], {type: 'image/png'});
+}
+
+////////////////////////////////////////////////
+//
+// Utility functions
+//
+////////////////////////////////////////////////
+
+circularTrack.prototype.showTrack = function(name) {
+    var i = this.findTrackbyName(name);
+
+    // We didn't find the track by that name
+    if(i < 0) {
+	return;
+    }
+
+    // Is it already visible? Do nothing
+    if(this.tracks[i].visible) {
+	return;
+    } else {
+	this.tracks[i].visible = true;
+    }
+
+    switch(this.tracks[i].trackType) {
+    case "plot":
+    this.drawPlot(i, true);
+        break;
+    case "track":
+    this.drawTrack(i, true);
+        break;
+    case "stranded":
+        this.drawTrack(i, true);
+        break;
+    case "gap":
+        this.drawGap(i, true);
+        break;
+    case "glyph":
+        // Do nothing for a glyph type, special case
+        // but leave this as a placeholder for now
+        break;
+    default:
+    // Do nothing for an unknown track type
+    }
+
+}
+
+circularTrack.prototype.hideTrack = function(name) {
+    var i = this.findTrackbyName(name);
+
+    // We didn't find the track by that name
+    if(i < 0) {
+	return;
+    }
+
+    // Is it already not visible? Do nothing
+    if(! this.tracks[i].visible) {
+	return;
+    }
+
+    switch(this.tracks[i].trackType) {
+    case "plot":
+        this.removePlot(i);
+        break;
+    case "track":
+        this.removeTrack(i);
+        break;
+    case "stranded":
+        this.removeTrack(i);
+        break;
+    case "gap":
+        this.removeGap(i);
+        break;
+    case "glyph":
+        // Do nothing for a glyph type, special case
+        // but leave this as a placeholder for now
+        break;
+    default:
+    // Do nothing for an unknown track type
+    }
+
+}
+
+circularTrack.prototype.hideGlyphTrackType = function(name, type) {
+    var i = this.findTrackbyName(name);
+
+    // We didn't find the track by that name
+    if(i < 0) {
+	return;
+    }
+
+    if(this.tracks[i].trackType !== "glyph") {
+	// Wrong track type, bail
+	return;
+    }
+
+    // Don't try to show if already visible
+    if(! this.isvisibleGlyphTrackType(name, type)) {
+	return;
+    }
+
+    for(var j = 0; j < this.tracks[i].visTypes.length; j++) {
+	if(this.tracks[i].visTypes[j] == type) {
+	    this.tracks[i].visTypes.splice(j, 1);
+	    j--;
+	}
+    }
+
+    this.drawGlyphTrack(i);
+
+}
+
+circularTrack.prototype.showGlyphTrackType = function(name, type) {
+    var i = this.findTrackbyName(name);
+
+    // We didn't find the track by that name
+    if(i < 0) {
+	return;
+    }
+
+    if(this.tracks[i].trackType !== "glyph") {
+	// Wrong track type, bail
+	return;
+    }
+
+    // Don't try to show if already visible
+    if(this.isvisibleGlyphTrackType(name, type)) {
+	return;
+    }
+
+    if(! this.tracks[i].visTypes.contains(type) ) {
+	this.tracks[i].visTypes.push(type);
+    }
+
+    this.drawGlyphTrack(i);
+
+}
+
+circularTrack.prototype.isvisibleGlyphTrackType = function(name, type) {
+    var i = this.findTrackbyName(name);
+
+    // We didn't find the track by that name
+    if(i < 0) {
+	return;
+    }
+
+    if(this.tracks[i].trackType !== "glyph") {
+	// Wrong track type, bail
+	return;
+    }
+
+    for(var j = 0; j < this.tracks[i].visTypes.length; j++) {
+	if(this.tracks[i].visTypes[j] == type) {
+	    return true;
+	}
+    }
+
+    return false;
+}
+
+circularTrack.prototype.dragresize = function() {
+    var newWidth = d3.event.x - this.layout.ExtraWidthX;
+    var newHeight = d3.event.y - this.layout.ExtraWidthY;
+
+    var newSize = Math.max(newWidth, newHeight);
+
+    // Don't allow going below 25px in size
+    if(newSize <= 25) {
+        return;
+    }
+
+//    console.log(this.layout.w);
+//    console.log("x " + newWidth);
+//    console.log("y " + newHeight);
+
+    this.layout.newSize = newSize
+//    this.layout.w = newSize;
+//    this.layout.h = newSize;
+
+    this.dragbar
+	.attr("transform", "translate(" + (newSize+this.layout.ExtraWidthX-25) + "," +  (newSize+this.layout.ExtraWidthY-25) + ")")
+
+    this.drag_shadow
+	.attr("width", (newSize+this.layout.ExtraWidthX))
+	.attr("height", (newSize+this.layout.ExtraWidthY));
+
+    if((newSize >= this.layout.w) || (newSize >= this.layout.h)) {
+	this.container
+	    .attr("width", newSize+this.layout.ExtraWidthX)
+	    .attr("height", newSize+this.layout.ExtraWidthY)
+    }
+//    this.resize(newSize);
+
+}
+
+circularTrack.prototype.dragresize_start = function() {
+    d3.event.sourceEvent.stopPropagation();
+
+    this.drag_shadow
+	.attr("class", "dragbar-shadow");
+}
+
+circularTrack.prototype.dragresize_end = function() {
+    var newSize = this.layout.newSize;
+
+    this.resize(this.layout.w);
+
+    this.layout.w = newSize;
+    this.layout.w2 = newSize / 2;
+    this.layout.h = newSize;
+    this.layout.h2 = this.layout.w2;
+
+    this.drag_shadow
+	.attr("class", "linear_hidden dragbar-shadow");
+
+    this.resize(newSize);
+
+}
+
+circularTrack.prototype.resize = function(newWidth) {
+    
+    var resize_ratio = newWidth / this.layout.radius / 2;
+
+    this.layout.radius = this.layout.factor*Math.min(newWidth/2, newWidth/2);
+
+    this.layout.w = newWidth;
+    this.layout.w2 = newWidth / 2;
+    this.layout.h = newWidth;
+    this.layout.h2 = this.layout.w2;
+
+    this.moveAxis();
+
+    // Resize the plots
+    for(var i=0; i < this.tracks.length; i++) {
+
+	//	if('undefined' !== typeof this.tracks[i].visible) {
+	//	    if(! this.tracks[i].visible) {
+	//		continue;
+	//	    }
+	//	}
+
+	// We're going to see what type of tracks we have
+	// and dispatch them appropriately
+
+	switch(this.tracks[i].trackType) {
+	case "plot":
+	    this.movePlot(i, (this.tracks[i].plot_radius*resize_ratio));
+	    break;
+	case "track":
+	    this.moveTrack(i, (this.tracks[i].inner_radius*resize_ratio), (this.tracks[i].outer_radius*resize_ratio));
+	    break;
+	case "stranded":
+	    this.moveTrack(i, (this.tracks[i].inner_radius*resize_ratio), (this.tracks[i].outer_radius*resize_ratio));
+	    break;
+	case "gap":
+	    this.moveGap(i, (this.tracks[i].inner_radius*resize_ratio), (this.tracks[i].outer_radius*resize_ratio));
+	    break;
+	case "glyph":
+	    this.tracks[i].radius = this.tracks[i].radius * resize_ratio;
+	    // We needed to save the new radius but if this
+	    // track isn't visible, do nothing
+	    if(this.tracks[i].visible) {
+		this.drawGlyphTrack(i);
+	    }
+	    break;
+	default:
+	    // Do nothing for an unknown track type
+	}
+    }
+
+    this.container
+	.attr("width", newWidth+this.layout.ExtraWidthX)
+	.attr("height", newWidth+this.layout.ExtraWidthY)
+
+    this.redrawBrush(this.currentStart, this.currentEnd);
+
+    this.dragbar
+	.attr("transform", "translate(" + (newWidth+this.layout.ExtraWidthX-25) + "," +  (newWidth+this.layout.ExtraWidthY-25) + ")")
+
+}
+
+////////////////////////////////////////////////
+//
+// Helper functions
+//
+////////////////////////////////////////////////
+
+circularTrack.prototype.findTrackbyName = function(name) {
+    var tracks = this.tracks;
+
+    for(var i=0; i < tracks.length; i++) {
+	if(tracks[i].trackName == name) {
+	    return i;
+	}
+    }
+
+    return -1;
+
+}
+
+circularTrack.prototype.findGlyphTypes = function(i) {
+
+    var classes = [];
+
+    if('undefined' == typeof this.tracks[i].visItems) {
+	this.tracks[i].visTypes = [];
+    }
+
+    for(var j=0; j < this.tracks[i].items.length; j++) {
+	if(! this.tracks[i].visTypes.contains(this.tracks[i].items[j].type)) {
+	    this.tracks[i].visTypes.push(this.tracks[i].items[j].type);
+	    classes.push(this.tracks[i].trackName + "_" + this.tracks[i].items[j].type);
+	}
+    }
+
+    this.tracks[i].visClasses = classes.join(' ');
+
+}
+
+circularTrack.prototype.maskGlyphTypes = function(i, types) {
+
+    for(var j = this.tracks[i].visTypes.length - 1; j >= 0; j--) {
+	if(types.contains(this.tracks[i].visTypes[j])) {
+	    this.tracks[i].visTypes.splice(j, 1);
+	}
+    }
+
+}
+
+Array.prototype.contains = function(obj) {
+    var i = this.length;
+    while (i--) {
+        if (this[i] == obj) {
+            return true;
+        }
+    }
+    return false;
+}
+
+// If we're displaying a stranded track, calculate
+// the inner radius depending on which strand the 
+// gene is on.
+
+function calcInnerRadius(inner, outer, strand) {
+    if('undefined' == typeof strand) {
+	return inner;
+    } else if(strand == -1) {
+	return inner;
+    } else {
+	return (inner+outer)/2;
+    }
+}
+
+// If we're displaying a stranded track, calculate
+// the outer radius depending on which strand the 
+// gene is on.
+    
+function calcOuterRadius (inner, outer, strand) {
+    if('undefined' == typeof strand) {
+	return outer;
+    } else if(strand == -1) {
+	return (inner+outer)/2;
+    } else {
+	return outer;
+    }
+}
+
+function calcRadBPfromXY (x,y,xScale) {
+    var rad = Math.PI/2 - Math.atan(y/x);
+    if(x < 0) {
+	// II & III quadrant
+	rad = rad + Math.PI;
+    }
+
+    return [rad,Math.floor(xScale.invert(rad))];
+}
+
+function calcMinSliceSize () {
+    var cfg = this.layout;
+
+    
+    //cfg.radians_pre_bp
+}
diff --git a/dammit/viewer/static/linearbrush.js b/dammit/viewer/static/linearbrush.js
new file mode 100644
index 00000000..ae5cfefe
--- /dev/null
+++ b/dammit/viewer/static/linearbrush.js
@@ -0,0 +1,97 @@
+var contextMargin = {top: 10, right: 40, bottom: 25, left: 60},
+contextWidth = 440 - contextMargin.left - contextMargin.right,
+contextHeight = 100 - contextMargin.top - contextMargin.bottom;
+
+function linearBrush(layout, callbackObj) {
+    this.layout;
+    this.callbackObj = callbackObj;
+
+    this.brushContainer = d3.select(layout.container)
+	.append("svg")
+	.attr("width", contextWidth + contextMargin.left + contextMargin.right)
+	.attr("height", contextHeight + contextMargin.top + contextMargin.bottom)
+	.attr("class", "contextTracks");
+
+    this.x1 = d3.scale.linear()
+	.range([0,contextWidth])
+       	.domain([0, layout.genomesize]);
+
+    this.mini = this.brushContainer.append("g")
+	.attr("transform", "translate(" + contextMargin.left + "," + contextMargin.top + ")")
+	.attr("width", contextWidth)
+	.attr("height", contextHeight)
+	.attr("class", "miniBrush");
+
+    this.brush = d3.svg.brush()
+	.x(this.x1)
+	.on("brush", this.brushUpdate.bind(this));
+
+    //    this.brush = brush;
+
+    this.brushContainer = this.mini.append("g")
+	.attr("class", "track brush")
+	.call(this.brush.bind(this))
+	.selectAll("rect")
+	.attr("y", 1)
+	.attr("height", contextHeight - 1);
+ 
+    this.axisContainer = this.mini.append("g")
+	.attr('class', 'brushAxis')
+	.attr("transform", "translate(" + 0 + "," + contextHeight + ")");
+
+    this.xAxis = d3.svg.axis().scale(this.x1).orient("bottom")
+	.tickFormat(d3.format("s"));
+
+    this.axisContainer.append("g")
+    .attr("class", "context axis bottom")
+    .attr("transform", "translate(0," + 0 + ")")
+    .call(this.xAxis);
+
+}
+
+linearBrush.prototype.brushUpdate = function(b) {
+    var minExtent = this.brush.extent()[0];
+    var maxExtent = this.brush.extent()[1];
+
+    if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) {
+        for(var obj in this.callbackObj) {
+            if(this.callbackObj.hasOwnProperty(obj)) {
+                this.callbackObj[obj].update(minExtent, maxExtent);
+            }
+        }
+    } else {
+        this.callbackObj.update(minExtent, maxExtent);
+    }
+
+}
+
+linearBrush.prototype.update = function(startBP, endBP) {
+
+	this.brush.extent([startBP, endBP]);
+	
+	d3.selectAll('.brush').call(this.brush);
+
+}
+
+linearBrush.prototype.update_finished = function(startBP, endBP) {
+
+}
+
+linearBrush.prototype.addBrushCallback = function(obj) {
+
+    // We allow multiple brushes to be associated with a linear plot, if we have
+    // a brush already, add this new one on.  Otherwise just remember it.
+
+    if('undefined' !== typeof this.callbackObj) {
+
+	if( Object.prototype.toString.call( obj ) === '[object Array]' ) { 
+	    this.callbackObj.push(obj);
+	} else {
+	    var tmpobj = this.callbackObj;
+	    this.callbackObj = [tmpobj, obj];
+	}
+    } else {
+	this.callbackObj = obj;
+    }
+
+}
diff --git a/dammit/viewer/static/linearplot.js b/dammit/viewer/static/linearplot.js
new file mode 100644
index 00000000..dd59e910
--- /dev/null
+++ b/dammit/viewer/static/linearplot.js
@@ -0,0 +1,1484 @@
+var linearTrackDefaults = {
+    width: 940,
+    height: 500,
+    left_margin: 15,
+    right_margin: 15,
+    bottom_margin: 5,
+    axis_height: 50,
+    name: "defaultlinear",
+    dragresize: true
+};
+
+function genomeTrack(layout,tracks) {
+
+    this.tracks = tracks;
+    this.layout = layout;
+    this.numTracks = this.countTracks();
+
+    if('undefined' !== typeof layout) {
+	// Copy over any defaults not passed in
+	// by the user
+	for(var i in linearTrackDefaults) {
+	    if('undefined' == typeof layout[i]) {
+		this.layout[i] = linearTrackDefaults[i];
+	    }
+	}
+    }
+
+    if('undefined' == typeof layout.plotid) {
+	this.layout.plotid = layout.container.slice(1);
+    }
+
+    this.layout.containerid = layout.container.slice(1);
+
+    this.layout.width_without_margins =
+	this.layout.width - this.layout.left_margin -
+	this.layout.right_margin;
+
+    this.layout.height_without_axis = this.layout.height -
+	this.layout.axis_height;
+
+    this.itemRects = [];
+
+    // Start with showing the entire genome unless otherwise stated
+    this.visStart = 'undefined' !== typeof layout.initStart ? layout.initStart : 0;
+    this.visEnd = 'undefined' !== typeof layout.initEnd ? layout.initEnd : layout.genomesize;
+
+    this.x = d3.scale.linear()
+//	.domain([0, layout.genomesize])
+	.domain([this.visStart, this.visEnd])
+	.range([0,this.layout.width_without_margins]);
+    this.x1 = d3.scale.linear()
+	.range([0,this.layout.width_without_margins])
+//       	.domain([0, layout.genomesize]);
+       	.domain([this.visStart, this.visEnd]);
+    this.y1 = d3.scale.linear()
+	.domain([0,this.numTracks])
+	.range([0,(this.layout.height_without_axis-this.layout.bottom_margin)]);
+    // We need x1 and y1 in the initialization's scope too
+    // to deal with passing it in to make the lollipops
+
+    this.zoom = d3.behavior.zoom()
+	.x(this.x1)
+	.on("zoomstart", function () {d3.event.sourceEvent.preventDefault()} )
+	.on("zoom", this.rescale.bind(this))
+	.on("zoomend", this.callBrushFinished.bind(this) );
+
+    if('undefined' == typeof layout.plotid) {
+	this.layout.plotid = layout.container.slice(1);
+    }
+
+    d3.select(layout.container).select("svg").remove();
+
+    this.chart = d3.select(layout.container)
+	.append("svg")
+	.attr("id", function() { return layout.container.slice(1) + "_svg"; })
+	.attr("width", this.layout.width)
+	.attr("height", this.layout.height)
+	.attr("class", "mainTracks")
+	.call(this.zoom);
+
+    this.defs = this.chart.append("defs");
+    this.clipPath = this.defs.append("clipPath")
+	.attr("id", "trackClip_" + this.layout.containerid)
+	.append("rect")
+	.attr("width", this.layout.width_without_margins)
+	//	.attr("width", this.layout.width_without_margins + this.layout.right_margin)
+	.attr("height", this.layout.height)
+	.attr("transform", "translate(0,0)");
+    //	.attr("transform", "translate(" + this.layout.left_margin + ",0)");
+    
+    this.drawFeatures();
+
+    this.main = this.chart.append("g")
+       	.attr("transform", "translate(" + this.layout.left_margin + ",0)")
+	.attr("width", this.layout.width_without_margins)
+	.attr("height", this.layout.height)
+	.attr("class", "mainTrack");
+
+    // Resize dragger
+    if(this.layout.dragresize == true) {
+	var dragright = d3.behavior.drag()
+	    .on("dragstart", function() {  d3.event.sourceEvent.stopPropagation(); })
+	    .on("drag", this.dragresize.bind(this));
+
+	this.dragbar_y_mid = this.layout.height/2;
+	this.dragbar = this.chart.append("g")
+	    .attr("transform", "translate(" + (this.layout.width-this.layout.right_margin) + "," + (this.dragbar_y_mid-10) + ")")
+	    .attr("width", 25)
+	    .attr("height", 20)
+	    .attr("fill", "lightblue")
+	    .attr("fill-opacity", .2)
+	    .attr("cursor", "ew-resize")
+	    .attr("id", "dragbar_" + this.layout.containerid)
+	    .call(dragright);
+
+	this.dragbar.append("rect")
+	    .attr("width", 25)
+	    .attr("height", 20)
+	    .attr("fill-opacity", 0);
+
+	this.dragbar.append("line")
+	    .attr("x1", 6)
+	    .attr("x2", 6)
+	    .attr("y1", 0)
+	    .attr("y2", 20)
+	    .attr("class", "dragbar-line");
+	this.dragbar.append("line")
+	    .attr("x1", 9)
+	    .attr("x2", 9)
+	    .attr("y1", 0)
+	    .attr("y2", 20)
+	    .attr("class", "dragbar-line");
+	this.dragbar.append("line")
+	    .attr("x1", 12)
+	    .attr("x2", 12)
+	    .attr("y1", 0)
+	    .attr("y2", 20)
+	    .attr("class", "dragbar-line");
+    }
+	
+
+    this.genomesize = layout.genomesize;
+
+    this.tip = d3.tip()
+	.attr('class', 'd3-tip')
+	.offset([-10, 0])
+	.html(function(d) {
+		return "<strong>Name:</strong> <span style='color:red'>" + d.name + "</span>";
+	    });
+    
+    this.chart.call(this.tip);
+
+    this.axisContainer = this.chart.append("g")
+	.attr('class', 'trackAxis')
+	.attr('width', this.layout.width_without_margins)
+	.attr("transform", "translate(" + (this.layout.left_margin + 5) + "," + this.layout.height_without_axis + ")");
+
+    this.xAxis = d3.svg.axis().scale(this.x1).orient("bottom")
+	.innerTickSize(-this.layout.height)
+	.outerTickSize(0)
+	.tickFormat(d3.format("s"));
+
+    this.axisContainer.append("g")
+	.attr("class", "xaxislinear")
+	.attr('width', this.layout.width_without_margins)
+
+	.attr("transform", "translate(0," + 10 + ")")
+	.call(this.xAxis);
+
+
+    for(var i=0; i < this.tracks.length; i++) {
+	// We're going to see what type of tracks we have
+	// and dispatch them appropriately
+
+	 if("undefined" !== typeof this.tracks[i].skipLinear
+	    &&  this.tracks[i].skipLinear == true) {
+	     continue;
+	 }
+
+	 if("undefined" == typeof this.tracks[i].trackFeatures) {
+	     this.tracks[i].trackFeatures = "simple";
+	 } else if(this.tracks[i].trackFeatures == "complex") {
+	     // We need to pre-calculate the stacking order for
+	     // all arrow type features
+
+	     // 0.77 * 0.9
+	     if(this.tracks[i].trackType == "stranded") {
+		 this.tracks[i].baseheight = (this.y1(1) * 0.693);
+	     } else {
+		 this.tracks[i].baseheight = (this.y1(1) * 0.616);
+	     }
+	     var inframe = [];
+	     this.tracks[i].maxStackOrder = 1;
+	     for(var j = 0; j < this.tracks[i].items.length; j++) {
+		 // If it's the arrow type we're looking for
+		 if("undefined" !== typeof this.tracks[i].items[j].feature && this.tracks[i].items[j].feature == "arrow") {
+		     item = this.tracks[i].items[j];
+		     // Is there anything else still in frame we need to check?
+
+		     this.tracks[i].items[j].stackOrder = 1;
+		     // Next one we encoutner will be 2
+		     var curr_stackorder = 2;
+		     // Go backwards through the possible inframe elements
+		     // and increase their stack order if needed
+		     for(var k = inframe.length - 1; k >= 0; k--) {
+			 curr_k = inframe[k];
+			 if(this.tracks[i].items[curr_k].end >= item.start) {
+			     // If the current item in the possible stack
+			     // items is overlapping...
+			     if(this.tracks[i].items[curr_k].stackOrder <= curr_stackorder) {
+				 // If the examined item is below or
+				 // equal to the current stack order
+				 this.tracks[i].items[curr_k].stackOrder = curr_stackorder;
+				 curr_stackorder++;
+			     }
+			     // This takes care of ignoring items that
+			     // are already well above the current stack order
+			     
+			 } else {
+			     // Or if it no longer overlaps, remove it
+			     inframe.splice(k, 1);
+			 }
+		     }
+
+		     // Push ourselves on the inframe so the next
+		     // guy can check us out
+		     inframe.push(j);
+		     this.tracks[i].maxStackOrder = Math.max(this.tracks[i].maxStackOrder, curr_stackorder);
+		     // Save the maximum stackorder we've seen
+		 }
+	     }
+	     this.tracks[i].increment = this.y1(0.23) / this.tracks[i].maxStackOrder;
+	 }
+
+	 if("undefined" == typeof this.tracks[i].featureThreshold) {
+	     this.tracks[i].featureThreshold = this.genomesize;
+	 }
+
+	switch(this.tracks[i].trackType) {
+	case "gap":
+	    this.itemRects[i] = this.main.append("g")
+		.attr("class", this.tracks[i].trackName)
+		.attr("width", this.layout.width_without_margins)
+		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
+	    this.displayGapTrack(this.tracks[i], i);
+	    break;
+	case "stranded":
+	    this.itemRects[i] = this.main.append("g")
+		.attr("class", this.tracks[i].trackName)
+		.attr("width", this.layout.width_without_margins)
+		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
+	    if('undefined' !== typeof this.tracks[i].linear_skipInit && this.tracks[i].linear_skipInit) {
+		break;
+	    }
+	    this.displayStranded(this.tracks[i], i);
+	    break;
+	case "track":
+	    this.itemRects[i] = this.main.append("g")
+		.attr("class", this.tracks[i].trackName)
+		.attr("width", this.layout.width_without_margins)
+		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
+	    if('undefined' !== typeof this.tracks[i].linear_skipInit && this.tracks[i].linear_skipInit) {
+		break;
+	    }
+	    this.displayTrack(this.tracks[i], i);
+	    break;
+	case "glyph":
+	    if(typeof this.tracks[i].linear_invert !== 'undefined' && this.tracks[i].linear_invert == true) {
+		this.tracks[i].invert = -1;
+	    } else {
+		this.tracks[i].invert = 1;
+	    }
+	    if(typeof this.tracks[i].linear_padding !== 'undefined') {
+		this.tracks[i].padding = this.tracks[i].linear_padding;
+	    } else {
+		this.tracks[i].padding = 0;
+	    }
+	    this.itemRects[i] = this.main.append("g")
+		.attr("class", this.tracks[i].trackName)
+		.attr("width", this.layout.width_without_margins)
+		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
+	    this.displayGlyphTrack(this.tracks[i], i);
+	    break;
+	case "plot":
+	    this.tracks[i].g = this.itemRects[i] = this.main.append("g")
+		.attr("class", this.tracks[i].trackName)
+		.attr("width", this.layout.width_without_margins)
+		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
+	    this.tracks[i].g.append("path")
+		.attr("class", this.tracks[i].trackName)
+		.attr("id", this.tracks[i].trackName)
+		.attr("stroke-width", 1)
+		.attr("fill", "none");
+
+	    this.displayPlotTrack(this.tracks[i], i);
+	    break;
+	default:
+	    // Do nothing for an unknown track type
+	}
+    }
+
+    //    this.main.append("g").attr("transform", "matrix(0.7, 0, 0, 0.7, 0, 0)").append("use").attr("xlink:href", "#lollipop");
+    //    this.main.append("g").attr("transform", "translate(100,137)").on("click", function() { console.log("click!");}).append("use").attr("xlink:href", "#lollipop_strand_pos");
+
+}
+
+// We can't display all track types, or some don't
+// add to the stacking (ie. graph type)
+
+genomeTrack.prototype.countTracks = function() {
+    var track_count = 0;
+
+     for(var i=0; i < this.tracks.length; i++) {
+
+	 if("undefined" !== this.tracks[i].skipLinear
+	    &&  this.tracks[i].skipLinear == true) {
+	     continue;
+	 }
+
+	switch(this.tracks[i].trackType) {
+	case "stranded":
+	    // a linear track counts as two
+	    track_count++;
+	    this.tracks[i].stackNum = track_count;
+	    track_count++;
+	    break;
+	case "track":
+	    this.tracks[i].stackNum = track_count;
+	    track_count++;
+	    break;
+	default:
+	    // Do nothing for an unknown track type
+	}
+    }
+   
+    return track_count;
+}
+
+genomeTrack.prototype.displayStranded = function(track, i) {
+    var visStart = this.visStart,
+    visEnd = this.visEnd,
+    visRange = visEnd - visStart,
+    x1 = this.x1,
+    y1 = this.y1;
+    var cfg = this.layout;
+
+    // Because of how the tooltip library binds to the SVG object we have to turn it
+    // on or off here rather than in the .on() call, we'll redirect the calls to
+    // a dummy do-nothing object if we're not showing tips in this context.
+    var tip = {show: function() {}, hide: function() {} };
+    if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
+	tip = this.tip;
+    }
+
+    var stackNum = this.tracks[i].stackNum;
+    //    console.log(visStart, visEnd);
+    var visItems = track.items.filter(function(d) {
+	    if(typeof d.feature !== 'undefined' && d.feature !== 'gene') {
+		if(track.featureThreshold < visRange) {
+		    return false;
+		}
+	    }
+	    return d.start < visEnd && d.end > visStart;
+	});
+
+    //    console.log(track.items);
+
+    var rects = this.itemRects[i].selectAll("g")
+    .data(visItems, function(d) { return d.id; })
+	.attr("transform", function(d,i) { 
+	    return "translate(" + x1(d.start) + ',' +  d.yshift + ")"; });
+
+    // Process the changed/moved rects
+    rects.selectAll("rect")
+    .each(function (d) { d.width = x1(d.end + 1) - x1(d.start); })
+    .attr("width", function(d) {return d.width;})
+    // Yes we really don't need to set the class here again
+    // except to deal with the _zoom class when zooming
+    // in and out
+    .attr("class", function(d) {
+	return track.trackName + '_' + d.suffix + ' ' + ((d.width > 5) ? (track.trackName + '_' + d.suffix + '_zoomed') : '' ) + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');});
+
+    // Process the text for changed/moved rects
+    rects.selectAll("text")
+    .attr("dx", "2px")
+    .attr("dy", "0.94em")
+    .each(function (d) {
+	    var bb = this.getBBox();
+	    var slice_length = x1(d.end) - x1(d.start) - 2; // -2 to offset the dx above
+	    d.visible = (slice_length > bb.width);
+	})
+    .attr("class", function(d) {
+	return track.trackName + '_text ' + track.trackName + '_' + d.suffix + '_text ' + (d.visible ? '' : "linear_hidden " ) + ('undefined' !== typeof d.extraclass ? d.extraclass : ''); });
+
+    this.itemRects[i].selectAll(".arrow")
+    .each(function(d) {
+	    d.width = x1(d.end + 1) - x1(d.start);
+
+	    if(d.strand == -1) {
+		headxtranslate = 0;
+		arrowline = "m " + d.width + ",0 " + "l 0," + (track.baseheight + d.height) + " -" + d.width + ",0";
+	    } else {
+		headxtranslate = d.width;
+		arrowline = "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
+	    }
+
+	    d3.select(this).select("path")
+		.attr("d", function(d) { 
+			return arrowline;
+		    });
+
+	    d3.select(this).select("use")
+		.attr("transform", function(d) {
+			return "translate(" + headxtranslate + "," + d.headytranslate + ")";
+		    });
+
+	});
+
+    var entering_rects = rects.enter().append("g")
+    .attr("transform", function(d,i) {
+	    if(d.strand == -1) {
+		ystack = stackNum;
+		d.suffix = 'neg';
+	    } else if(d.strand == "1") {
+		ystack = stackNum -1;
+		d.suffix = 'pos';
+	    } else {
+		ystack = stackNum - 0.3;
+		d.suffix = 'none';
+	    }
+	    var shift_gene = 0;
+	    if(typeof d.feature !== 'undefined' && d.feature == "terminator") {
+		ystack = ystack - 0.5;
+	    } else if (track.trackFeatures == 'complex' && d.strand == "1") {
+		    var shift_gene = y1(1) * .2;
+
+	    }
+	    d.yshift = y1(ystack) + 10 + shift_gene;
+	    return "translate(" + x1(d.start) + ',' +  d.yshift + ")"; })
+    //	    return "translate(" + x1(d.start) + ',' +  (y1(ystack) + 10 + shift_gene) + ")"; })
+    .attr("id", function(d,i) { return track.trackName + '_' + d.id; })
+    .attr("class", function(d) {
+	    return track.trackName + '_' + d.suffix + '_group ' + (typeof d.feature === 'undefined' ? 'gene' : d.feature); })//;
+	   
+    //        entering_rects
+    .each(function(d) {
+	    d.width = x1(d.end) - x1(d.start);
+
+	    if (typeof d.feature === 'undefined' || d.feature == "gene") {
+		d3.select(this)
+		.append("rect")
+		.attr("class", function(d) {
+
+			return track.trackName + '_' + d.suffix + ' ' + ((d.width > 5) ? (track.trackName + '_' + d.suffix + '_zoomed') : '') + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');})
+		.attr("width", function(d) {return d.width;})
+		.attr("height", function(d) {
+			if(track.trackFeatures == 'complex') { 
+			    var scale_factor = 0.77;
+			} else {
+			    var scale_factor = 1;
+			}
+			return (d.strand == 0 ? .4 : .9) * scale_factor * y1(1);
+		    })
+    .on("click", function(d,i) {
+	    if (d3.event.defaultPrevented) return; // click suppressed
+	    if('undefined' !== typeof track.linear_mouseclick) {
+		var fn = window[track.linear_mouseclick];
+		if('object' ==  typeof fn) {
+		    return fn.onclick(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    } else {
+		null;
+	    }
+	})
+    .on('mouseover', function(d) { 
+	    tip.show(d);
+	    if('undefined' !== typeof track.linear_mouseover) {
+		var fn = window[track.linear_mouseover];
+		if('object' ==  typeof fn) {
+		    return fn.mouseover(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    }	
+	})
+    .on('mouseout', function(d) { 
+	    tip.hide(d);
+	    if('undefined' !== typeof track.linear_mouseout) {
+		var fn = window[track.linear_mouseout];
+		if('object' ==  typeof fn) {
+		    return fn.mouseout(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    }	
+	});
+
+	    } else if(d.feature == "terminator") {
+		if(d.strand == 1) {
+		    lollipop = "#lollipop_strand_pos";
+		} else {
+		    lollipop = "#lollipop_strand_neg";
+		}
+		d3.select(this).append("use").attr("xlink:href", lollipop);
+
+	    } else if(d.feature == "arrow") {
+
+		if(d.strand == -1) {
+		    d.height = y1(0.23) - (d.stackOrder * track.increment);
+		    arrowhead = "#leftarrow";
+		    headxtranslate = 0;
+		    d.headytranslate = track.baseheight + d.height;
+		    //		    console.log(track.increment);
+		    //		    console.log(d.headytranslate);
+		    arrowline = "m " + d.width + ",0 " + "l 0," + (track.baseheight + d.height) + " -" + d.width + ",0";
+		    //		    console.log(arrowline);
+		} else {
+		    d.height = d.stackOrder * track.increment;
+		    arrowhead = "#rightarrow";
+		    headxtranslate = d.width;
+		    d.headytranslate = d.height * -1;
+		    arrowline = "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
+
+		}
+		arrowclass = track.trackName + '_arrow_' + d.suffix + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');
+		arrowbase = d3.select(this)
+		
+		arrowbase.append("path")
+		.attr("class", arrowclass)
+		.attr("d", function(d) { 
+			// 0.77 * 0.9
+			
+			return arrowline;
+		    })
+		.attr("fill-opacity", 0)
+		arrowbase.append("use").attr("xlink:href", arrowhead)
+		.attr("transform", function(d) {
+			return "translate(" + headxtranslate + "," + d.headytranslate + ")";
+		    })
+		.attr("class", arrowclass);
+
+
+	    } //else
+	});
+
+    if(('undefined' !== typeof track.showLabels) && typeof track.showLabels) {
+	entering_rects.each(function(d) {
+		if(typeof d.feature == 'undefined' || d.feature == 'gene') {
+		    d3.select(this).append("text")
+			.text(function(d) {return d.name;})
+			.attr("dx", "2px")
+			.attr("dy", "1em")
+			.each(function (d) {
+				var bb = this.getBBox();
+				var slice_length = x1(d.end - d.start);
+				d.visible = (slice_length > bb.width);
+			    })
+			.attr("class", function(d) {
+				return track.trackName + '_text ' +  track.trackName + '_' + d.suffix + '_text ' + (d.visible ? null : "linear_hidden"  ); });
+		}
+	    });
+    }
+
+    rects.exit().remove();
+}
+
+genomeTrack.prototype.displayTrack = function(track, i) {
+    var visStart = this.visStart,
+    visEnd = this.visEnd,
+    visRange = visEnd - visStart,
+    x1 = this.x1,
+    y1 = this.y1;
+    var cfg = this.layout;
+
+    // Because of how the tooltip library binds to the SVG object we have to turn it
+    // on or off here rather than in the .on() call, we'll redirect the calls to
+    // a dummy do-nothing object if we're not showing tips in this context.
+    var tip = {show: function() {}, hide: function() {} };
+    if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
+	tip = this.tip;
+    }
+
+    var stackNum = this.tracks[i].stackNum;
+    //    console.log(visStart, visEnd, visRange);
+    var visItems = track.items.filter(function(d) {
+	    if(typeof d.feature !== 'undefined' && d.feature !== 'gene') {
+		if(track.featureThreshold < visRange) {
+		    return false;
+		}
+	    }
+	    return d.start < visEnd && d.end > visStart;}
+	);
+
+    //    console.log(track.items);
+
+    var rects = this.itemRects[i].selectAll("g")
+    .data(visItems, function(d) { return d.id; })
+    .attr("transform", function(d,i) { 
+	    return "translate(" + x1(d.start) + ',' + d.yshift  + ")"; 
+	});
+
+
+    this.itemRects[i].selectAll("rect")
+    .each(function (d) { d.width = x1(d.end) - x1(d.start); })
+    .attr("width", function(d) {return d.width; })
+    // Yes we really don't need to set the class here again
+    // except to deal with the _zoom class when zooming
+    // in and out
+    .attr("class", function(d) {return track.trackName + ' ' + ((d.width > 5) ? (track.trackName + '_zoomed') : '' ) + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');});
+
+    rects.selectAll("text")
+    .attr("dx", "2px")
+    .attr("dy", "1em")
+    .each(function (d) {
+	    var bb = this.getBBox();
+	    var slice_length = x1(d.end) - x1(d.start) - 2; // -2 to offset the dx above
+	    d.visible = (slice_length > bb.width);
+	})
+    .attr("class", function(d) {return track.trackName + '_text ' + (d.visible ? null : "linear_hidden" ); });
+
+    this.itemRects[i].selectAll(".arrow")
+    .each(function(d) {
+	    //	console.log(d);
+	    d.width = x1(d.end + 1) - x1(d.start);
+
+	    d3.select(this).select("path")
+		.attr("d", function(d) { 
+			return "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
+		    });
+
+	    d3.select(this).select("use")
+		.attr("transform", function(d) {
+			return "translate(" + d.width + ",-" + d.headytranslate + ")";
+		    });
+
+	});
+
+    var entering_rects = rects.enter().append("g")
+    .attr("transform", function(d,i) { 
+	    ystack = stackNum;
+	    shift_gene = 0;
+	    if(typeof d.feature !== 'undefined' && d.feature == "terminator") {
+		ystack = ystack - 0.6;
+	    } else if (track.trackFeatures == 'complex') {
+		    var shift_gene = y1(1) * .175;
+
+	    }
+
+	    d.yshift = y1(ystack) + 10 + shift_gene;
+	    return "translate(" + x1(d.start) + ',' + d.yshift  + ")"; 
+	})
+    .attr("id", function(d,i) { return track.trackName + '_' + d.id; })
+    .attr("class", function(d) {return track.trackName + '_group ' + (typeof d.feature === 'undefined' ? 'gene' : d.feature); })//;
+
+    //    entering_rects
+    .each(function (d) { 
+	    d.width = x1(d.end) - x1(d.start); 
+
+	    if (typeof d.feature === 'undefined' || d.feature == "gene") {
+
+		d3.select(this).append("rect")
+
+		    .attr("class", function(d) {return track.trackName + ' ' + ((d.width > 5) ? (track.trackName + '_zoomed') : '' ) + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');})
+		    .attr("width", function(d) {return d.width; })
+		    .attr("height", function(d) {
+			    if(track.trackFeatures == 'complex') {
+				var scale_factor = 0.77;
+			    } else {
+				var scale_factor = 1;
+			    }
+
+			    return .8 * scale_factor * y1(1);
+			})
+		    .on("click", function(d,i) {
+			    if (d3.event.defaultPrevented) return; // click suppressed
+			    if('undefined' !== typeof track.linear_mouseclick) {
+				var fn = window[track.linear_mouseclick];
+				if('object' ==  typeof fn) {
+				    return fn.onclick(track.trackName, d, cfg.plotid);
+				} else if('function' == typeof fn) {
+				    return fn(track.trackName, d, cfg.plotid);
+				}
+			    } else {
+				null;
+			    }
+			})
+		    .on('mouseover', function(d) { 
+			    tip.show(d);
+			    if('undefined' !== typeof track.linear_mouseover) {
+				var fn = window[track.linear_mouseover];
+				if('object' ==  typeof fn) {
+				    return fn.mouseover(track.trackName, d, cfg.plotid);
+				} else if('function' == typeof fn) {
+				    return fn(track.trackName, d, cfg.plotid);
+				}
+			    }	
+			})
+		    .on('mouseout', function(d) { 
+			    tip.hide(d);
+			    if('undefined' !== typeof track.linear_mouseout) {
+				var fn = window[track.linear_mouseout];
+				if('object' ==  typeof fn) {
+				    return fn.mouseout(track.trackName, d, cfg.plotid);
+				} else if('function' == typeof fn) {
+				    return fn(track.trackName, d, cfg.plotid);
+				}
+			    }	
+			})
+		    
+		    if('undefined' !== typeof track.showLabels) {
+			//		entering_rects
+			d3.select(this).append("text")
+			    .text(function(d) {return d.name;})
+			    .attr("dx", "2px")
+			    .attr("dy", "1em")
+			    .each(function (d) {
+				    var bb = this.getBBox();
+				    var slice_length = x1(d.end) - x1(d.start) -2 ; // -2 to offset the dx above
+				    d.visible = (slice_length > bb.width);
+				})
+			    .attr("class", function(d) {return track.trackName + '_text ' + (d.visible ? null : "linear_hidden" ); });
+		    }
+	    } else if(d.feature == "terminator") {
+		d3.select(this).append("use").attr("xlink:href", "#lollipop");
+	    } else if(d.feature == "arrow") {
+
+		d.height = d.stackOrder * track.increment;
+		d.headytranslate = d.height;
+
+		arrowclass = track.trackName + '_arrow' + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');
+		arrowbase = d3.select(this)
+		
+		arrowbase.append("path")
+		.attr("class", arrowclass)
+		.attr("d", function(d) { 
+			// 0.77 * 0.9
+			return "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
+			
+		    })
+		.attr("fill-opacity", 0)
+		arrowbase.append("use").attr("xlink:href", "#rightarrow")
+		.attr("transform", function(d) {
+			return "translate(" + d.width + ",-" + d.headytranslate + ")";
+		    })
+		.attr("class", arrowclass);
+
+
+	    } //else
+	});
+
+
+    rects.exit().remove();
+}
+
+genomeTrack.prototype.displayPlotTrack = function(track, i) {
+    var visStart = this.visStart,
+    visEnd = this.visEnd,
+    x1 = this.x1,
+    y1 = this.y1;
+
+    if((typeof track.visible == 'undefined') || (track.visible == false)) {
+    	return;
+    }
+
+    if((typeof track.linear_plot_width == 'undefined') || (typeof track.linear_plot_height == 'undefined')) {
+//    if((typeof track.linear_plot_width == 'undefined')) {
+	return;
+    }
+
+    var startItem = parseInt(visStart / track.bp_per_element);
+    var endItem = Math.min(parseInt(visEnd / track.bp_per_element), track.items.length);
+    var offset = ((startItem+1) * track.bp_per_element) - visStart;
+
+    var items = track.items.filter(function(d, i) { return i >= startItem && i <= endItem } );
+
+    track.plotScale = d3.scale.linear()
+	.domain([track.plot_min, track.plot_max])
+	.range([track.linear_plot_height+(track.linear_plot_width/2), track.linear_plot_height-(track.linear_plot_width/2)]);
+
+    var lineFunction = d3.svg.line()
+	.x(function(d, i) { return x1((i*track.bp_per_element)); } )
+	.y(function(d, i) { return track.plotScale(d); } )
+	.interpolate("linear");
+
+     var plot = this.itemRects[i].selectAll("path")
+	.attr("d", lineFunction(track.items))
+
+//    plot.exit().remove();
+
+}
+
+genomeTrack.prototype.displayGapTrack = function(track, i) {
+    var visStart = this.visStart,
+    visEnd = this.visEnd,
+    x1 = this.x1,
+    y1 = this.y1;
+    var cfg = this.layout;
+    var self = this;
+
+    // Because of how the tooltip library binds to the SVG object we have to turn it
+    // on or off here rather than in the .on() call, we'll redirect the calls to
+    // a dummy do-nothing object if we're not showing tips in this context.
+    var tip = {show: function() {}, hide: function() {} };
+    if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
+	tip = this.tip;
+    }
+
+    if((typeof track.visible !== 'undefined') && (track.visible == false)) {
+    	return;
+    }
+
+//    var gap_range = d3.range(0, this.layout.height, 5);
+    var gap_range = d3.range(0, y1(this.numTracks)+(this.numTracks*3), 5);
+
+    var items = track.items.filter(function(d) {return (d.start <= visEnd && d.start >= visStart) || (d.end <= visEnd && d.end >= visStart);});
+
+    var gaps = this.itemRects[i].selectAll("path")
+    .data(items, function(d) { return d.id; })
+    .attr("transform", function(d,i) { 
+	    return "translate(" + x1(d.start) + ', 0)'; 
+	})
+    .each(function (d) { d.width = x1(d.end) - x1(d.start); })
+    .attr('d', function(d) { return self.jaggedPathGenerator(d.width, gap_range); } );
+
+    var entering_gaps = gaps.enter().append("path")
+    .each(function (d) { d.width = x1(d.end) - x1(d.start); })
+    .attr('d', function(d) { return self.jaggedPathGenerator(d.width, gap_range); } )
+    .attr("transform", function(d,i) { 
+	    return "translate(" + x1(d.start) + ', 0)'; 
+	})
+    .attr("id", function(d,i) { return track.trackName + '_' + d.id; })
+    .attr("class", function(d) {return track.trackName + ' linearplot ' + (typeof d.feature === 'undefined' ? 'gene' : d.feature); })//;
+    .on("click", function(d,i) {
+	    if (d3.event.defaultPrevented) return; // click suppressed
+	    if('undefined' !== typeof track.linear_mouseclick) {
+		var fn = window[track.linear_mouseclick];
+		if('object' ==  typeof fn) {
+		    return fn.onclick(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    } else {
+		null;
+	    }
+	})
+    .on('mouseover', function(d) { 
+	    tip.show(d);
+	    if('undefined' !== typeof track.linear_mouseover) {
+		var fn = window[track.linear_mouseover];
+		if('object' ==  typeof fn) {
+		    return fn.mouseover(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    }	
+	})
+    .on('mouseout', function(d) { 
+	    tip.hide(d);
+	    if('undefined' !== typeof track.linear_mouseout) {
+		var fn = window[track.linear_mouseout];
+		if('object' ==  typeof fn) {
+		    return fn.mouseout(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    }	
+	});
+
+    gaps.exit().remove();
+
+}
+
+genomeTrack.prototype.jaggedPathGenerator = function(width, data) {
+
+    var down = [];
+    //    var up = [];
+    for(var i = 0; i < data.length; i++) {
+	var offset = ((i % 2 === 0) ? 3 : -3);
+	down.push({ x: offset, y: data[i] });
+	down.unshift({ x: offset+width, y: data[i] });
+    }
+    down.push(down[0]);
+
+    var generator = d3.svg.line()
+    .x(function(d,i) { return d.x; })
+    .y(function(d,i) { return d.y; })
+    .interpolate("linear");
+
+    return generator(down);
+    //    return generator(down.concat(up));
+}
+
+genomeTrack.prototype.displayGlyphTrack = function(track, i) {
+    var visStart = this.visStart,
+    visEnd = this.visEnd,
+    x1 = this.x1,
+    y1 = this.y1;
+    var cfg = this.layout;
+
+    if((typeof track.visible !== 'undefined') && (track.visible == false)) {
+    	return;
+    }
+
+    // Because of how the tooltip library binds to the SVG object we have to turn it
+    // on or off here rather than in the .on() call, we'll redirect the calls to
+    // a dummy do-nothing object if we're not showing tips in this context.
+    var tip = {show: function() {}, hide: function() {} };
+    if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
+	tip = this.tip;
+    }
+
+    var items = track.items.filter(function(d) {return d.bp <= visEnd && d.bp >= visStart;});
+
+    // When we move we need to recalculate the stacking order
+    var stackCount = 0;
+    for(var j = 0; j < items.length; j++) {
+	if(items[j].bp < visStart || items[j].bp > visEnd) {
+	    continue;
+	}
+	if(j < 1) {
+	    items[j].stackCount = 0;
+	    continue;
+	}
+
+	var dist = x1(items[j].bp) - x1(items[j-1].bp);
+
+	if(dist < track.linear_pixel_spacing) {
+	    items[j].stackCount = items[j-1].stackCount + 1;
+	    continue;
+	}
+
+	items[j].stackCount = 0;
+    }
+
+    // Because SVG coordinates are from the top-left, the "height" is pixels DOWN from
+    // the top of the image to start stacking the glyphs
+
+    var glyphs = this.itemRects[i].selectAll("path")
+    .data(items, function(d) { return d.id; })
+    .attr("transform", function(d,i) { return "translate(" + (x1(d.bp) + track.padding) + ',' + (track.linear_height - (track.linear_glyph_buffer * d.stackCount * track.invert))  + ")"; });
+   
+    var entering_glyphs = glyphs.enter()
+    .append('path')
+    .attr('id', function(d,i) { return track.trackName + "_glyph" + d.id; })
+    .attr('class', function(d) {return track.trackName + '_' + d.type + " linear_" + track.trackName + '_' + d.type; })
+    .attr("d", d3.svg.symbol().type(track.glyphType).size(track.linear_glyphSize))
+    .attr("transform", function(d,i) {  return "translate(" + (x1(d.bp) + track.padding) + ',' + (track.linear_height - (track.linear_glyph_buffer * d.stackCount * track.invert))  + ")"; })
+    .on("click", function(d,i) {
+	    if('undefined' !== typeof track.linear_mouseclick) {
+		var fn = window[track.linear_mouseclick];
+		if('object' ==  typeof fn) {
+		    return fn.onclick(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    } else {
+		null;
+	    }
+	})
+    .on('mouseover', function(d) { 
+	tip.show(d);
+	    if('undefined' !== typeof track.linear_mouseover) {
+		var fn = window[track.linear_mouseover];
+		if('object' ==  typeof fn) {
+		    return fn.mouseover(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    }	
+	})
+    .on('mouseout', function(d) { 
+	tip.hide(d);
+	    if('undefined' !== typeof track.linear_mouseout) {
+		var fn = window[track.linear_mouseout];
+		if('object' ==  typeof fn) {
+		    return fn.mouseout(track.trackName, d, cfg.plotid);
+		} else if('function' == typeof fn) {
+		    return fn(track.trackName, d, cfg.plotid);
+		}
+	    }	
+	});
+
+    glyphs.exit()
+    .remove();
+    
+}
+
+genomeTrack.prototype.displayAxis = function() {
+    this.axisContainer.select(".xaxislinear").call(this.xAxis);
+}
+
+    genomeTrack.prototype.update = function(startbp, endbp, params) {
+    //    console.log(startbp, endbp);
+
+    this.visStart = startbp;
+    this.visEnd = endbp;
+
+    this.zoom.x(this.x1.domain([startbp,endbp]));
+
+    this.redraw();
+}
+
+genomeTrack.prototype.update_finished = function(startbp, endbp, params) {
+    //    console.log("Thank you, got: " + startbp, endbp);
+
+}
+
+genomeTrack.prototype.resize = function(newWidth) {
+    this.layout.width = newWidth;
+
+    this.dragbar
+    .attr("transform", "translate(" + (newWidth -
+				       this.layout.right_margin) + "," + (this.dragbar_y_mid-15) + ")")
+
+    this.layout.width_without_margins =
+	this.layout.width - this.layout.left_margin -
+	this.layout.right_margin;
+
+    this.x
+	.range([0,this.layout.width_without_margins]);
+    this.x1
+	.range([0,this.layout.width_without_margins]);
+
+    this.chart
+	.attr("width", this.layout.width)
+
+    this.clipPath
+	.attr("width", this.layout.width_without_margins)
+    
+    this.main
+	.attr("width", this.layout.width_without_margins)
+
+    this.redraw();
+
+}
+
+genomeTrack.prototype.dragresize = function(d) {
+    var newWidth = d3.event.x;
+
+    //    console.log(this.layout.containerid);
+    this.resize(newWidth);
+    //    d3.event.preventDefault();
+
+}
+
+genomeTrack.prototype.redraw = function() {
+
+    for(var i = 0; i < this.tracks.length; i++) {
+
+	 if("undefined" !== this.tracks[i].skipLinear
+	    &&  this.tracks[i].skipLinear == true) {
+	     continue;
+	 }
+
+	switch(this.tracks[i].trackType) {
+	case 'gap':
+	    this.displayGapTrack(this.tracks[i], i);
+            break;
+	case "stranded":
+	    this.displayStranded(this.tracks[i], i);
+	    break;
+	case "track":
+	    this.displayTrack(this.tracks[i], i);
+	    break;
+	case "glyph":
+	    this.displayGlyphTrack(this.tracks[i], i);
+	    break;
+	case "plot":
+	    this.displayPlotTrack(this.tracks[i], i);
+	    break;
+	default:
+	    // Do nothing for an unknown track type
+	}
+    }
+    
+    this.axisContainer.select(".xaxislinear").call(this.xAxis);
+
+}
+
+genomeTrack.prototype.rescale = function() {
+    var cfg = this.layout;
+
+    var reset_s = 0;
+    if ((this.x1.domain()[1] - this.x1.domain()[0]) >= (this.genomesize - 0)) {
+	this.zoom.x(this.x1.domain([0, this.genomesize]));
+	reset_s = 1;
+    }
+
+    if (reset_s == 1) { // Both axes are full resolution. Reset.
+	this.zoom.scale(1);
+	this.zoom.translate([0,0]);
+    }
+    else {
+	if (this.x1.domain()[0] < 0) {
+	    this.x1.domain([0, this.x1.domain()[1] - this.x1.domain()[0] + 0]);
+	}
+	if (this.x1.domain()[1] > this.genomesize) {
+	    var xdom0 = this.x1.domain()[0] - this.x1.domain()[1] + this.genomesize;
+	    this.x1.domain([xdom0, this.genomesize]);
+	}
+    }
+
+    var cur_domain = this.x1.domain();
+    this.visStart = cur_domain[0];
+    this.visEnd = cur_domain[1];
+
+    if('undefined' !== typeof this.callbackObj) {
+	if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
+	    for(var obj in this.callbackObj) {
+		if(this.callbackObj.hasOwnProperty(obj)) {
+		    this.callbackObj[obj].update(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
+		}
+	    }
+	} else {
+	    this.callbackObj.update(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
+	}
+    }
+
+    this.redraw();
+
+}
+
+genomeTrack.prototype.addBrushCallback = function(obj) {
+
+    // We allow multiple brushes to be associated with a linear plot, if we have
+    // a brush already, add this new one on.  Otherwise just remember it.
+
+    if('undefined' !== typeof this.callbackObj) {
+
+	if( Object.prototype.toString.call( obj ) === '[object Array]' ) { 
+	    this.callbackObj.push(obj);
+	} else {
+	    var tmpobj = this.callbackObj;
+	    this.callbackObj = [tmpobj, obj];
+	}
+    } else {
+	this.callbackObj = obj;
+    }
+
+    // And make sure our new brush is updated to reflect
+    // the current visible area
+    obj.update(this.visStart, this.visEnd);
+}
+
+genomeTrack.prototype.callBrushFinished = function() {
+    var cfg = this.layout;
+
+    if('undefined' !== typeof this.callbackObj) {
+	if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
+	    for(var obj in this.callbackObj) {
+		if(this.callbackObj.hasOwnProperty(obj)) {
+		    this.callbackObj[obj].update_finished(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
+		}
+	    }
+	} else {
+	    this.callbackObj.update_finished(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
+	}
+    }
+
+}
+
+////////////////////////////////////////////////
+//
+// Export functionality
+//
+////////////////////////////////////////////////
+
+// Allowed export formats are 'png' and 'svg'
+// The extension will be added, just summply the base
+// filename.
+
+// Saving to raster format is dependent on FileSaver.js
+// and canvg.js (which include rgbcolor.js & StackBlur.js),
+// they must be loaded before circularplot.js
+
+genomeTrack.prototype.savePlot = function(scaling, filename, stylesheetfile, format) {
+        // First lets get the stylesheet
+    var sheetlength = stylesheetfile.length;
+    var style = document.createElementNS("http://www.w3.org/1999/xhtml", "style");
+	style.textContent += "<![CDATA[\n";
+    for (var i=0;i<document.styleSheets.length; i++) {
+	str = document.styleSheets[i].href;
+	if(null == str) continue;
+
+	if (str.substr(str.length-sheetlength)==stylesheetfile){
+            var rules;
+            if(document.styleSheets[i].cssRules) {
+                rules = document.styleSheets[i].cssRules;
+            } else if (document.styleSheets[i].rules) {
+                rules = document.styleSheets[i].rules;
+            }
+            if(rules) {
+                for (var j=0; j<rules.length;j++){
+                    style.textContent += (rules[j].cssText + "\n");
+                }
+            }
+            break;
+    	}
+    }
+    style.textContent += "]]>";
+
+    // Now we clone the SVG element, resize and scale it up
+    var container = this.layout.container.slice(1);
+    var containertag = document.getElementById(container);
+    var clonedSVG = containertag.cloneNode(true);
+    var svg = clonedSVG.getElementsByTagName("svg")[0];
+
+    // Remove any hidden elements such as text that's not being shown
+    var tags = svg.getElementsByClassName("linear_hidden")
+    for(var i=tags.length-1; i>=0; i--) {
+//	if(tags[i].getAttributeNS(null, "name") === name) {
+	    tags[i].parentNode.removeChild(tags[i]);
+//        }
+    }
+
+    // We need to resize the svg with the new canvas size
+    svg.removeAttribute('width');
+    svg.removeAttribute('height');
+    svg.setAttribute('width', this.layout.width*scaling);
+    svg.setAttribute('height', this.layout.height*scaling);
+
+    // Update first g tag with the scaling
+    g = svg.getElementsByTagName("g")[0];
+    transform = g.getAttribute("transform");
+//    g.setAttribute("transform", transform + " scale(" + scaling + ")");
+
+    // Append the stylehsheet to the cloned svg element
+    // so when we export it the style are inline and 
+    // get rendered
+    svg.getElementsByTagName("defs")[0].appendChild(style);
+
+    // Fetch the actual SVG tag and convert it to a canvas
+    // element
+    var content = clonedSVG.innerHTML.trim();
+
+    if(format == 'svg') {
+	var a = document.createElement('a');
+	a.href = "data:application/octet-stream;base64;attachment," + btoa(content);
+	a.download = filename + ".svg";
+	a.click();
+
+    } else if(format == 'png') {
+	var canvas = document.createElement('canvas');
+	canvg(canvas, content);
+
+	// Convert the canvas to a data url (this could
+	// be displayed inline by inserting it in to an 
+	// <img> tag in the src attribute, ie
+	// <img src="'+imgData+'">
+	var theImage = canvas.toDataURL('image/png');
+
+	// Convert to a blob
+	var blob = this.dataURLtoBlob(theImage);
+
+	// Prompt to save
+	saveAs(blob, filename);
+    }
+}
+
+genomeTrack.prototype.dataURLtoBlob = function(dataURL) {
+  // Decode the dataURL    
+  var binary = atob(dataURL.split(',')[1]);
+  // Create 8-bit unsigned array
+  var array = [];
+  for(var i = 0; i < binary.length; i++) {
+      array.push(binary.charCodeAt(i));
+  }
+  // Return our Blob object
+  return new Blob([new Uint8Array(array)], {type: 'image/png'});
+}
+
+genomeTrack.prototype.drawFeatures = function() {
+    var x1 = this.x1;
+    var y1 = this.y1;
+
+    // Quick debugging variable to show click rects
+    var opacity = 0;
+
+    // Lollipop for terminator glyph (stranded, positive)
+    var lollipop_strand_pos = this.defs.append("g").attr("id", "lollipop_strand_pos");
+    lollipop_strand_pos.append("path")
+	.attr("class", "lollipophead")
+	.attr("d", function() {
+		arc = "m 0,";
+		arc += y1(1) * 0.69;
+		arc += " a ";
+		arc += y1(1) * 0.13;
+		arc += ",";
+		arc += y1(1) * 0.13;
+		arc += " 0 1 1 ";
+		arc += y1(1) * 0.09;
+		arc += ",0";
+		//		console.log(arc);
+		return arc;
+		//		"m 0,60 a 12,12 0 1 1 8,0"
+	    });
+    lollipop_strand_pos.append("path")
+	.attr("class", "lollipopstemend")
+	.attr("d", function() {
+		line = "m " + (y1(1) * 0.09) + ",";
+		line += y1(1) * 0.69;
+		line += " l 0,";
+		line += y1(1) * 0.70;
+		//		console.log("line " + line);
+		return line;
+		//		"m 8,60 l 0,65"
+		    });
+    lollipop_strand_pos.append("path")
+	.attr("class", "lollipopstemstart")
+	.attr("d", function() {
+		line = "m 0,";
+		line += y1(1) * 0.69;
+		line += " l 0,";
+		line += y1(1) * 0.70;
+		//		console.log(line);
+		return line;
+		//		"m 0,60 l 0,65"
+	    });
+    lollipop_strand_pos.append("rect")
+	.attr("transform", function () {
+		return "translate(-" + (y1(1) * 0.1) + "," + (y1(1) * 0.43) + ")";
+	    })
+	.attr("width", function() { 
+		return y1(1) * 0.3;
+	    })
+	.attr("height", function() { 
+		return y1(1) * 0.26;
+	    })
+	.attr("fill-opacity", opacity);
+    lollipop_strand_pos.append("rect")
+        .attr("transform", function() {
+		return "translate(0, " + (y1(1) * 0.68) + ")";
+		//		"translate(0,60)"
+		    })
+	.attr("width", 8)
+	.attr("height", function() {
+		return  y1(1) * 0.72;
+	    })
+	.attr("fill-opacity", opacity);
+
+    // Lollipop for terminator glyph (stranded, negative)
+    var lollipop_strand_neg = this.defs.append("g").attr("id", "lollipop_strand_neg");
+    lollipop_strand_neg.append("path")
+	.attr("class", "lollipophead")
+	.attr("d", function() {
+		arc = "m 0,";
+		arc += y1(1) * 1.20;
+		arc += " a ";
+		arc += y1(1) * 0.13;
+		arc += ",";
+		arc += y1(1) * 0.13;
+		arc += " 0 1 0 ";
+		arc += y1(1) * 0.09;
+		arc += ",0";
+		//		console.log(arc);
+		return arc;
+		//		"m 0,60 a 12,12 0 1 1 8,0"
+	    });
+    lollipop_strand_neg.append("path")
+	.attr("class", "lollipopstemstart")
+	.attr("d", function() {
+		line = "m " + (y1(1) * 0.09) + ",";
+		line += y1(1) * 1.20;
+		line += " l 0,";
+		line += y1(1) * 0.71 * -1;
+		//		console.log(line);
+		return line;
+		//		"m 8,60 l 0,65"
+		    });
+    lollipop_strand_neg.append("path")
+	.attr("class", "lollipopstemend")
+	.attr("d", function() {
+		line = "m 0,";
+		line += y1(1) * 1.20;
+		line += " l 0,";
+		line += y1(1) * 0.71 * -1;
+		//		console.log(line);
+		return line;
+		//		"m 0,60 l 0,65"
+	    });
+    lollipop_strand_neg.append("rect")
+	.attr("transform", function () {
+		return "translate(-" + (y1(1) * 0.1) + "," + (y1(1) * 1.20) + ")";
+	    })
+	.attr("width", function() { 
+		return y1(1) * 0.3;
+	    })
+	.attr("height", function() { 
+		return y1(1) * 0.26;
+	    })
+	.attr("fill-opacity", opacity);
+    lollipop_strand_neg.append("rect")
+	.attr("transform", function() {
+		return "translate(0, " + (y1(1) * 0.50) + ")";
+		//		"translate(0,60)"
+		    })
+	.attr("width", 8)
+	.attr("height", function() {
+		return  y1(1) * 0.71;
+	    })
+	.attr("fill-opacity", opacity);
+
+    // Lollipop for terminator glyph (unstranded)
+    var lollipop = this.defs.append("g").attr("id", "lollipop");
+    lollipop.append("path")
+        .attr("class", "lollipophead")
+	.attr("d", function() {
+		arc = "m 0,";
+		arc += y1(1) * 0.77;
+		arc += " a ";
+		arc += y1(1) * 0.13;
+		arc += ",";
+		arc += y1(1) * 0.13;
+		arc += " 0 1 1 ";
+		arc += y1(1) * 0.09;
+		arc += ",0";
+		//		console.log(arc);
+		return arc;
+		//		"m 0,60 a 12,12 0 1 1 8,0"
+	    });
+    lollipop.append("path")
+	.attr("class", "lollipopstemend")
+	.attr("d", function() {
+		line = "m " + (y1(1) * 0.09) + ",";
+		line += y1(1) * 0.77;
+		line += " l 0,";
+		line += y1(1) * 0.62;
+		//		console.log(line);
+		return line;
+		//		"m 8,60 l 0,65"
+		    });
+    lollipop.append("path")
+	.attr("class", "lollipopstemstart")
+	.attr("d", function() {
+		line = "m 0,";
+		line += y1(1) * 0.77;
+		line += " l 0,";
+		line += y1(1) * 0.62;
+		//		console.log(line);
+		return line;
+		//		"m 0,60 l 0,65"
+	    });
+    lollipop.append("rect")
+	.attr("transform", function () {
+		return "translate(-" + (y1(1) * 0.1) + "," + (y1(1) * 0.51) + ")";
+	    })
+	.attr("width", function() { 
+		return y1(1) * 0.3;
+	    })
+	.attr("height", function() { 
+		return y1(1) * 0.26;
+	    })
+	.attr("fill-opacity", opacity);
+    lollipop.append("rect")
+        .attr("transform", function() {
+		return "translate(0, " + (y1(1) * 0.76) + ")";
+		//		"translate(0,60)"
+		    })
+	.attr("width", 8)
+	.attr("height", function() {
+		return  y1(1) * 0.64;
+	    })
+	.attr("fill-opacity", opacity);
+
+    // Right arrow
+    var rightarrow = this.defs.append("g").attr("id", "rightarrow");
+    rightarrow.append("path")
+        .attr("class", "rightarrow")
+        .attr("d", function() {
+		return "m 0,0 l -4,4 m 0,-8 l 4,4";
+	    });
+
+    // Left arrow
+    var leftarrow = this.defs.append("g").attr("id", "leftarrow");
+    leftarrow.append("path")
+        .attr("class", "rightarrow")
+        .attr("d", function() {
+		return "m 0,0 l 4,4 m 0,-8 l -4,4";
+		//		return "m 0," + y1(1) + " l 4,4 m 0,-8 l -4,4";
+	    });
+
+}
diff --git a/dammit/viewer/static/mygene_autocomplete_jqueryui.js b/dammit/viewer/static/mygene_autocomplete_jqueryui.js
new file mode 100644
index 00000000..33c13141
--- /dev/null
+++ b/dammit/viewer/static/mygene_autocomplete_jqueryui.js
@@ -0,0 +1,120 @@
+/*! jquery.ui.genequery_autocomplete.js
+ *  A JQuery UI widget for gene query autocomplete
+ *  This autocomplete widget for gene query provides suggestions while you type a gene
+ *  symbol or name into the field. By default the gene suggestions are displayed as
+ *  "<Symbol>:<Name>", automatically triggered when at least two characters are entered
+ *  into the field.
+ *  Copyright (c) 2013 Chunlei Wu; Apache License, Version 2.0.
+ */
+
+
+//Ref: http://stackoverflow.com/questions/1038746/equivalent-of-string-format-in-jquery
+//Example usage: alert("Hello {name}".format({ name: 'World' }));
+String.prototype.format = function (args) {
+    var newStr = this;
+    for (var key in args) {
+        var regex = new RegExp('{'+key+'}', "igm");
+        newStr = newStr.replace(regex, args[key]);
+    }
+    return newStr;
+};
+
+//Subclass default jQuery UI autocomplete widget
+//Ref: http://stackoverflow.com/questions/5218300/how-do-subclass-a-widget
+//Ref: https://gist.github.com/962848
+$.widget("my.genequery_autocomplete", $.ui.autocomplete, {
+
+	options: {
+        mygene_url: 'http://mygene.info/v2/query',
+        //exact match with symbol is boosted.
+        q: "(symbol:{term} OR symbol: {term}* OR name:{term}* OR alias: {term}* OR summary:{term}*)",
+//        q: "{term}*",
+        species: "human",
+        fields: "name,symbol,taxid,entrezgene",
+        limit:20,
+        gene_label: "{symbol}: {name}",
+        value_attr: 'symbol',
+        minLength: 2
+	},
+
+	_create: function() {
+		//this._super("_create");
+        $.ui.autocomplete.prototype._create.call(this);
+		var self = this;
+        var _options = self.options;
+
+        this.source = function( request, response ) {
+                $.ajax({
+                    url: _options.mygene_url,
+                    dataType: "jsonp",
+                    jsonp: 'callback',
+                    data: {
+                        q: _options.q.format({term:request.term}),
+                        sort:_options.sort,
+                        limit:_options.limit,
+                        fields: _options.fields,
+                        species: _options.species
+                    },
+                    success: function( data ) {
+                        var species_d = {3702: 'thale-cress',
+                                         6239: 'nematode',
+                                         7227: 'fruitfly',
+                                         7955: 'zebrafish',
+                                         8364: 'frog',
+                                         9606: 'human',
+                                         9823: 'pig',
+                                         10090: 'mouse',
+                                         10116: 'rat'};
+                        if (data.total > 0){
+                            response( $.map( data.hits, function( item ) {
+                                var obj = {
+                                    id: item._id,
+                                    value: item[_options.value_attr]
+                                }
+                                $.extend(obj, item);
+                                if (species_d[obj.taxid]){
+                                    obj.species = species_d[obj.taxid];
+                                }
+                                obj.label = _options.gene_label.format(obj);
+                                return obj;
+                            }));
+                        }else{
+                            response([{label:'no matched gene found.', value:''}]);
+                        }
+                    }
+                });
+            };
+
+        //set default title attribute if not set already.
+        if (this.element.attr("title") === undefined){
+            this.element.attr("title", 'Powered by mygene.info');
+        }
+        //set default select callback if not provided.
+        _options.select = _options.select || this._default_select_callback;
+
+        //set default loading icon
+        this._add_css('.ui-autocomplete-loading { background: white url("'+this._url_root+'img/ui-anim_basic_16x16.gif") right center no-repeat; }');
+
+	},
+
+    _url_root : 'http://mygene.info/widget/autocomplete/',
+
+    //helper function for adding custom css style.
+    _add_css : function(cssCode) {
+        var styleElement = document.createElement("style");
+        styleElement.type = "text/css";
+        if (styleElement.styleSheet) {
+        styleElement.styleSheet.cssText = cssCode;
+        } else {
+        styleElement.appendChild(document.createTextNode(cssCode));
+        }
+        document.getElementsByTagName("head")[0].appendChild(styleElement);
+    },
+
+    _default_select_callback: function(event, ui) {
+                alert( ui.item ?
+                    "Selected: " + ui.item.label + '('+ui.item.id+')':
+                    "Nothing selected, input was " + this.value);
+    }
+
+});
diff --git a/dammit/viewer/static/rgbcolor.js b/dammit/viewer/static/rgbcolor.js
new file mode 100644
index 00000000..04423f29
--- /dev/null
+++ b/dammit/viewer/static/rgbcolor.js
@@ -0,0 +1,288 @@
+/**
+ * A class to parse color values
+ * @author Stoyan Stefanov <sstoo@gmail.com>
+ * @link   http://www.phpied.com/rgb-color-parser-in-javascript/
+ * @license Use it if you like it
+ */
+function RGBColor(color_string)
+{
+    this.ok = false;
+
+    // strip any leading #
+    if (color_string.charAt(0) == '#') { // remove # if any
+        color_string = color_string.substr(1,6);
+    }
+
+    color_string = color_string.replace(/ /g,'');
+    color_string = color_string.toLowerCase();
+
+    // before getting into regexps, try simple matches
+    // and overwrite the input
+    var simple_colors = {
+        aliceblue: 'f0f8ff',
+        antiquewhite: 'faebd7',
+        aqua: '00ffff',
+        aquamarine: '7fffd4',
+        azure: 'f0ffff',
+        beige: 'f5f5dc',
+        bisque: 'ffe4c4',
+        black: '000000',
+        blanchedalmond: 'ffebcd',
+        blue: '0000ff',
+        blueviolet: '8a2be2',
+        brown: 'a52a2a',
+        burlywood: 'deb887',
+        cadetblue: '5f9ea0',
+        chartreuse: '7fff00',
+        chocolate: 'd2691e',
+        coral: 'ff7f50',
+        cornflowerblue: '6495ed',
+        cornsilk: 'fff8dc',
+        crimson: 'dc143c',
+        cyan: '00ffff',
+        darkblue: '00008b',
+        darkcyan: '008b8b',
+        darkgoldenrod: 'b8860b',
+        darkgray: 'a9a9a9',
+        darkgreen: '006400',
+        darkkhaki: 'bdb76b',
+        darkmagenta: '8b008b',
+        darkolivegreen: '556b2f',
+        darkorange: 'ff8c00',
+        darkorchid: '9932cc',
+        darkred: '8b0000',
+        darksalmon: 'e9967a',
+        darkseagreen: '8fbc8f',
+        darkslateblue: '483d8b',
+        darkslategray: '2f4f4f',
+        darkturquoise: '00ced1',
+        darkviolet: '9400d3',
+        deeppink: 'ff1493',
+        deepskyblue: '00bfff',
+        dimgray: '696969',
+        dodgerblue: '1e90ff',
+        feldspar: 'd19275',
+        firebrick: 'b22222',
+        floralwhite: 'fffaf0',
+        forestgreen: '228b22',
+        fuchsia: 'ff00ff',
+        gainsboro: 'dcdcdc',
+        ghostwhite: 'f8f8ff',
+        gold: 'ffd700',
+        goldenrod: 'daa520',
+        gray: '808080',
+        green: '008000',
+        greenyellow: 'adff2f',
+        honeydew: 'f0fff0',
+        hotpink: 'ff69b4',
+        indianred : 'cd5c5c',
+        indigo : '4b0082',
+        ivory: 'fffff0',
+        khaki: 'f0e68c',
+        lavender: 'e6e6fa',
+        lavenderblush: 'fff0f5',
+        lawngreen: '7cfc00',
+        lemonchiffon: 'fffacd',
+        lightblue: 'add8e6',
+        lightcoral: 'f08080',
+        lightcyan: 'e0ffff',
+        lightgoldenrodyellow: 'fafad2',
+        lightgrey: 'd3d3d3',
+        lightgreen: '90ee90',
+        lightpink: 'ffb6c1',
+        lightsalmon: 'ffa07a',
+        lightseagreen: '20b2aa',
+        lightskyblue: '87cefa',
+        lightslateblue: '8470ff',
+        lightslategray: '778899',
+        lightsteelblue: 'b0c4de',
+        lightyellow: 'ffffe0',
+        lime: '00ff00',
+        limegreen: '32cd32',
+        linen: 'faf0e6',
+        magenta: 'ff00ff',
+        maroon: '800000',
+        mediumaquamarine: '66cdaa',
+        mediumblue: '0000cd',
+        mediumorchid: 'ba55d3',
+        mediumpurple: '9370d8',
+        mediumseagreen: '3cb371',
+        mediumslateblue: '7b68ee',
+        mediumspringgreen: '00fa9a',
+        mediumturquoise: '48d1cc',
+        mediumvioletred: 'c71585',
+        midnightblue: '191970',
+        mintcream: 'f5fffa',
+        mistyrose: 'ffe4e1',
+        moccasin: 'ffe4b5',
+        navajowhite: 'ffdead',
+        navy: '000080',
+        oldlace: 'fdf5e6',
+        olive: '808000',
+        olivedrab: '6b8e23',
+        orange: 'ffa500',
+        orangered: 'ff4500',
+        orchid: 'da70d6',
+        palegoldenrod: 'eee8aa',
+        palegreen: '98fb98',
+        paleturquoise: 'afeeee',
+        palevioletred: 'd87093',
+        papayawhip: 'ffefd5',
+        peachpuff: 'ffdab9',
+        peru: 'cd853f',
+        pink: 'ffc0cb',
+        plum: 'dda0dd',
+        powderblue: 'b0e0e6',
+        purple: '800080',
+        red: 'ff0000',
+        rosybrown: 'bc8f8f',
+        royalblue: '4169e1',
+        saddlebrown: '8b4513',
+        salmon: 'fa8072',
+        sandybrown: 'f4a460',
+        seagreen: '2e8b57',
+        seashell: 'fff5ee',
+        sienna: 'a0522d',
+        silver: 'c0c0c0',
+        skyblue: '87ceeb',
+        slateblue: '6a5acd',
+        slategray: '708090',
+        snow: 'fffafa',
+        springgreen: '00ff7f',
+        steelblue: '4682b4',
+        tan: 'd2b48c',
+        teal: '008080',
+        thistle: 'd8bfd8',
+        tomato: 'ff6347',
+        turquoise: '40e0d0',
+        violet: 'ee82ee',
+        violetred: 'd02090',
+        wheat: 'f5deb3',
+        white: 'ffffff',
+        whitesmoke: 'f5f5f5',
+        yellow: 'ffff00',
+        yellowgreen: '9acd32'
+    };
+    for (var key in simple_colors) {
+        if (color_string == key) {
+            color_string = simple_colors[key];
+        }
+    }
+    // emd of simple type-in colors
+
+    // array of color definition objects
+    var color_defs = [
+        {
+            re: /^rgb\((\d{1,3}),\s*(\d{1,3}),\s*(\d{1,3})\)$/,
+            example: ['rgb(123, 234, 45)', 'rgb(255,234,245)'],
+            process: function (bits){
+                return [
+                    parseInt(bits[1]),
+                    parseInt(bits[2]),
+                    parseInt(bits[3])
+                ];
+            }
+        },
+        {
+            re: /^(\w{2})(\w{2})(\w{2})$/,
+            example: ['#00ff00', '336699'],
+            process: function (bits){
+                return [
+                    parseInt(bits[1], 16),
+                    parseInt(bits[2], 16),
+                    parseInt(bits[3], 16)
+                ];
+            }
+        },
+        {
+            re: /^(\w{1})(\w{1})(\w{1})$/,
+            example: ['#fb0', 'f0f'],
+            process: function (bits){
+                return [
+                    parseInt(bits[1] + bits[1], 16),
+                    parseInt(bits[2] + bits[2], 16),
+                    parseInt(bits[3] + bits[3], 16)
+                ];
+            }
+        }
+    ];
+
+    // search through the definitions to find a match
+    for (var i = 0; i < color_defs.length; i++) {
+        var re = color_defs[i].re;
+        var processor = color_defs[i].process;
+        var bits = re.exec(color_string);
+        if (bits) {
+            channels = processor(bits);
+            this.r = channels[0];
+            this.g = channels[1];
+            this.b = channels[2];
+            this.ok = true;
+        }
+
+    }
+
+    // validate/cleanup values
+    this.r = (this.r < 0 || isNaN(this.r)) ? 0 : ((this.r > 255) ? 255 : this.r);
+    this.g = (this.g < 0 || isNaN(this.g)) ? 0 : ((this.g > 255) ? 255 : this.g);
+    this.b = (this.b < 0 || isNaN(this.b)) ? 0 : ((this.b > 255) ? 255 : this.b);
+
+    // some getters
+    this.toRGB = function () {
+        return 'rgb(' + this.r + ', ' + this.g + ', ' + this.b + ')';
+    }
+    this.toHex = function () {
+        var r = this.r.toString(16);
+        var g = this.g.toString(16);
+        var b = this.b.toString(16);
+        if (r.length == 1) r = '0' + r;
+        if (g.length == 1) g = '0' + g;
+        if (b.length == 1) b = '0' + b;
+        return '#' + r + g + b;
+    }
+
+    // help
+    this.getHelpXML = function () {
+
+        var examples = new Array();
+        // add regexps
+        for (var i = 0; i < color_defs.length; i++) {
+            var example = color_defs[i].example;
+            for (var j = 0; j < example.length; j++) {
+                examples[examples.length] = example[j];
+            }
+        }
+        // add type-in colors
+        for (var sc in simple_colors) {
+            examples[examples.length] = sc;
+        }
+
+        var xml = document.createElement('ul');
+        xml.setAttribute('id', 'rgbcolor-examples');
+        for (var i = 0; i < examples.length; i++) {
+            try {
+                var list_item = document.createElement('li');
+                var list_color = new RGBColor(examples[i]);
+                var example_div = document.createElement('div');
+                example_div.style.cssText =
+                        'margin: 3px; '
+                        + 'border: 1px solid black; '
+                        + 'background:' + list_color.toHex() + '; '
+                        + 'color:' + list_color.toHex()
+                ;
+                example_div.appendChild(document.createTextNode('test'));
+                var list_item_value = document.createTextNode(
+                    ' ' + examples[i] + ' -> ' + list_color.toRGB() + ' -> ' + list_color.toHex()
+                );
+                list_item.appendChild(example_div);
+                list_item.appendChild(list_item_value);
+                xml.appendChild(list_item);
+
+            } catch(e){}
+        }
+        return xml;
+
+    }
+
+}
+
diff --git a/dammit/viewer/static/test_tracks.js b/dammit/viewer/static/test_tracks.js
new file mode 100644
index 00000000..f856ef03
--- /dev/null
+++ b/dammit/viewer/static/test_tracks.js
@@ -0,0 +1,92 @@
+var tracks = [
+    {
+        "inner_radius": 100,
+        "trackName": "dammit.HMMER",
+        "showTooltip": true,
+        "items": [
+            {
+                "start": 3583,
+                "end": 4095,
+                "id": 0,
+                "name": "DEAD/DEAH box helicase"
+            },
+            {
+                "start": 4189,
+                "end": 4551,
+                "id": 1,
+                "name": "Helicase conserved C-terminal domain"
+            },
+            {
+                "start": 5206,
+                "end": 5310,
+                "id": 2,
+                "name": "Helicase conserved C-terminal domain"
+            }
+        ],
+        "visible": true,
+        "outer_radius": 140,
+        "min_slice": true,
+        "trackType": "track",
+        "trackFeatures": "complex"
+    },
+    {
+        "inner_radius": 150,
+        "trackName": "dammit.LAST",
+        "showTooltip": true,
+        "items": [
+            {
+                "start": 1,
+                "end": 5663,
+                "id": 0,
+                "name": "TLH2_SCHPO"
+            }
+        ],
+        "visible": true,
+        "outer_radius": 190,
+        "min_slice": true,
+        "trackType": "track",
+        "trackFeatures": "complex"
+    },
+    {
+        "inner_radius": 200,
+        "trackName": "transdecoder",
+        "showTooltip": true,
+        "items": [
+            {
+                "start": 1,
+                "end": 5662,
+                "id": 0,
+                "name": "cds.Transcript_0|m.1"
+            },
+            {
+                "start": 1,
+                "end": 5663,
+                "id": 1,
+                "name": "Transcript_0|m.1.exon1"
+            },
+            {
+                "start": 1,
+                "end": 5663,
+                "id": 2,
+                "name": "ORF%20Transcript_0%7Cg.1%20Transcript_0%7Cm.1%20type%3A3prime_partial%20len%3A1888%20%28%2B%29"
+            },
+            {
+                "start": 1,
+                "end": 5663,
+                "id": 3,
+                "name": "ORF%20Transcript_0%7Cg.1%20Transcript_0%7Cm.1%20type%3A3prime_partial%20len%3A1888%20%28%2B%29"
+            },
+            {
+                "start": 5662,
+                "end": 5663,
+                "id": 4,
+                "name": "Transcript_0|m.1.utr3p1"
+            }
+        ],
+        "visible": true,
+        "outer_radius": 240,
+        "min_slice": true,
+        "trackType": "track",
+        "trackFeatures": "complex"
+    }
+]
diff --git a/dammit/viewer/static/tracks.css b/dammit/viewer/static/tracks.css
new file mode 100644
index 00000000..5bd0426e
--- /dev/null
+++ b/dammit/viewer/static/tracks.css
@@ -0,0 +1,286 @@
+/* Classes for the demo's controls */
+#demo-controls {
+  padding: 10px;
+}
+
+.control-item {
+  padding: 5px;
+}
+
+/* Render the chart as cleanly as possible */
+#circularchart {
+    shape-rendering: geometricPrecision;
+}
+
+/* Text on the demo */
+.mini text {
+    font: 9px sans-serif;
+}
+
+.main text {
+    font: 12px sans-serif;
+}
+
+/* Definitions for the plot resize dragger, and
+   resizing shadow */
+.dragbar-line {
+    stroke-width: 1;
+    stroke: lightgrey;
+    pointer-events: inherit;
+}
+
+.dragbar-shadow {
+    stroke-width: 1;
+    stroke: lightgrey;
+    fill: transparent;
+}
+
+/* Style for the plot move arrow if active */
+.move-cross {
+    stroke-width: 1;
+    stroke: lightgrey;
+    fill: lightgrey;
+    cursor:move;
+}
+
+.move-shadow {
+    cursor:move !important;
+}
+
+/* For resizing the linear chart */
+#linearchart {
+    cursor: -webkit-grab; cursor: -moz-grab;
+}
+
+#linearchart:active {
+    cursor: -webkit-grabbing; cursor: -moz-grabbing;
+}
+
+.mainTrack {
+    cursor: pointer;
+    cursor: hand;
+}
+
+/* Definitions for first stranded track, colour, stroke */
+."dammit.HMMER"_pos {
+    fill: darksalmon;
+    stroke: #d1876d;
+    stroke-opacity: 0.8;
+    stroke-width: 1;
+}
+
+."dammit.HMMER"_neg {
+    fill: #FFCC00;
+    fill-opacity: .7;
+    /*stroke-width: 1;
+    stroke: #4c602a;*/
+}
+
+/* In a linear track if an intergenic
+   region is defined, give it a colour */
+."dammit.HMMER"_none {
+    fill: #cccccc;
+    fill-opacity: .7;
+    stroke-width: 1;
+}
+
+/* And we want to show the user as they hover
+   over a track, change the colour */
+."dammit.HMMER"_pos:hover {
+    fill: red;
+    stroke-width: 1;
+    stroke: 1;
+}
+
+."dammit.HMMER"_neg:hover {
+    fill: red;
+    fill-opacity: .9;
+    stroke-width: 1;
+    stroke: red;
+}
+
+/* In a linear track, if there are regulatory
+   elements such as transcription factors and
+   terminators, give them a colour for the stroke */
+."dammit.HMMER"_arrow_pos, ."dammit.HMMER"_arrow_neg, ."dammit.LAST"_arrow {
+    stroke-width: 1;
+    stroke: black;
+}
+
+/* Labels on the linear track */
+."dammit.HMMER"_text {
+    fill: white;
+    font-weight: bold;
+    font: 12px arial;
+}
+
+/* Track 2 is also a stranded track, give it
+   a different set of colours */
+.transdecoder_pos {
+    fill: #000099;
+    fill-opacity: .7;
+}
+
+/* When a linear track is zoomed to the point
+   it's text is visible an extra class is added
+   to the element we can hook in to */
+.transdecoder_pos_zoomed {
+    stroke-width: 1px;
+    stroke: #647381;
+}
+
+.transdecoder_neg {
+    fill: #006600;
+    fill-opacity: .7;
+}
+
+.transdecoder_neg_zoomed {
+    stroke-width: 1px;
+    stroke: #007300;
+    stroke-opacity: 0.7;
+}
+
+.transdecoder_text {
+    fill: white;
+    font-weight: bold;
+    font: 12px arial;
+}
+
+/* Track 3 is a non-stranded track, so no _pos
+   and _neg modifiers on the classes */
+.dammit\.LAST {
+    fill: #3399FF;
+    fill-opacity: .7;
+}
+
+.dammit\.LAST:hover {
+    fill: blue;
+    fill-opacity: .9;
+}
+
+.dammit\.LAST_text {
+    fill: white;
+    font-weight: bold;
+    font: 12px arial;
+}
+
+/* The GC Plot type track, give the stroke a colour */
+.gcplot {
+    stroke: black;
+}
+
+/* Track 5 is the glyphs, classes of a concatenation
+   of the track name and the type of glyph in the track */
+.track5_vfdb {
+    fill: #663300;
+}
+
+.track5_adb {
+    fill: #FF9933;
+}
+
+/* Give a colour to the glyph track's stroke */
+.gapTrack {
+    stroke: grey;
+}
+
+/* Set the stroke width of the axis lines */
+.trackAxis .domain {
+    stroke-width: 1;
+}
+
+/* In a linear track, we need to set the
+   colours for the drag brush */
+.brush .background {
+    stroke: black;
+    stroke-width: 2;
+    fill: slategray;
+    fill-opacity: .3;
+}
+
+.brush .extent {
+    stroke: gray;
+    fill: dodgerblue;
+    fill-opacity: .365;
+}
+
+/* In a circular plot if there's a
+   drag brush for zoomed region, define the
+   colours and style */
+.polarbrush {
+    fill: lightgrey;
+    opacity: 0.5;
+}
+
+/* In the circular plot, the circular end points
+   for the drag brush */
+.brushEnd {
+    fill: "red";
+}
+
+.brushStart {
+    fill: "green";
+}
+
+/* If we need to set an element to hidden, give
+   ourselves a class */
+.linear_hidden {
+	visibility: hidden;
+}
+
+/* For regulatory elements in a linear plot,
+   define the colours and stroke for the lollipop
+   head (terminator site) */
+.lollipophead {
+  stroke:#000000;
+  stroke-opacity: 1;
+  fill: none;
+}
+
+.lollipopstemstart {
+  fill:none;
+  stroke:#000000;
+  stroke-width: 1px;
+  stroke-linecap:butt;
+  stroke-linejoin:miter;
+  stroke-dasharray: 5,5;
+}
+
+.lollipopstemend {
+  fill:none;
+  stroke:#000000;
+  stroke-width: 1px;
+  stroke-linecap:butt;
+  stroke-linejoin:miter;
+}
+
+/* For our tooltips, how should we display them? */
+.d3-tip {
+  line-height: 1;
+  font: 12px arial;
+  font-weight: bold;
+  padding: 12px;
+  background: rgba(0, 0, 0, 0.8);
+  color: #fff;
+  border-radius: 2px;
+}
+
+/* Creates a small triangle extender for the tooltip */
+.d3-tip:after {
+  box-sizing: border-box;
+  display: inline;
+  font-size: 10px;
+  width: 100%;
+  line-height: 1;
+  color: rgba(0, 0, 0, 0.8);
+  content: "\25BC";
+  position: absolute;
+  text-align: center;
+}
+
+/* Style northward tooltips differently */
+.d3-tip.n:after {
+  margin: -1px 0 0 0;
+  top: 100%;
+  left: 0;
+}
diff --git a/dammit/viewer/templates/404.html b/dammit/viewer/templates/404.html
new file mode 100644
index 00000000..f1e6b5cb
--- /dev/null
+++ b/dammit/viewer/templates/404.html
@@ -0,0 +1,6 @@
+<html>
+<body>
+<h1>dammit, 404 error!</h1>
+<p> {{ msg }} </p>
+</body>
+</html>
diff --git a/dammit/viewer/templates/index.html b/dammit/viewer/templates/index.html
new file mode 100644
index 00000000..647853eb
--- /dev/null
+++ b/dammit/viewer/templates/index.html
@@ -0,0 +1,38 @@
+<!doctype html>
+<html>
+
+<head>
+    <title>Annotation Report, Dammit</title>
+    <link rel="stylesheet" href="http://code.jquery.com/ui/1.11.1/themes/ui-lightness/jquery-ui.min.css" type="text/css" media="all" />
+    <script src="http://code.jquery.com/jquery-2.1.1.min.js" type="text/javascript"></script>
+    <script src="http://code.jquery.com/ui/1.11.1/jquery-ui.min.js" type="text/javascript"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.16/d3.min.js"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3-tip/0.6.7/d3-tip.js"></script>
+    <script src="{{ url_for('static', filename='mygene_autocomplete_jqueryui.js') }}" type="text/javascript"></script>
+
+    <style>
+      body {
+        overflow: hidden;
+        margin: 0;
+        font-size: 14px;
+        font-family: "Helvetica Neue", Helvetica;
+      }
+
+      #circularchart {
+        position: absolute;
+        top: 0px;
+        left: 125px;
+      }
+    </style>
+    <link href="{{ url_for('static', filename='tracks.css') }}" rel="stylesheet">
+</head>
+
+<body class="ui-widget">
+    <div>
+        <h1> Annotation Report, Dammit </h1>
+        <h2> <em><small>for</small></em> {{ name }}</h2>
+    </div>
+
+    {% include 'transcript_model.html' %}
+
+</body>
diff --git a/dammit/viewer/templates/js_imports.html b/dammit/viewer/templates/js_imports.html
new file mode 100644
index 00000000..d1452cc6
--- /dev/null
+++ b/dammit/viewer/templates/js_imports.html
@@ -0,0 +1,2 @@
+<script src="//d3js.org/d3.v3.min.js"></script>
+<script src="{{ url_for('static', filename='biojs-io-newick.min.js')}}"></script>
diff --git a/dammit/viewer/templates/search.html b/dammit/viewer/templates/search.html
new file mode 100644
index 00000000..5b08a4f5
--- /dev/null
+++ b/dammit/viewer/templates/search.html
@@ -0,0 +1,5 @@
+<label for="gene_query">Enter a gene here: </label>
+<input id="gene_query" style="width:250px" class="mygene_query_target">
+<script type="text/javascript">
+    $('input.mygene_query_target').genequery_autocomplete();
+</script>
diff --git a/dammit/viewer/templates/sunburst.html b/dammit/viewer/templates/sunburst.html
new file mode 100644
index 00000000..98bf01a3
--- /dev/null
+++ b/dammit/viewer/templates/sunburst.html
@@ -0,0 +1,25 @@
+<meta charset="utf-8">
+<style>
+
+body {
+  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
+  margin: auto;
+  position: relative;
+  width: 960px;
+}
+
+form {
+  position: absolute;
+  right: 10px;
+  top: 10px;
+}
+
+</style>
+{% include 'js_imports.html' %}
+<form>
+  <label><input type="radio" name="mode" value="size"> Size</label>
+  <label><input type="radio" name="mode" value="count" checked> Count</label>
+</form>
+<script>
+{% include 'sunburst.js' %}
+</script>
diff --git a/dammit/viewer/templates/sunburst.js b/dammit/viewer/templates/sunburst.js
new file mode 100644
index 00000000..a269becd
--- /dev/null
+++ b/dammit/viewer/templates/sunburst.js
@@ -0,0 +1,72 @@
+var width = 960,
+    height = 700,
+    radius = Math.min(width, height) / 2,
+    color = d3.scale.category20c();
+
+var svg = d3.select("body").append("svg")
+    .attr("width", width)
+    .attr("height", height)
+  .append("g")
+    .attr("transform", "translate(" + width / 2 + "," + height * .52 + ")");
+
+var partition = d3.layout.partition()
+    .sort(null)
+    .size([2 * Math.PI, radius * radius])
+    .value(function(d) { return 1; });
+
+var arc = d3.svg.arc()
+    .startAngle(function(d) { return d.x; })
+    .endAngle(function(d) { return d.x + d.dx; })
+    .innerRadius(function(d) { return Math.sqrt(d.y); })
+    .outerRadius(function(d) { return Math.sqrt(d.y + d.dy); });
+
+var parser = require("biojs-io-newick");
+
+//d3.json("{{ url_for('static', filename='flare.json') }}", function(error, root) {
+d3.text("{{ url_for('static', filename='itis.nwk') }}", function(error, nwk) {
+    if (error) throw error;
+
+  root = parser.parse_newick(nwk);
+  if (error) throw error;
+
+  var path = svg.datum(root).selectAll("path")
+      .data(partition.nodes)
+    .enter().append("path")
+      .attr("display", function(d) { return d.depth ? null : "none"; }) // hide inner ring
+      .attr("d", arc)
+      .style("stroke", "#fff")
+      .style("fill", function(d) { return color((d.children ? d : d.parent).name); })
+      .style("fill-rule", "evenodd")
+      .each(stash);
+
+  d3.selectAll("input").on("change", function change() {
+    var value = this.value === "count"
+        ? function() { return 1; }
+        : function(d) { return d.size; };
+
+    path
+        .data(partition.value(value).nodes)
+      .transition()
+        .duration(1500)
+        .attrTween("d", arcTween);
+  });
+});
+
+// Stash the old values for transition.
+function stash(d) {
+  d.x0 = d.x;
+  d.dx0 = d.dx;
+}
+
+// Interpolate the arcs in data space.
+function arcTween(a) {
+  var i = d3.interpolate({x: a.x0, dx: a.dx0}, a);
+  return function(t) {
+    var b = i(t);
+    a.x0 = b.x;
+    a.dx0 = b.dx;
+    return arc(b);
+  };
+}
+
+d3.select(self.frameElement).style("height", height + "px");
diff --git a/dammit/viewer/templates/transcript_model.html b/dammit/viewer/templates/transcript_model.html
new file mode 100644
index 00000000..2f6eedec
--- /dev/null
+++ b/dammit/viewer/templates/transcript_model.html
@@ -0,0 +1,114 @@
+<div id="plotbody">
+  <!-- The container that will hold the SVG of the plot -->
+  <div id="circularchart"></div>
+</div>
+
+<script type="text/javascript"
+        src="{{ url_for('static', filename='rgbcolor.js') }}"></script>
+<script type="text/javascript"
+        src="{{ url_for('static', filename='canvg.js') }}"></script>
+<script type="text/javascript"
+        src="{{ url_for('static', filename='FileSaver.js') }}"></script>
+
+<!-- Circular plot library -->
+<script type="text/javascript"
+        src="{{ url_for('static', filename='circularplot.js') }}"></script>
+
+<!-- Initialization code to initialize the plot, this is what you would write
+     and place in your application. -->
+<script type="text/javascript">
+
+// Sample routines to initialize the plot for rendering
+// and add some basic functionality.
+
+// Initialize the defaults for the chart such as
+// the genome size, the div container to put the
+// SVG object in, what function to call during a
+// double click and the initial chart size.
+
+d3.json("{{ url_for('transcript_pane.tracks', transcript='Transcript_0') }}", function(error, result) {
+
+    var genomesize = result.data.length;
+    var circularlayout = {genomesize: genomesize,
+                  spacing: 100,
+                  container: "#circularchart",
+                  dblclick: "doubleClick",
+                          w: 550, h: 550
+            };
+
+    // The actual initialization call which takes two
+    // parameters, the layout (above) for the plot and
+    // the dataset to visualize (from data.js, a json
+    // data structure)
+    var cTrack = new circularTrack(circularlayout, result.data.tracks);
+
+    // If we're showing both a circular and linear chart,
+    // and have a linear brush, attach it (see combo plot demo)
+    if('undefined' !== typeof linearTrack) {
+        console.log("Attaching linear track");
+        cTrack.attachBrush(linearTrack);
+        cTrack.showBrush();
+    }
+
+    if('undefined' !== typeof brush) {
+        console.log("Attaching linear track brush");
+        cTrack.attachBrush(brush);
+    }
+
+    // Now some callbacks to make the interactive functionality work.
+
+    // Attached to the onchange callback for the GC Plot checkbox,
+    // call the plot to add/remove the GC Plot as needed
+    function saveImage() {
+        cTrack.savePlot(4.0, "islandviewer.png", "tracks.css", 'png');
+    }
+
+    // Demo of the hover over timer, we had to
+    // do it this way to get around IE <9 not supporting
+    // parameters to the function called by setTimeout()
+    //
+    // If you have over an island, the console log will
+    // display the callback parameters when the timer expires
+    //
+    // The callback for hover (along with click) are defined in
+    // the data definition for each track in the dataset (data.js)
+    var timer;
+    var d_callback;
+    function islandPopup(d) {
+        d_callback = d;
+        timer = setTimeout(function() {console.log(d_callback);}, 1000);
+    }
+
+    function islandPopupClear(d) {
+        clearTimeout(timer);
+    }
+
+    // Callback defined at the top of this file, for
+    // double clicks on the plot
+    function doubleClick(plotid, bp) {
+        // If we have an attached linear plot, we're going
+        // to refocus the zoomed area, otherwise we'll just
+        // alert the user that a double click happened
+        if('undefined' !== typeof linearTrack) {
+            var halfBP = (cTrack.brushEndBP - cTrack.brushStartBP) /2;
+
+        var newStart = Math.max(0, (bp - halfBP));
+        var newEnd = Math.min(genomesize, (bp + halfBP));
+
+            console.log("Moving zoom area to: " + newStart + ", " + newEnd);
+            cTrack.moveBrushbyBP(newStart,
+                                 newEnd);
+            linearTrack.update(newStart, newEnd);
+        } else {
+          alert("Double click! From " + plotid + " at " + bp + " bp" )
+          console.log("double click!");
+          console.log(plotid);
+          console.log(bp);
+
+        }
+    }
+})
+</script>
+<div id="demo-controls">
+  <div class="control-item"><button name="saveImage" onclick="saveImage(); return false">Save Image</button></div>
+</div>
diff --git a/dammit/viewer/transcript_pane.py b/dammit/viewer/transcript_pane.py
new file mode 100644
index 00000000..7b025efb
--- /dev/null
+++ b/dammit/viewer/transcript_pane.py
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import json
+import logging
+import os
+
+from flask import Flask, Blueprint, current_app, abort, jsonify
+from flask import render_template, redirect, url_for
+from jinja2 import TemplateNotFound
+import pandas as pd
+
+from .. import common
+from .. import parsers
+from . import genomed3plot as gd3
+from .database import db
+
+from . import static_folder, template_folder
+
+views = Blueprint('transcript_pane', __name__,
+                  static_folder=static_folder,
+                  template_folder=template_folder)
+
+@views.errorhandler(404)
+def error_404_page(error):
+    return render_template('404.html', msg=error.description), 404
+
+@views.route('/tracks/<transcript>')
+def tracks(transcript):
+    try:
+        transcript_info = db['transcripts'][transcript]
+    except KeyError:
+        abort(404, 'No transcript named {0} in the annotation database :('.format(transcript))
+    else:
+        tracks = gd3.create_tracks(transcript, transcript_info['annotations'])
+        length = transcript_info['length']
+        result = {'data': {'tracks': tracks, 'length': length}}
+    return jsonify(result)
+
+@views.route('/transcripts')
+def transcript_list():
+    return jsonify({'transcripts': db['annotations'].keys()})
+
+@views.route('/transcript/<transcript>')
+def transcript(transcript):
+    print (transcript)
+    return render_template('index.html',
+                           name=current_app.config['DIRECTORY'],
+                           transcript=transcript)
diff --git a/setup.py b/setup.py
index c8a6cc09..ccafb85b 100755
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@ def main():
             license = 'BSD',
             test_suite = 'nose.collector',
             tests_require = ['nose'],
-            packages = ['dammit'],
+            packages = find_packages(),
             scripts = glob('bin/*'),
             install_requires = ['setuptools>=0.6.35',
                                 'pandas>=0.17',
@@ -49,6 +49,6 @@ def main():
                                 'numexpr>=2.3.1'],
             include_package_data = True,
             zip_safe = False,  )
-        
+
 if __name__ == "__main__":
     main()