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Essex.C
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/*
BOOM : Bioinformatics Object Oriented Modules
Copyright (C)2012 William H. Majoros ([email protected]).
This is OPEN SOURCE SOFTWARE governed by the Gnu General Public
License (GPL) version 3, as described at www.opensource.org.
*/
#include "Essex.H"
#include <ctype.h>
#include "ElasVector.H"
using namespace std;
using namespace BOOM;
//using namespace Essex;
namespace Essex {
int TAB_SIZE=3;
Regex Query::R("(\\S+)([<>=!~]+)(\\S+)");
// **************************************************
// Query methods
// **************************************************
Query::Query(const String &q)
{
parse(q);
}
void Query::parse(const String &q)
{
Vector<BOOM::String> &fields=*q.getFields("/");
int n=fields.size();
if(n<1) throw "error in Essex::Query";
tag=fields[0];
for(int i=1 ; i<n-1 ; ++i)
path.push_back(fields[i]);
String predicate=fields[n-1];
if(!R.match(predicate)) throw "Syntax error in Essex query";
path.push_back(R[1]);
String opStr=R[2];
strVal=R[3];
floatVal=strVal.asFloat();
if(opStr=="<") op=LESS;
else if(opStr=="<=") op=LESS_EQ;
else if(opStr==">") op=GREATER;
else if(opStr==">=") op=GREATER_EQ;
else if(opStr=="=") op=EQUAL;
else if(opStr=="!=") op=NOT_EQUAL;
else if(opStr=="~") op=SUBSTRING;
else throw "Invalid operator in Essex query";
delete &fields;
}
void Query::deleteResults(Vector<Node*> &results)
{
for(Vector<Node*>::iterator cur=results.begin(), end=results.end() ;
cur!=end ; ++cur) delete *cur;
}
void Query::search(Node *root,Vector<Node*> &results)
{
if(!results.empty()) throw "Query::search(): results is not empty";
Vector<Node*> candidates;
root->findDescendents(tag,candidates);
if(root->getNodeType()==COMPOSITE &&
static_cast<CompositeNode*>(root)->getTag()==tag)
candidates.push_back(root);
for(Vector<Node*>::iterator cur=candidates.begin(), end=candidates.end() ;
cur!=end ; ++cur) {
Node *candidate=*cur;
if(testCandidate(candidate)) results.push_back(candidate);
}
}
Vector<Node*> *Query::search(Node *root)
{
Vector<Node*> &results=*new Vector<Node*>;
search(root,results);
return &results;
}
bool Query::testCandidate(Node *node)
{
int n=path.size();
for(int i=0 ; i<n ; ++i) {
node=node->findChild(path[i]);
if(!node) return false;
}
node=static_cast<CompositeNode*>(node)->getIthChild(0);
return testValue(node);
}
bool Query::testValue(Node *node)
{
NodeType nodeType=node->getNodeType();
if(nodeType==STRING) {
StringNode *strNode=static_cast<StringNode*>(node);
const String &s=strNode->getValue();
switch(op)
{
case EQUAL: return s==strVal;
case NOT_EQUAL: return s!=strVal;
case SUBSTRING: return s.contains(strVal);
}
}
else {
NumericNode *nNode=static_cast<NumericNode*>(node);
float num=nNode->getValue();
switch(op)
{
case LESS: return num<floatVal;
case GREATER: return num>floatVal;
case LESS_EQ: return num<=floatVal;
case GREATER_EQ: return num>=floatVal;
case EQUAL: return num==floatVal;
case NOT_EQUAL: return num!=floatVal;
}
}
throw "Internal error";
}
// **************************************************
// Node methods
// **************************************************
ostream &operator<<(ostream &os,const Node &node)
{
node.printOn(os);
return os;
}
Node::Node(NodeType nodeType)
: nodeType(nodeType)
{
// ctor
}
Node::~Node()
{
// dtor
}
NodeType Node::getNodeType() const
{
return nodeType;
}
Node *Node::findChild(const String &tag)
{
return NULL;
}
void Node::findChildren(const String &,Vector<Node*> &)
{
return;
}
void Node::findDescendents(const String &,Vector<Node*> &)
{
return;
}
String Node::getAttribute(const String &tag)
{
return "";
}
NumericNode::NumericNode(float value)
: Node(NUMBER), value(value)
{
// ctor
}
float NumericNode::getValue() const
{
return value;
}
void NumericNode::acceptVisitor(NodeVisitor &v)
{
v.visit(*this);
}
void NumericNode::printOn(ostream &os) const
{
if(float(int(value))==value) os<<int(value);
else os<<value;
}
void NumericNode::printXML(ostream &os) const
{
printOn(os);
}
StringNode::StringNode(const String &value)
: Node(STRING), value(value)
{
// ctor
}
const String &StringNode::getValue() const
{
return value;
}
String &StringNode::getValue()
{
return value;
}
void StringNode::acceptVisitor(NodeVisitor &v)
{
v.visit(*this);
}
void StringNode::printXML(ostream &os) const
{
String escaped=value.substitute("&","&");
escaped=escaped.substitute("\"",""");
escaped=escaped.substitute("'","'");
escaped=escaped.substitute("<","<");
escaped=escaped.substitute(">",">");
os<<escaped;
}
void StringNode::printOn(ostream &os) const
{
String escaped=value.substitute("\"","\\\"");
bool needsQuotes=false;
const char *cstr=value.c_str();
for(; *cstr ; ++cstr)
if(isspace(*cstr)) needsQuotes=true;
if(needsQuotes) os<<'"'<<escaped<<'"';
else {
escaped=escaped.substitute("(","&lparen;");
escaped=escaped.substitute(")","&rparen;");
os<<escaped;
}
}
CompositeNode::CompositeNode(const String &tag)
: Node(COMPOSITE), tag(tag)
{
// ctor
}
CompositeNode::~CompositeNode()
{
for(Vector<Node*>::iterator cur=children.begin(), end=children.end() ;
cur!=end ; ++cur) delete *cur;
}
void CompositeNode::appendChild(Node *child)
{
if(child) children.push_back(child);
}
void CompositeNode::append(int x)
{
appendChild(new NumericNode(float(x)));
}
void CompositeNode::append(float x)
{
appendChild(new NumericNode(x));
}
void CompositeNode::append(const String &s)
{
appendChild(new StringNode(s));
}
void CompositeNode::prepend(const String &s)
{
children.push_front(new StringNode(s));
}
void CompositeNode::append(const String &tag,int value)
{
CompositeNode *node=new CompositeNode(tag);
node->append(value);
children.push_back(node);
}
void CompositeNode::append(const String &tag,float value)
{
CompositeNode *node=new CompositeNode(tag);
node->append(value);
children.push_back(node);
}
void CompositeNode::append(const String &tag,const String &value)
{
CompositeNode *node=new CompositeNode(tag);
node->append(value);
children.push_back(node);
}
void CompositeNode::append(const String &tag,const char *value)
{
CompositeNode *node=new CompositeNode(tag);
node->append(value);
children.push_back(node);
}
const String &CompositeNode::getTag() const
{
return tag;
}
String &CompositeNode::getTag()
{
return tag;
}
int CompositeNode::getNumChildren() const
{
return children.size();
}
Node *CompositeNode::getIthChild(int i) const
{
if(i>=children.size())
throw "Index out of range in CompositeNode::getIthChild()";
return children[i];
}
void CompositeNode::setIthChild(int i,Node *child)
{
children[i]=child;
}
void CompositeNode::acceptVisitor(NodeVisitor &v)
{
int n=children.size();
for(int i=0 ; i<n ; ++i)
children[i]->acceptVisitor(v);
v.visit(*this);
}
Node *CompositeNode::findChild(const String &tag)
{
int n=getNumChildren();
for(int i=0 ; i<n ; ++i) {
Node *child=getIthChild(i);
if(child->getNodeType()==COMPOSITE &&
static_cast<CompositeNode*>(child)->getTag()==tag)
return child;
}
return NULL;
}
void CompositeNode::findChildren(const String &tag,Vector<Node*> &v)
{
int n=getNumChildren();
for(int i=0 ; i<n ; ++i) {
Node *child=getIthChild(i);
if(child->getNodeType()==COMPOSITE &&
static_cast<CompositeNode*>(child)->getTag()==tag)
v.push_back(child);
}
}
void CompositeNode::findDescendents(const String &tag,Vector<Node*> &v)
{
int n=getNumChildren();
for(int i=0 ; i<n ; ++i) {
Node *child=getIthChild(i);
if(child->getNodeType()==COMPOSITE) {
CompositeNode *cNode=static_cast<CompositeNode*>(child);
if(cNode->getTag()==tag) v.push_back(child);
cNode->findDescendents(tag,v);
}
}
}
String CompositeNode::getAttribute(const String &tag)
{
Node *child=findChild(tag);
if(!child) return "";
child=static_cast<CompositeNode*>(child)->getIthChild(0);
if(!child) throw "No 0 element in CompositeNode::getAttribute()";
String attr;
switch(child->getNodeType())
{
case COMPOSITE:
throw "Can't convert composite attribute in Essex structure";
case NUMBER:
attr=String(static_cast<NumericNode*>(child)->getValue());
break;
case STRING:
attr=static_cast<StringNode*>(child)->getValue();
break;
}
return attr;
}
void CompositeNode::setAttribute(const String &tag,const String &value)
{
Node *child=findChild(tag);
if(!child) return;
CompositeNode *attrNode=static_cast<CompositeNode*>(child);
delete attrNode->getIthChild(0);
attrNode->setIthChild(0,new StringNode(value));
}
void CompositeNode::printXML(ostream &os) const
{
printXMLrecursive(os,0);
}
void CompositeNode::printOn(ostream &os) const
{
printRecursive(os,0);
}
bool CompositeNode::hasCompositeChildren() const
{
for(Vector<Node*>::const_iterator cur=children.begin(), end=children.end() ;
cur!=end ; ++cur)
if((*cur)->getNodeType()==COMPOSITE) return true;
return false;
}
void CompositeNode::printRecursive(ostream &os,int depth) const
{
String tab;
tab.padOrTruncate(TAB_SIZE*depth);
os<<tab<<'('<<tag;
int n=getNumChildren();
if(hasCompositeChildren()) {
for(int i=0 ; i<n ; ++i) {
Node *child=getIthChild(i);
if(child->getNodeType()==COMPOSITE) {
os<<"\n";
static_cast<CompositeNode*>(child)->printRecursive(os,depth+1);
}
else {
String tab;
tab.padOrTruncate(TAB_SIZE*(depth+1));
os<<"\n"<<tab<<*child;
}
}
}
else for(int i=0 ; i<n ; ++i) os<<" "<<*getIthChild(i);
os<<')';//<<endl;
}
void CompositeNode::printXMLrecursive(ostream &os,int depth) const
{
String tab;
tab.padOrTruncate(TAB_SIZE*depth);
os<<tab<<'<'<<tag<<'>';
int n=getNumChildren();
if(hasCompositeChildren()) {
os<<endl;
for(int i=0 ; i<n ; ++i) {
Node *child=getIthChild(i);
if(child->getNodeType()==COMPOSITE)
static_cast<CompositeNode*>(child)->printXMLrecursive(os,depth+1);
else {
String tab;
tab.padOrTruncate(TAB_SIZE*(depth+1));
os<<tab; child->printXML(os); os<<endl;
}
}
os<<tab;
}
else {
for(int i=0 ; i<n ; ++i) {
getIthChild(i)->printXML(os);
if(i+1<n) os<<" ";
}
}
os<<"</"<<tag<<'>'<<endl;
}
void CompositeNode::deleteChild(const String &tag)
{
int n=getNumChildren();
for(int i=0 ; i<n ; ++i) {
Node *child=getIthChild(i);
if(child->getNodeType()==COMPOSITE &&
static_cast<CompositeNode*>(child)->getTag()==tag) {
children.cut(i);
delete child;
}
}
}
// **************************************************
// Token methods
// **************************************************
ostream &operator<<(ostream &os,TokenType tokenType)
{
switch(tokenType)
{
case TOK_IDENT: // any-identifier
os << "identifier";
break;
case TOK_STRING_LIT: // "any string literal"
os << "string literal";
break;
case TOK_INT_LIT: // 123
os << "number";
break;
case TOK_FLOAT_LIT: // 3.14
os << "number";
break;
case TOK_LEFT_PAREN: // (
os << "'('";
break;
case TOK_RIGHT_PAREN: // )
os << "')'";
break;
case TOK_EOF: // end of file
os << "end of file";
break;
}
}
ostream &operator<<(ostream &os,const Token &token)
{
token.printOn(os);
return os;
}
Token::Token(const String &lexeme,TokenType tokenType,
int lineNum)
: lexeme(lexeme), tokenType(tokenType), lineNum(lineNum)
{
// ctor
}
const String &Token::getLexeme() const
{
return lexeme;
}
TokenType Token::getTokenType() const
{
return tokenType;
}
int Token::getLineNum() const
{
return lineNum;
}
void Token::printOn(ostream &os) const
{
os<<tokenType<< "\t" << lexeme;
}
void Token::changeLexeme(const String &newValue)
{
lexeme=newValue;
}
// **************************************************
// TokenStream methods
// **************************************************
TokenStream::TokenStream(Scanner *scanner)
: scanner(*scanner), pushedBack(NULL)
{
// ctor
}
TokenStream::TokenStream(istream &is)
: scanner(*new Scanner(is)), pushedBack(NULL)
{
// ctor
}
TokenStream::~TokenStream()
{
// dtor
delete &scanner;
}
TokenType TokenStream::peekTokenType()
{
if(!pushedBack)
pushedBack=scanner.nextToken();
return pushedBack->getTokenType();
}
Token *TokenStream::nextToken()
{
Token *retval;
if(pushedBack) {
retval=pushedBack;
pushedBack=NULL;
}
else retval=scanner.nextToken();
return retval;
}
void TokenStream::pushBack(Token *token)
{
if(pushedBack)
throw "Pushing back more than one token in Essex::TokenStream";
pushedBack=token;
}
// **************************************************
// Scanner methods
// **************************************************
Scanner::Scanner(istream &is)
: is(is), lineNum(1)
{
// ctor
}
void Scanner::skipWhiteSpace()
{
// This method skips whitespace and keeps count of newlines
// in the process
int ic;
char c=' ';
while(isspace(c)) {
ic=is.get();
if(isEofChar(ic)) return;
c=char(ic);
if(c=='#') {
do {
ic=is.get();
if(isEofChar(ic)) return;
c=char(ic);
} while(c!='\r' && c!='\n');
}
if(c=='\r' || c=='\n') ++lineNum;
}
is.putback(c);
}
bool Scanner::isEofChar(int ic)
{
return ic==EOF || ic==0;
}
Token *Scanner::nextToken()
{
skipWhiteSpace();
while(!is.eof()) {
int ic=is.get();
if(isEofChar(ic)) break;
char c=static_cast<char>(ic);
switch(c)
{
case '\"': // string literal
return scanStringLit();
case '-': // - or negative number
return scanMinus();
case '#': // comment
skipComment();
skipWhiteSpace();
continue;
case '(': // (
return new Token("(",TOK_LEFT_PAREN,lineNum);
case ')': // )
return new Token(")",TOK_RIGHT_PAREN,lineNum);
default:
if(isdigit(c)) {
is.putback(c);
return scanNumber();
}
else if(isalpha(c) || c=='_') {
is.putback(c);
return scanIdent();
}
is.putback(c);
return scanFreeformString();
}
}
return new Token("",TOK_EOF,lineNum);
}
Token *Scanner::scanMinus()
{
// Precondition: a '-' has already been read
int ic=is.get();
char c=static_cast<char>(ic);
if(isEofChar(ic)) return new Token("-",TOK_STRING_LIT,lineNum);
if(isdigit(c)) {
is.putback(c);
Token *token=scanNumber();
const String &lexeme=token->getLexeme();
if(lexeme.contains('.')) { // float
float value=lexeme.asFloat();
value *= -1;
token->changeLexeme(String(value));
}
else { // int
int value=lexeme.asInt();
value *= -1;
token->changeLexeme(String((long)value));
}
return token;
}
else {
is.putback(c);
return scanFreeformString("-");
}
}
Token *Scanner::scanNumber() {
char buffer[256];
int i=0;
bool periodSeen=false;
while(!is.eof() && i<255) {
int ic=is.get();
char c=static_cast<char>(ic);
if(isEofChar(ic)) break;
if(!(isdigit(c) || c=='.')) {
is.putback(c);
break;
}
buffer[i]=c;
++i;
if(c=='.')
if(periodSeen)
lexicalError(c,lineNum);
else
periodSeen=true;
}
buffer[i]='\0';
TokenType tokenType=periodSeen ? TOK_FLOAT_LIT : TOK_INT_LIT;
return new Token(buffer,tokenType,lineNum);
}
void Scanner::lexicalError(char c,int lineNum)
{
throw String("Lexical error in Essex file, on line number ")+lineNum;
}
bool Scanner::validIdentChar(char c)
{
return isalpha(c) || isdigit(c) || c=='_' || c=='-' || c=='?';
}
Token *Scanner::scanIdent()
{
char buffer[256];
int i=0;
while(!is.eof() && i<255) {
int ic=is.get();
char c=static_cast<char>(ic);
if(isEofChar(ic)) break;
if(!validIdentChar(c)) {
is.putback(c);
break;
}
buffer[i]=c;
++i;
}
buffer[i]='\0';
return new Token(buffer,TOK_IDENT,lineNum);
}
Token *Scanner::scanStringLit()
{
// Precondition: A '\"' has already been read
ElasCharVect array;
int i=0;
// Read string literal into elastic array
while(!is.eof()) {
int ic=is.get();
char c=static_cast<char>(ic);
if(isEofChar(ic)) lexicalError(c,lineNum);
if(c=='\"') break;
if(c=='\\') {
ic=is.get();
c=static_cast<char>(ic);
if(isEofChar(ic)) lexicalError(c,lineNum);
switch(c)
{
case 'n':
c='\n';
break;
case 'r':
c='\r';
break;
case 't':
c='\t';
break;
}
}
array[i]=c;
++i;
}
const int len=i;
// Copy elastic array into a char string
char *buffer=new char[len+1];
for(i=0 ; i<len ; ++i) buffer[i]=array[i];
buffer[i]='\0';
// Create token
String lexeme=buffer;
lexeme=lexeme.substitute("&lparen;","(");
lexeme=lexeme.substitute("&rparen;",")");
lexeme=lexeme.substitute("&tab;","\t");
lexeme=lexeme.substitute("&space;"," ");
Token *token=new Token(lexeme,TOK_STRING_LIT,lineNum);
// Clean up and return
delete [] buffer;
return token;
}
void Scanner::skipComment()
{
// Precondition: A '#' has already been read
while(!is.eof()) {
int ic=is.get();
char c=static_cast<char>(ic);
if(isEofChar(ic) || c=='\n') break;
}
++lineNum;
}
Token *Scanner::scanFreeformString(String prefix)
{
ElasCharVect array;
int i=0;
// Read string literal into elastic array
while(!is.eof()) {
int ic=is.get();
char c=static_cast<char>(ic);
if(isEofChar(ic)) break;