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Bryan Bartley
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Merged development branch to master
2 parents 6ef68ce + 0e79ee7 commit ffabe29

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‎CMakeLists.txt‎

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PROJECT( SBOL )
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CMAKE_MINIMUM_REQUIRED( VERSION 2.8 )
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if(CMAKE_SIZEOF_VOID_P EQUAL 8)
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MESSAGE(64)
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else()
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MESSAGE(32)
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endif()
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# set up folder structure
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SET( SBOL_ROOT_DIR ${CMAKE_CURRENT_SOURCE_DIR} )
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SET( SBOL_SOURCE_DIR ${SBOL_ROOT_DIR}/source )
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SET( SBOL_EXAMPLE_DIR ${SBOL_ROOT_DIR}/examples )
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SET( SBOL_TEST_DIR ${SBOL_ROOT_DIR}/tests )
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SET( SBOL_MANUAL_DIR ${SBOL_ROOT_DIR}/manual )
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SET( SBOL_WRAPPER_DIR ${SBOL_ROOT_DIR}/wrapper )
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SET( SBOL_BUILD_DIR ${SBOL_ROOT_DIR}/build )
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SET( SBOL_RELEASE_DIR ${SBOL_ROOT_DIR}/release )
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SET( EXECUTABLE_OUTPUT_PATH ${SBOL_RELEASE_DIR} )
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SET( LIBRARY_OUTPUT_PATH ${SBOL_RELEASE_DIR}/library )
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SET( HEADER_OUTPUT_PATH ${LIBRARY_OUTPUT_PATH}/include )
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# set build options
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OPTION( SBOL_BUILD_STATIC "Build statically linked library" FALSE )
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OPTION( SBOL_BUILD_COMBINED "Build libxml2 and libSBOL combined" FALSE )
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OPTION( SBOL_DEBUG_STATEMENTS "Add some print statements for debugging" FALSE )
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OPTION( SBOL_BUILD_EXAMPLES "Build the example programs" FALSE )
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OPTION( SBOL_BUILD_TESTS "Build the unit tests and example tests" FALSE )
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OPTION( SBOL_GENERATE_PYTHON "Generate Python wrapper using SWIG" FALSE )
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OPTION( SBOL_GENERATE_MANUAL "Generate SBOL documentation using Doxygen" FALSE )
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# build libSBOLc
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#ADD_SUBDIRECTORY( schema )
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ADD_SUBDIRECTORY( source )
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# build examples
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#IF( SBOL_BUILD_EXAMPLES )
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# ADD_SUBDIRECTORY( examples )
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#ENDIF()
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# build tests
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#IF( SBOL_BUILD_TESTS )
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# ADD_SUBDIRECTORY( tests )
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#ENDIF()
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# generate documentation
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#IF( SBOL_GENERATE_MANUAL )
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# ADD_SUBDIRECTORY( manual )
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#ENDIF()
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# generate python wrapper
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#IF( SBOL_GENERATE_PYTHON )
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# ADD_SUBDIRECTORY( wrapper )
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#ENDIF()
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‎source/CMakeLists.txt‎

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ADD_SUBDIRECTORY( libxml2 )
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ADD_SUBDIRECTORY( raptor )
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# gather headers
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INCLUDE_DIRECTORIES( ${HEADER_DIR} )
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INCLUDE_DIRECTORIES( ${XML2_HEADER_DIR})
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INCLUDE_DIRECTORIES( ${RAPTOR_HEADER_DIR})
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# gather source files
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FILE(GLOB SBOL_HEADER_FILES
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validation.h
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sbolerror.h
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property.h
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identified.h
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toplevel.h
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generictoplevel.h
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sequenceannotation.h
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component.h
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componentdefinition.h
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sequence.h
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document.h
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sequenceannotationextension.h
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interaction.h
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participation.h
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location.h
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sequenceconstraint.h
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moduledefinition.h
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module.h
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mapsto.h
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model.h
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sbol.h)
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FILE(GLOB SBOL_SOURCE_FILES
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validation.cpp
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sbolerror.cpp
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property.cpp
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identified.cpp
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toplevel.cpp
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componentdefinition.cpp
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document.cpp
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serializer.cpp)
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FILE(COPY ${SBOL_HEADER_FILES} DESTINATION ${HEADER_OUTPUT_PATH} )
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#ADD_EXECUTABLE(sbol ${SBOL_SOURCE_FILES})
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ADD_LIBRARY( sbol
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STATIC
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${SBOL_HEADER_FILES}
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${SBOL_SOURCE_FILES}
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)
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# build static library for release
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# by default, GCC exports everything;
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# this tells it to stick to SBOLAPIEXPORTS functions
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IF(CMAKE_COMPILER_IS_GNUCC)
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SET_TARGET_PROPERTIES( sbol
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PROPERTIES COMPILE_FLAGS -fvisibility=hidden
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)
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
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ENDIF()
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# link against raptor
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
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SET_TARGET_PROPERTIES(sbol PROPERTIES LINKER_LANGUAGE CXX)
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ADD_DEFINITIONS(-DLIBXML_STATIC -DRAPTOR_STATIC)
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MESSAGE(${raptor2})
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IF (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
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TARGET_LINK_LIBRARIES( sbol
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${raptor2}
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${xml2}
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${zlib}
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${iconv}
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Ws2_32.lib )
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ELSE ()
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TARGET_LINK_LIBRARIES( sbol
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${raptor2}
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${xml2}
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${zlib}
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${iconv} )
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ENDIF ()
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# generate python wrapper
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IF( SBOL_GENERATE_PYTHON )
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ADD_SUBDIRECTORY( wrapper )
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ENDIF()
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INSTALL(TARGETS sbol DESTINATION lib)
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INSTALL(DIRECTORY ${HEADER_OUTPUT_PATH} DESTINATION ${CMAKE_INSTALL_PREFIX})
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‎source/component.h‎

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#ifndef COMPONENT_INCLUDED
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#define COMPONENT_INCLUDED
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#include "identified.h"
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#include "mapsto.h"
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#include <string>
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namespace sbol
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{
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class ComponentInstance : public Identified
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{
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public:
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ReferencedObject definition;
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URIProperty access;
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List<OwnedObject<MapsTo>> mapsTos;
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protected:
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ComponentInstance(sbol_type type = SBOL_COMPONENT, std::string uri_prefix = SBOL_URI "/Component", std::string id = "example", std::string access = SBOL_ACCESS_PRIVATE) :
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Identified(type, uri_prefix, id, "", "", ""),
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definition(SBOL_DEFINITION, this, UNDEFINED, {}),
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access(SBOL_ACCESS, this, access),
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mapsTos(SBOL_MAPS_TO, this)
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{
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};
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};
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class Component : public ComponentInstance
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{
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public:
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Component(std::string uri_prefix = SBOL_URI "/Component", std::string id = "example", std::string access = SBOL_ACCESS_PRIVATE) :
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Component(SBOL_COMPONENT, uri_prefix, id, access)
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{
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};
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~Component();
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protected:
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Component(sbol_type type, std::string uri_prefix, std::string id, std::string access) :
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ComponentInstance(type, uri_prefix, id, access)
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{
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};
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};
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class FunctionalComponent : public ComponentInstance
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{
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public:
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URIProperty direction;
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FunctionalComponent(std::string uri_prefix = SBOL_URI "/FunctionalComponent", std::string id = "example") :
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FunctionalComponent(SBOL_FUNCTIONAL_COMPONENT, uri_prefix, id)
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{
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};
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~FunctionalComponent();
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protected:
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FunctionalComponent(sbol_type type, std::string uri_prefix, std::string id) :
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ComponentInstance(type, uri_prefix, id),
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direction(SBOL_DIRECTION, this, SBOL_DIRECTION_NONE)
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{};
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};
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}
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#endif

‎source/componentdefinition.cpp‎

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#include "componentdefinition.h"
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using namespace std;
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using namespace sbol;
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//ComponentDefinition::ComponentDefinition(std::string uri_prefix, std::string display_id)
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//{
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// identity.set(uri_prefix + "/" + display_id + "/1.0.0");
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// persistentIdentity.set(uri_prefix + "/" + display_id + "/1.0.0");
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// displayID.set(display_id);
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// name.set("");
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// description.set("");
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//}

‎source/componentdefinition.h‎

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#include "toplevel.h"
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#include "component.h"
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#include "sequenceannotation.h"
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#include "sequenceconstraint.h"
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#include <string>
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namespace sbol
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{
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class ComponentDefinition : public TopLevel
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{
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public:
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List<URIProperty> types;
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List<URIProperty> roles;
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ReferencedObject sequence;
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List<OwnedObject<SequenceAnnotation>> sequenceAnnotations;
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List<OwnedObject<Component>> components;
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List<OwnedObject<SequenceConstraint>> sequenceConstraints;
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ComponentDefinition(std::string uri_prefix = SBOL_URI "/ComponentDefinition",
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std::string display_id = "example",
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std::string type = SO_UNDEFINED,
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std::string role = SO_UNDEFINED,
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std::string name = "",
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std::string description = "",
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std::string version = "1.0.0") :
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ComponentDefinition(SBOL_COMPONENT_DEFINITION, uri_prefix, display_id, type, role, name, description, version)
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{
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}
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~ComponentDefinition() { };
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protected:
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// This protected constructor is a delegate constructor. It initializes ComponentDefinitions with the corresponding sbol_type_uri
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ComponentDefinition(sbol_type sbol_type_uri, std::string uri_prefix, std::string display_id, std::string type, std::string role, std::string name, std::string description, std::string version) :
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TopLevel(sbol_type_uri, uri_prefix, display_id, name, description, version),
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types(SBOL_TYPES, this, type),
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roles(SBOL_ROLES, this, role),
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sequence(SBOL_SEQUENCE_PROPERTY, this, ""),
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sequenceAnnotations(SBOL_SEQUENCE_ANNOTATIONS, this),
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components(SBOL_COMPONENTS, this),
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sequenceConstraints(SBOL_SEQUENCE_CONSTRAINTS, this)
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{
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}
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};
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}

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