Merged development branch to master

SynBioDex · Jan 12, 2016 · ffabe29 · ffabe29
2 parents 6ef68ce + 0e79ee7
commit ffabe29
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,54 @@
+PROJECT( SBOL )
+CMAKE_MINIMUM_REQUIRED( VERSION 2.8 )
+if(CMAKE_SIZEOF_VOID_P EQUAL 8)
+        MESSAGE(64)
+    else()
+        MESSAGE(32)
+    endif()
+
+# set up folder structure
+SET( SBOL_ROOT_DIR          ${CMAKE_CURRENT_SOURCE_DIR} )
+SET( SBOL_SOURCE_DIR        ${SBOL_ROOT_DIR}/source     )
+SET( SBOL_EXAMPLE_DIR       ${SBOL_ROOT_DIR}/examples   )
+SET( SBOL_TEST_DIR          ${SBOL_ROOT_DIR}/tests      )
+SET( SBOL_MANUAL_DIR        ${SBOL_ROOT_DIR}/manual     )
+SET( SBOL_WRAPPER_DIR       ${SBOL_ROOT_DIR}/wrapper    )
+SET( SBOL_BUILD_DIR         ${SBOL_ROOT_DIR}/build      )
+SET( SBOL_RELEASE_DIR       ${SBOL_ROOT_DIR}/release    )
+SET( EXECUTABLE_OUTPUT_PATH ${SBOL_RELEASE_DIR}         )
+SET( LIBRARY_OUTPUT_PATH    ${SBOL_RELEASE_DIR}/library )
+SET( HEADER_OUTPUT_PATH		${LIBRARY_OUTPUT_PATH}/include )
+
+# set build options
+OPTION( SBOL_BUILD_STATIC     "Build statically linked library"           FALSE )
+OPTION( SBOL_BUILD_COMBINED  "Build libxml2 and libSBOL combined" FALSE )
+OPTION( SBOL_DEBUG_STATEMENTS "Add some print statements for debugging"   FALSE )
+OPTION( SBOL_BUILD_EXAMPLES   "Build the example programs"                FALSE )
+OPTION( SBOL_BUILD_TESTS      "Build the unit tests and example tests"    FALSE )
+OPTION( SBOL_GENERATE_PYTHON  "Generate Python wrapper using SWIG"        FALSE )
+OPTION( SBOL_GENERATE_MANUAL  "Generate SBOL documentation using Doxygen" FALSE )
+
+# build libSBOLc
+#ADD_SUBDIRECTORY( schema )
+ADD_SUBDIRECTORY( source )
+
+# build examples
+#IF( SBOL_BUILD_EXAMPLES )
+#    ADD_SUBDIRECTORY( examples )
+#ENDIF()
+
+# build tests
+#IF( SBOL_BUILD_TESTS )
+#    ADD_SUBDIRECTORY( tests )
+#ENDIF()
+
+# generate documentation
+#IF( SBOL_GENERATE_MANUAL )
+#    ADD_SUBDIRECTORY( manual )
+#ENDIF()
+
+# generate python wrapper
+#IF( SBOL_GENERATE_PYTHON )
+#    ADD_SUBDIRECTORY( wrapper )
+#ENDIF()
+
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
@@ -0,0 +1,96 @@
+
+ADD_SUBDIRECTORY( libxml2 )
+ADD_SUBDIRECTORY( raptor )
+
+# gather headers
+INCLUDE_DIRECTORIES( ${HEADER_DIR} )
+INCLUDE_DIRECTORIES( ${XML2_HEADER_DIR})
+INCLUDE_DIRECTORIES( ${RAPTOR_HEADER_DIR})
+# gather source files
+FILE(GLOB SBOL_HEADER_FILES 
+	validation.h
+	sbolerror.h
+	property.h
+	identified.h
+	toplevel.h
+	generictoplevel.h
+	sequenceannotation.h
+	component.h
+	componentdefinition.h
+	sequence.h
+	document.h
+	sequenceannotationextension.h
+	interaction.h
+	participation.h
+	location.h
+	sequenceconstraint.h
+	moduledefinition.h
+	module.h
+	mapsto.h
+	model.h
+	sbol.h)
+FILE(GLOB SBOL_SOURCE_FILES	
+	validation.cpp
+	sbolerror.cpp
+	property.cpp
+	identified.cpp
+	toplevel.cpp
+	componentdefinition.cpp
+	document.cpp
+	serializer.cpp)
+
+
+FILE(COPY ${SBOL_HEADER_FILES} DESTINATION  ${HEADER_OUTPUT_PATH} )
+
+
+#ADD_EXECUTABLE(sbol ${SBOL_SOURCE_FILES})
+ADD_LIBRARY( sbol
+		STATIC
+		${SBOL_HEADER_FILES}
+		${SBOL_SOURCE_FILES}
+	)
+
+
+# build static library for release
+
+# by default, GCC exports everything;
+# this tells it to stick to SBOLAPIEXPORTS functions
+IF(CMAKE_COMPILER_IS_GNUCC)
+	SET_TARGET_PROPERTIES( sbol
+		PROPERTIES COMPILE_FLAGS -fvisibility=hidden
+	)
+	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+ENDIF()
+
+# link against raptor
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+SET_TARGET_PROPERTIES(sbol PROPERTIES LINKER_LANGUAGE CXX)
+ADD_DEFINITIONS(-DLIBXML_STATIC -DRAPTOR_STATIC)
+
+
+
+MESSAGE(${raptor2})
+
+IF (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+    TARGET_LINK_LIBRARIES( sbol
+        ${raptor2}
+        ${xml2}
+        ${zlib}
+        ${iconv}
+        Ws2_32.lib )
+ELSE ()
+    TARGET_LINK_LIBRARIES( sbol
+        ${raptor2}
+        ${xml2}
+        ${zlib}
+        ${iconv} )
+ENDIF ()
+
+# generate python wrapper
+IF( SBOL_GENERATE_PYTHON )
+    ADD_SUBDIRECTORY( wrapper )
+ENDIF()
+
+INSTALL(TARGETS sbol DESTINATION lib)
+INSTALL(DIRECTORY ${HEADER_OUTPUT_PATH} DESTINATION ${CMAKE_INSTALL_PREFIX})
+
diff --git a/source/component.h b/source/component.h
@@ -0,0 +1,64 @@
+#ifndef COMPONENT_INCLUDED
+#define COMPONENT_INCLUDED
+
+#include "identified.h"
+#include "mapsto.h"
+
+#include <string>
+
+namespace sbol
+{
+	class ComponentInstance : public Identified
+	{
+
+	public:
+		ReferencedObject definition;
+		URIProperty access;
+		List<OwnedObject<MapsTo>> mapsTos;
+
+	protected:
+		ComponentInstance(sbol_type type = SBOL_COMPONENT, std::string uri_prefix = SBOL_URI "/Component", std::string id = "example", std::string access = SBOL_ACCESS_PRIVATE) :
+			Identified(type, uri_prefix, id, "", "", ""),
+			definition(SBOL_DEFINITION, this, UNDEFINED, {}),
+			access(SBOL_ACCESS, this, access),
+			mapsTos(SBOL_MAPS_TO, this)
+			{
+			};
+	};
+
+	class Component : public ComponentInstance
+	{
+	public:
+		Component(std::string uri_prefix = SBOL_URI "/Component", std::string id = "example", std::string access = SBOL_ACCESS_PRIVATE) :
+			Component(SBOL_COMPONENT, uri_prefix, id, access)
+			{
+			};
+		~Component();
+
+	protected:
+		Component(sbol_type type, std::string uri_prefix, std::string id, std::string access) :
+			ComponentInstance(type, uri_prefix, id, access) 
+			{
+			};
+	};
+
+	class FunctionalComponent : public ComponentInstance
+	{
+	public:
+		URIProperty direction;
+		FunctionalComponent(std::string uri_prefix = SBOL_URI "/FunctionalComponent", std::string id = "example") :
+			FunctionalComponent(SBOL_FUNCTIONAL_COMPONENT, uri_prefix, id)
+			{
+			};
+		~FunctionalComponent();
+
+	protected:
+		FunctionalComponent(sbol_type type, std::string uri_prefix, std::string id) : 
+			ComponentInstance(type, uri_prefix, id),
+			direction(SBOL_DIRECTION, this, SBOL_DIRECTION_NONE)
+		{};
+
+	};
+}
+
+#endif
diff --git a/source/componentdefinition.cpp b/source/componentdefinition.cpp
@@ -0,0 +1,13 @@
+#include "componentdefinition.h"
+
+using namespace std;
+using namespace sbol;
+
+//ComponentDefinition::ComponentDefinition(std::string uri_prefix, std::string display_id)
+//{
+//	identity.set(uri_prefix + "/" + display_id + "/1.0.0");
+//	persistentIdentity.set(uri_prefix + "/" + display_id + "/1.0.0");
+//	displayID.set(display_id);
+//	name.set("");
+//	description.set("");
+//}
diff --git a/source/componentdefinition.h b/source/componentdefinition.h
@@ -0,0 +1,43 @@
+#include "toplevel.h"
+#include "component.h"
+#include "sequenceannotation.h"
+#include "sequenceconstraint.h"
+#include <string>
+
+namespace sbol 
+{
+	class ComponentDefinition : public TopLevel
+	{
+	public:
+		List<URIProperty> types;
+		List<URIProperty> roles;
+		ReferencedObject sequence;
+		List<OwnedObject<SequenceAnnotation>> sequenceAnnotations;
+		List<OwnedObject<Component>> components;
+		List<OwnedObject<SequenceConstraint>> sequenceConstraints;
+
+		ComponentDefinition(std::string uri_prefix = SBOL_URI "/ComponentDefinition",
+			std::string display_id = "example",
+			std::string type = SO_UNDEFINED,
+			std::string role = SO_UNDEFINED,
+			std::string name = "",
+			std::string description = "",
+			std::string version = "1.0.0") :
+			ComponentDefinition(SBOL_COMPONENT_DEFINITION, uri_prefix, display_id, type, role, name, description, version)
+			{
+			}
+		~ComponentDefinition() {  };
+	protected:
+		// This protected constructor is a delegate constructor.  It initializes ComponentDefinitions with the corresponding sbol_type_uri 
+		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) :
+			TopLevel(sbol_type_uri, uri_prefix, display_id, name, description, version),
+			types(SBOL_TYPES, this, type),
+			roles(SBOL_ROLES, this, role),
+			sequence(SBOL_SEQUENCE_PROPERTY, this, ""),
+			sequenceAnnotations(SBOL_SEQUENCE_ANNOTATIONS, this),
+			components(SBOL_COMPONENTS, this),
+			sequenceConstraints(SBOL_SEQUENCE_CONSTRAINTS, this)
+			{
+			}
+	};
+}