CCellDesignerImporter Member List

This is the complete list of members for CCellDesignerImporter, including all inherited members.

addAllPositions(std::vector< POSITION > &v)	CCellDesignerImporter	protectedstatic
addDependency(const std::string &parent, const std::string &child)	CCellDesignerImporter	protected
addProteinModifications(RenderGroup *pGroup, const BoundingBox &bounds, const std::vector< ProteinModification > &modifications, const std::vector< SpeciesModification > &speciesModifications, const std::string &stroke_color)	CCellDesignerImporter	protected
angle(const Point &v)	CCellDesignerImporter	protectedstatic
calculateAbsoluteValue(const Point &p, const Point &p1, const Point &p2, const Point &p3)	CCellDesignerImporter	protectedstatic
CCellDesignerImporter(SBMLDocument *pDocument=0)	CCellDesignerImporter
checkLinkAnchor(LinkTarget &link, const Point &p)	CCellDesignerImporter	protected
checkLinkAnchors(LinkTarget &substrate, LinkTarget &product)	CCellDesignerImporter	protected
classToEnum(std::string cl)	CCellDesignerImporter	protectedstatic
cleanString(const std::string &text)	CCellDesignerImporter	protectedstatic
connectionPolicyToEnum(std::string s)	CCellDesignerImporter	protectedstatic
convertCellDesignerLayout(const XMLNode *pCellDesignerAnnotation)	CCellDesignerImporter	protected
convertCompartmentAnnotations()	CCellDesignerImporter	protected
convertReactionAnnotation(Reaction *pReaction, const Model *pModel)	CCellDesignerImporter	protected
convertReactionAnnotations()	CCellDesignerImporter	protected
convertSpeciesAnnotations()	CCellDesignerImporter	protected
createBiUniCurve(ReactionAnnotation &ranno, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle)	CCellDesignerImporter
createCatalysisStyles()	CCellDesignerImporter	protected
createCompartmentGlyph(const CompartmentAlias &ca)	CCellDesignerImporter	protected
createCompartmentGlyphs(const XMLNode *pLoCA)	CCellDesignerImporter	protected
createCompartmentStyle(const CompartmentAlias &ca, const CompartmentGlyph *pCGlyph)	CCellDesignerImporter	protected
createDefaultActivatorStyle()	CCellDesignerImporter	protected
createDefaultInhibitorStyle()	CCellDesignerImporter	protected
createDefaultModifierStyle()	CCellDesignerImporter	protected
createDefaultProductStyle()	CCellDesignerImporter	protected
createDefaultReactionGlyphStyle()	CCellDesignerImporter	protected
createDefaultStyles()	CCellDesignerImporter	protected
createDefaultSubstrateStyle()	CCellDesignerImporter	protected
createLineSegments(Curve *pCurve, ITERATOR start, ITERATOR end)	CCellDesignerImporter	inlineprotectedstatic
createOrthogonal(const Point &v1, Point &v2)	CCellDesignerImporter	protectedstatic
createPrimitive(RenderGroup *pGroup, const SpeciesIdentity &si, const BoundingBox &bounds, const Point &offset, double stroke_width, const std::string &stroke_color, const std::string &fill_color, const std::string &text="")	CCellDesignerImporter	protected
createProduct(std::vector< Point > &productPoints, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle, ReactionAnnotation &ranno)	CCellDesignerImporter
createProteinModification(RenderGroup *pGroup, SPECIES_MODIFICATION_TYPE type, const BoundingBox &bounds, const std::string &stroke_color, double angle=0.0)	CCellDesignerImporter	protected
createSpeciesGlyph(const SpeciesAlias &sa)	CCellDesignerImporter	protected
createSpeciesGlyphs(const XMLNode *pLoSA)	CCellDesignerImporter	protected
createSpeciesReferenceGlyphs(ReactionGlyph *pRGlyph, const std::vector< LinkTarget > &link, std::map< SpeciesReferenceGlyph *, Point > &startsMap, bool reactants)	CCellDesignerImporter	protected
createSpeciesStyles()	CCellDesignerImporter	protected
createStyleFromLine(Line &line, const std::string &glyphId)	CCellDesignerImporter	protected
createSubstrate(std::vector< Point > &reactantPoints, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle, ReactionAnnotation &ranno)	CCellDesignerImporter
createTextGlyphStyle(double size, Text::TEXT_ANCHOR hAlign, Text::TEXT_ANCHOR vAlign, const std::string &objectReference)	CCellDesignerImporter	protected
createUniBiCurve(ReactionAnnotation &ranno, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle)	CCellDesignerImporter
createUniqueId(const std::string &prefix)	CCellDesignerImporter	protected
createUniUniCurve(ReactionAnnotation &ranno, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle)	CCellDesignerImporter
determineVersion(const XMLNode *pNode)	CCellDesignerImporter	static
directionToEnum(std::string s)	CCellDesignerImporter	protectedstatic
distance(const Point &p1, const Point &p2)	CCellDesignerImporter	protectedstatic
enforceSquare(const ConnectScheme &connectScheme, Point &p, const Point &pStart, const Point &pEnd, int &directionCount, bool isLast, const std::vector< Point > &points)	CCellDesignerImporter
findCellDesignerAnnotation(SBMLDocument *pDocument, const XMLNode *pAnnotation)	CCellDesignerImporter	static
findCellDesignerNamespace(const SBMLDocument *pDocument)	CCellDesignerImporter	static
findChildNode(const XMLNode *pNode, const std::string &prefix, const std::string &name, bool recursive=false)	CCellDesignerImporter	protectedstatic
findOrCreateColorDefinition(const std::string &color_string, std::string &id)	CCellDesignerImporter	protected
findOrCreateColorDefinition(const Paint &paint, std::string &id)	CCellDesignerImporter	protected
findRootElementId(const std::string &id) const	CCellDesignerImporter	protected
findShortestConnection(std::vector< POSITION > &pos1, std::vector< POSITION > &pos2, const BoundingBox &box1, const BoundingBox &box2)	CCellDesignerImporter	protectedstatic
findShortestConnection(const Point &p, std::vector< POSITION > &pos, const BoundingBox &box)	CCellDesignerImporter	protectedstatic
getColorString(const std::string &color_id) const	CCellDesignerImporter	protected
getLayout() const	CCellDesignerImporter
getPositionPoint(const BoundingBox &box, POSITION position)	CCellDesignerImporter	protectedstatic
getSBMLDocument() const	CCellDesignerImporter
handleExtraReactionElements(ReactionGlyph *pRGlyph, ReactionAnnotation &ranno, bool substrate)	CCellDesignerImporter	protected
handleIncludedSpecies(const XMLNode *pNode)	CCellDesignerImporter	protected
handleModificationLinks(ReactionGlyph *pRGlyph, ReactionAnnotation &ranno)	CCellDesignerImporter	protected
isDefaultOrEmpty(const Line &line)	CCellDesignerImporter	protectedstatic
mCDBounds	CCellDesignerImporter	protected
mCDIdToLayoutElement	CCellDesignerImporter	protected
mColorStringMap	CCellDesignerImporter	protected
mCompartmentAliasMap	CCellDesignerImporter	protected
mCompartmentAnnotationMap	CCellDesignerImporter	protected
mCompartmentNamePointMap	CCellDesignerImporter	protected
mComplexDependencies	CCellDesignerImporter	protected
mFont	CCellDesignerImporter	protected
mIdMap	CCellDesignerImporter	protected
mIncludedSpeciesNameMap	CCellDesignerImporter	protected
mModelIdToLayoutElement	CCellDesignerImporter	protected
mModificationLinkStyleMap	CCellDesignerImporter	protected
modificationLinkTypeToEnum(std::string s)	CCellDesignerImporter	protectedstatic
modificationTypeToEnum(std::string s)	CCellDesignerImporter	protectedstatic
mpDocument	CCellDesignerImporter	protected
mpLayout	CCellDesignerImporter	protected
mpLocalRenderInfo	CCellDesignerImporter	protected
mpModel	CCellDesignerImporter	protected
mProteinInformationMap	CCellDesignerImporter	protected
mSpeciesAliases	CCellDesignerImporter	protected
mSpeciesAliasMap	CCellDesignerImporter	protected
mSpeciesAnnotationMap	CCellDesignerImporter	protected
paintSchemeToEnum(std::string s)	CCellDesignerImporter	protectedstatic
parseBounds(const XMLNode *pNode, BoundingBox &box)	CCellDesignerImporter	protectedstatic
parseBoxSize(const XMLNode *pNode, Dimensions &d)	CCellDesignerImporter	protectedstatic
parseCompartmentAlias(const XMLNode *pNode, CompartmentAlias &ca, const Dimensions &layout_dimensions)	CCellDesignerImporter	protectedstatic
parseCompartmentAnnotation(const XMLNode *pNode, CompartmentAnnotation &anno)	CCellDesignerImporter	protectedstatic
parseConnectScheme(const XMLNode *pNode, ConnectScheme &scheme)	CCellDesignerImporter	protectedstatic
parseDoubleLine(const XMLNode *pNode, DoubleLine &dl)	CCellDesignerImporter	protectedstatic
parseEditPoints(const XMLNode *pNode, EditPoints &editpoints)	CCellDesignerImporter	protectedstatic
parseExtraLink(const XMLNode *pNode, ReactantLink &l)	CCellDesignerImporter	protectedstatic
parseExtraLinks(const XMLNode *pNode, std::vector< ReactantLink > &rlinks)	CCellDesignerImporter	protectedstatic
parseLine(const XMLNode *pNode, Line &line)	CCellDesignerImporter	protectedstatic
parseLineDirection(const XMLNode *pNode, LineDirection &d)	CCellDesignerImporter	protectedstatic
parseLinkTarget(const XMLNode *pNode, LinkTarget &l)	CCellDesignerImporter	protectedstatic
parseModelDisplay(const XMLNode *pNode, Dimensions &d)	CCellDesignerImporter	protectedstatic
parsePaint(const XMLNode *pNode, Paint &p)	CCellDesignerImporter	protectedstatic
parsePoint(const XMLNode *pNode, Point &p)	CCellDesignerImporter	protectedstatic
parsePointsString(const std::string &s, std::vector< Point > &points)	CCellDesignerImporter	protectedstatic
parseProteinModification(const XMLNode *pNode, ProteinModification &mod)	CCellDesignerImporter	protectedstatic
parseProteins(const XMLNode *pNode)	CCellDesignerImporter	protected
parseReactionAnnotation(const XMLNode *pNode, ReactionAnnotation &ranno)	CCellDesignerImporter	protectedstatic
parseReactionElements(const XMLNode *pNode, std::vector< LinkTarget > &elements)	CCellDesignerImporter	protectedstatic
parseReactionModification(const XMLNode *pNode, ReactionModification &mod)	CCellDesignerImporter	protectedstatic
parseReactionModifications(const XMLNode *pNode, std::vector< ReactionModification > &rmods)	CCellDesignerImporter	protectedstatic
parseSpeciesAlias(const XMLNode *pNode, SpeciesAlias &sa)	CCellDesignerImporter	protectedstatic
parseSpeciesAnnotation(const XMLNode *pNode, SpeciesAnnotation &anno)	CCellDesignerImporter	protectedstatic
parseSpeciesIdentity(const XMLNode *pNode, SpeciesIdentity &identity)	CCellDesignerImporter	protectedstatic
parseSpeciesModification(const XMLNode *pNode, SpeciesModification &mod)	CCellDesignerImporter	protectedstatic
parseSpeciesState(const XMLNode *pNode, SpeciesState &state)	CCellDesignerImporter	protectedstatic
parseUsualView(const XMLNode *pNode, UsualView &view)	CCellDesignerImporter	protectedstatic
positionToCompartmentToEnum(std::string s)	CCellDesignerImporter	protectedstatic
positionToEnum(std::string pos)	CCellDesignerImporter	protectedstatic
reactionTypeToEnum(std::string s)	CCellDesignerImporter	protectedstatic
removeCurrentLayout()	CCellDesignerImporter
replaceStringInPlace(std::string &subject, const std::string &search, const std::string &replace)	CCellDesignerImporter	protectedstatic
rotate(const Point &p, double a, Point &r)	CCellDesignerImporter	protectedstatic
setProductStyle(const std::string &id, LocalStyle *pReactionStyle)	CCellDesignerImporter
setSBMLDocument(SBMLDocument *pDocument)	CCellDesignerImporter
setSpeciesGlyphId(SpeciesReferenceGlyph *pGlyph, const LinkTarget &link)	CCellDesignerImporter	protected
setSpeciesReferenceId(SpeciesReferenceGlyph *pGlyph, const LinkTarget &link, const std::string &reactionId)	CCellDesignerImporter	protected
speciesModificationTypeToEnum(std::string cl)	CCellDesignerImporter	protectedstatic
splitString(const std::string &s, std::vector< std::string > &parts, const std::string &splitChars)	CCellDesignerImporter	protectedstatic