COPASI API
4.40.278
|
#include <CCellDesignerImporter.h>
Public Member Functions | |
CCellDesignerImporter (SBMLDocument *pDocument=0) | |
bool | createBiUniCurve (ReactionAnnotation &ranno, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle) |
creates a curve connecting two substrates to one product More... | |
bool | createProduct (std::vector< Point > &productPoints, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle, ReactionAnnotation &ranno) |
bool | createSubstrate (std::vector< Point > &reactantPoints, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle, ReactionAnnotation &ranno) |
bool | createUniBiCurve (ReactionAnnotation &ranno, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle) |
creates a curve connecting one substrate to two products More... | |
bool | createUniUniCurve (ReactionAnnotation &ranno, ReactionGlyph *pRGlyph, LocalStyle *pReactionStyle) |
creates a curve connecting one substrate to one product More... | |
void | enforceSquare (const ConnectScheme &connectScheme, Point &p, const Point &pStart, const Point &pEnd, int &directionCount, bool isLast, const std::vector< Point > &points) |
const Layout * | getLayout () const |
const SBMLDocument * | getSBMLDocument () const |
void | removeCurrentLayout () |
void | setProductStyle (const std::string &id, LocalStyle *pReactionStyle) |
void | setSBMLDocument (SBMLDocument *pDocument) |
Static Public Member Functions | |
static double | determineVersion (const XMLNode *pNode) |
static const XMLNode * | findCellDesignerAnnotation (SBMLDocument *pDocument, const XMLNode *pAnnotation) |
static std::pair< bool, std::string > | findCellDesignerNamespace (const SBMLDocument *pDocument) |
Protected Member Functions | |
void | addDependency (const std::string &parent, const std::string &child) |
bool | addProteinModifications (RenderGroup *pGroup, const BoundingBox &bounds, const std::vector< ProteinModification > &modifications, const std::vector< SpeciesModification > &speciesModifications, const std::string &stroke_color) |
adds the given protein modifications to the given group More... | |
void | checkLinkAnchor (LinkTarget &link, const Point &p) |
void | checkLinkAnchors (LinkTarget &substrate, LinkTarget &product) |
bool | convertCellDesignerLayout (const XMLNode *pCellDesignerAnnotation) |
bool | convertCompartmentAnnotations () |
bool | convertReactionAnnotation (Reaction *pReaction, const Model *pModel) |
bool | convertReactionAnnotations () |
bool | convertSpeciesAnnotations () |
bool | createCatalysisStyles () |
bool | createCompartmentGlyph (const CompartmentAlias &ca) |
bool | createCompartmentGlyphs (const XMLNode *pLoCA) |
bool | createCompartmentStyle (const CompartmentAlias &ca, const CompartmentGlyph *pCGlyph) |
bool | createDefaultActivatorStyle () |
bool | createDefaultInhibitorStyle () |
bool | createDefaultModifierStyle () |
bool | createDefaultProductStyle () |
bool | createDefaultReactionGlyphStyle () |
bool | createDefaultStyles () |
bool | createDefaultSubstrateStyle () |
bool | 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="") |
bool | createProteinModification (RenderGroup *pGroup, SPECIES_MODIFICATION_TYPE type, const BoundingBox &bounds, const std::string &stroke_color, double angle=0.0) |
bool | createSpeciesGlyph (const SpeciesAlias &sa) |
bool | createSpeciesGlyphs (const XMLNode *pLoSA) |
bool | createSpeciesReferenceGlyphs (ReactionGlyph *pRGlyph, const std::vector< LinkTarget > &link, std::map< SpeciesReferenceGlyph *, Point > &startsMap, bool reactants) |
bool | createSpeciesStyles () |
LocalStyle * | createStyleFromLine (Line &line, const std::string &glyphId) |
bool | createTextGlyphStyle (double size, Text::TEXT_ANCHOR hAlign, Text::TEXT_ANCHOR vAlign, const std::string &objectReference) |
std::string | createUniqueId (const std::string &prefix) |
bool | findOrCreateColorDefinition (const Paint &paint, std::string &id) |
bool | findOrCreateColorDefinition (const std::string &color_string, std::string &id) |
std::string | findRootElementId (const std::string &id) const |
std::string | getColorString (const std::string &color_id) const |
bool | handleExtraReactionElements (ReactionGlyph *pRGlyph, ReactionAnnotation &ranno, bool substrate) |
bool | handleIncludedSpecies (const XMLNode *pNode) |
bool | handleModificationLinks (ReactionGlyph *pRGlyph, ReactionAnnotation &ranno) |
bool | parseProteins (const XMLNode *pNode) |
bool | setSpeciesGlyphId (SpeciesReferenceGlyph *pGlyph, const LinkTarget &link) |
bool | setSpeciesReferenceId (SpeciesReferenceGlyph *pGlyph, const LinkTarget &link, const std::string &reactionId) |
Static Protected Member Functions | |
static void | addAllPositions (std::vector< POSITION > &v) |
static double | angle (const Point &v) |
static Point | calculateAbsoluteValue (const Point &p, const Point &p1, const Point &p2, const Point &p3) |
static SPECIES_CLASS | classToEnum (std::string cl) |
static std::string | cleanString (const std::string &text) |
cleanString replaces sequences within the given text string More... | |
static CONNECTION_POLICY | connectionPolicyToEnum (std::string s) |
template<typename ITERATOR > | |
static bool | createLineSegments (Curve *pCurve, ITERATOR start, ITERATOR end) |
static bool | createOrthogonal (const Point &v1, Point &v2) |
static DIRECTION_VALUE | directionToEnum (std::string s) |
static double | distance (const Point &p1, const Point &p2) |
static const XMLNode * | findChildNode (const XMLNode *pNode, const std::string &prefix, const std::string &name, bool recursive=false) |
static POSITION | findShortestConnection (const Point &p, std::vector< POSITION > &pos, const BoundingBox &box) |
static bool | findShortestConnection (std::vector< POSITION > &pos1, std::vector< POSITION > &pos2, const BoundingBox &box1, const BoundingBox &box2) |
static Point | getPositionPoint (const BoundingBox &box, POSITION position) |
static bool | isDefaultOrEmpty (const Line &line) |
static MODIFICATION_LINK_TYPE | modificationLinkTypeToEnum (std::string s) |
static MODIFICATION_TYPE | modificationTypeToEnum (std::string s) |
static PAINT_SCHEME | paintSchemeToEnum (std::string s) |
static bool | parseBounds (const XMLNode *pNode, BoundingBox &box) |
static bool | parseBoxSize (const XMLNode *pNode, Dimensions &d) |
static bool | parseCompartmentAlias (const XMLNode *pNode, CompartmentAlias &ca, const Dimensions &layout_dimensions) |
static bool | parseCompartmentAnnotation (const XMLNode *pNode, CompartmentAnnotation &anno) |
static bool | parseConnectScheme (const XMLNode *pNode, ConnectScheme &scheme) |
static bool | parseDoubleLine (const XMLNode *pNode, DoubleLine &dl) |
static bool | parseEditPoints (const XMLNode *pNode, EditPoints &editpoints) |
static bool | parseExtraLink (const XMLNode *pNode, ReactantLink &l) |
static bool | parseExtraLinks (const XMLNode *pNode, std::vector< ReactantLink > &rlinks) |
static bool | parseLine (const XMLNode *pNode, Line &line) |
static bool | parseLineDirection (const XMLNode *pNode, LineDirection &d) |
static bool | parseLinkTarget (const XMLNode *pNode, LinkTarget &l) |
static bool | parseModelDisplay (const XMLNode *pNode, Dimensions &d) |
static bool | parsePaint (const XMLNode *pNode, Paint &p) |
static bool | parsePoint (const XMLNode *pNode, Point &p) |
static bool | parsePointsString (const std::string &s, std::vector< Point > &points) |
static bool | parseProteinModification (const XMLNode *pNode, ProteinModification &mod) |
static bool | parseReactionAnnotation (const XMLNode *pNode, ReactionAnnotation &ranno) |
static bool | parseReactionElements (const XMLNode *pNode, std::vector< LinkTarget > &elements) |
static bool | parseReactionModification (const XMLNode *pNode, ReactionModification &mod) |
static bool | parseReactionModifications (const XMLNode *pNode, std::vector< ReactionModification > &rmods) |
static bool | parseSpeciesAlias (const XMLNode *pNode, SpeciesAlias &sa) |
static bool | parseSpeciesAnnotation (const XMLNode *pNode, SpeciesAnnotation &anno) |
static bool | parseSpeciesIdentity (const XMLNode *pNode, SpeciesIdentity &identity) |
static bool | parseSpeciesModification (const XMLNode *pNode, SpeciesModification &mod) |
static bool | parseSpeciesState (const XMLNode *pNode, SpeciesState &state) |
static bool | parseUsualView (const XMLNode *pNode, UsualView &view) |
static POSITION_TO_COMPARTMENT | positionToCompartmentToEnum (std::string s) |
static POSITION | positionToEnum (std::string pos) |
static REACTION_TYPE | reactionTypeToEnum (std::string s) |
static void | replaceStringInPlace (std::string &subject, const std::string &search, const std::string &replace) |
static void | rotate (const Point &p, double a, Point &r) |
static SPECIES_MODIFICATION_TYPE | speciesModificationTypeToEnum (std::string cl) |
static bool | splitString (const std::string &s, std::vector< std::string > &parts, const std::string &splitChars) |
Protected Attributes | |
std::map< std::string, BoundingBox > | mCDBounds |
std::map< std::string, GraphicalObject * > | mCDIdToLayoutElement |
std::map< std::string, std::string > | mColorStringMap |
std::map< const CompartmentGlyph *, CompartmentAlias > | mCompartmentAliasMap |
std::map< std::string, CompartmentAnnotation > | mCompartmentAnnotationMap |
std::map< const CompartmentGlyph *, Point > | mCompartmentNamePointMap |
std::list< CCopasiNode< std::string > * > | mComplexDependencies |
std::string | mFont |
std::map< std::string, const SBase * > | mIdMap |
std::map< std::string, std::pair< std::string, SpeciesIdentity > > | mIncludedSpeciesNameMap |
std::multimap< std::string, GraphicalObject * > | mModelIdToLayoutElement |
std::map< MODIFICATION_LINK_TYPE, LocalStyle * > | mModificationLinkStyleMap |
SBMLDocument * | mpDocument |
Layout * | mpLayout |
LocalRenderInformation * | mpLocalRenderInfo |
Model * | mpModel |
std::map< std::string, Protein > | mProteinInformationMap |
std::map< std::string, SpeciesAlias > | mSpeciesAliases |
std::map< const SpeciesGlyph *, SpeciesAlias > | mSpeciesAliasMap |
std::map< std::string, SpeciesAnnotation > | mSpeciesAnnotationMap |
This class converts CellDesigner layout information into SBML layout. Maybe later versions will also be able to handle the render information part.
CCellDesignerImporter::CCellDesignerImporter | ( | SBMLDocument * | pDocument = 0 | ) |
Constructor that takes a pointer to an SBMLDocument. The SBMLDocument will not be copied and it will not be owned by the importer. If the pointer is not NULL, the class will try to directly convert the CellDesigner layout if there is one.
References setSBMLDocument().
|
staticprotected |
Adds all possible POSITION enums to the given vector. The vector is cleared first.
|
protected |
Adds a new entry to the dependency tree for complex species aliases.
References CCopasiNode< _Data >::addChild(), CCopasiNode< _Data >::getChild(), CCopasiNode< _Data >::getData(), CCopasiNode< _Data >::getNext(), CCopasiNode< _Data >::getSibling(), mComplexDependencies, and CCopasiNode< _Data >::setData().
Referenced by createSpeciesGlyph().
|
protected |
adds the given protein modifications to the given group
pGroup | the render group to add the modification to |
bounds | the bounds of the element |
modifications | list of angles where to attach the modifications |
speciesModifications | list of modification types |
stroke_color | the stroke color |
Create a primitive that corresponds to the given class The promitive is created in the given group object. The complete primitive is translated by the given offset.
If creation of the primitive fails, false is returned.
References createProteinModification(), and getTypeFrom().
Referenced by createPrimitive().
|
staticprotected |
Calculates the angle between the given vector and the positive x axis. The result is returned in radians.
Referenced by createProteinModification().
|
staticprotected |
Calculates the absolute position for point p based on the three other points (p1,p2,p3) given. The formula for that is: p1 + p.x * (p2 - p1) + p.y * (p3 - p1)
Referenced by createBiUniCurve(), and createUniUniCurve().
|
protected |
Checks if the given ReactantLink object has a valid linkAnchor If not, we try to determine the best anchor be finding the one that is closest to the given point.
Referenced by createBiUniCurve(), and createUniBiCurve().
|
protected |
Checks if the given ReactantLink objects have valid linkAnchors If not, we try to determine the best anchor be finding the ones that give the shortest connection between the two objects
Referenced by createUniUniCurve().
|
staticprotected |
Converts the given class string to the corresponding SPECIES_CLASS enum value. If no enum is found, UNDEFINED is returned.
References ANTISENSE_RNA_CLASS, CHANNEL_CLASS, COMPLEX_CLASS, DEGRADED_CLASS, DRUG_CLASS, GENE_CLASS, ION_CLASS, OVAL_CLASS, PHENOTYPE_CLASS, PROTEIN_CLASS, RECEPTOR_CLASS, RNA_CLASS, SIMPLE_MOLECULE_CLASS, SQUARE_CLASS, SQUARE_E_CLASS, SQUARE_N_CLASS, SQUARE_NE_CLASS, SQUARE_NW_CLASS, SQUARE_S_CLASS, SQUARE_SE_CLASS, SQUARE_SW_CLASS, SQUARE_W_CLASS, TRUNCATED_CLASS, UNDEFINED_CLASS, and UNKNOWN_CLASS.
Referenced by parseProteins(), and parseSpeciesIdentity().
|
staticprotected |
cleanString replaces sequences within the given text string
text | the string to be cleaned |
Referenced by convertCompartmentAnnotations(), convertSpeciesAnnotations(), and createPrimitive().
|
staticprotected |
Converts the given connection policy string to the corresponding enum. If there is no enum that corresponds to the string, POLICY_UNDEFINED is returned.
References POLICY_DIRECT, POLICY_SQUARE, and POLICY_UNDEFINED.
Referenced by parseConnectScheme().
|
protected |
This method tries to convert the CellDesigner annotation to an SBML Layout. On success the method will return true and false otherwise.
References SBMLUtils::collectIds(), convertCompartmentAnnotations(), convertReactionAnnotations(), convertSpeciesAnnotations(), COULD_NOT_CREATE, createCompartmentGlyphs(), createDefaultStyles(), createSpeciesGlyphs(), createSpeciesStyles(), createUniqueId(), determineVersion(), FAIL_WITH_ERROR_AND_RETURN, findChildNode(), handleIncludedSpecies(), mCDBounds, mCDIdToLayoutElement, mColorStringMap, mCompartmentAliasMap, mCompartmentAnnotationMap, mCompartmentNamePointMap, mComplexDependencies, mIdMap, mModelIdToLayoutElement, mpLayout, mpLocalRenderInfo, mpModel, mProteinInformationMap, mSpeciesAliases, mSpeciesAliasMap, mSpeciesAnnotationMap, parseModelDisplay(), parseProteins(), and removeCurrentLayout().
Referenced by setSBMLDocument().
|
protected |
Traverses the compartments of the model and looks for CellDesigner annotations. These are used to create text glyphs associated with compartments.
References cleanString(), createTextGlyphStyle(), createUniqueId(), FAIL_WITH_ERROR, findCellDesignerAnnotation(), getCenter(), mCompartmentAliasMap, mCompartmentAnnotationMap, mCompartmentNamePointMap, mIdMap, mModelIdToLayoutElement, CompartmentAnnotation::mName, mpDocument, mpLayout, mpModel, and parseCompartmentAnnotation().
Referenced by convertCellDesignerLayout().
|
protected |
Looks for CellDesigner annotation in the given reaction and tries to convert the information in that annotation into a ReactionGlyph.
References CATALYSIS_RTYPE, COULD_NOT_CREATE, createBiUniCurve(), createStyleFromLine(), createUniBiCurve(), createUniqueId(), createUniUniCurve(), DISSOCIATION_RTYPE, FAIL_WITH_ERROR, FAIL_WITH_ERROR_AND_RETURN, findCellDesignerAnnotation(), handleExtraReactionElements(), handleModificationLinks(), HETERODIMER_ASSOCIATION_RTYPE, INHIBITION_RTYPE, KNOWN_TRANSITION_OMITTED_RTYPE, mIdMap, ReactionAnnotation::mLine, mpDocument, mpLayout, ReactionAnnotation::mType, parseReactionAnnotation(), STATE_TRANSITION_RTYPE, TRANSCRIPTION_RTYPE, TRANSCRIPTIONAL_ACTIVATION_RTYPE, TRANSCRIPTIONAL_INHIBITION_RTYPE, TRANSLATION_RTYPE, TRANSLATIONAL_ACTIVATION_RTYPE, TRANSLATIONAL_INHIBITION_RTYPE, TRANSPORT_RTYPE, TRUNCATION_RTYPE, UNKNOWN_CATALYSIS_RTYPE, UNKNOWN_INHIBITION_RTYPE, and UNKNOWN_TRANSITION_RTYPE.
Referenced by convertReactionAnnotations().
|
protected |
Traverses the reactions of the model and looks for CellDesigner annotations. These are used to create reaction glyphs.
References convertReactionAnnotation(), FAIL_WITH_ERROR_AND_RETURN, mpDocument, and mpModel.
Referenced by convertCellDesignerLayout().
|
protected |
Traverses the species of the model and looks for CellDesigner annotations. These are used to create text glyphs associated with species.
References cleanString(), createTextGlyphStyle(), createUniqueId(), DEGRADED_CLASS, FAIL_WITH_ERROR, findCellDesignerAnnotation(), SpeciesAnnotation::mIdentity, mIdMap, mModelIdToLayoutElement, mpDocument, mpLayout, mpModel, mSpeciesAliasMap, mSpeciesAnnotationMap, SpeciesIdentity::mSpeciesClass, and parseSpeciesAnnotation().
Referenced by convertCellDesignerLayout().
bool CCellDesignerImporter::createBiUniCurve | ( | ReactionAnnotation & | ranno, |
ReactionGlyph * | pRGlyph, | ||
LocalStyle * | pReactionStyle | ||
) |
creates a curve connecting two substrates to one product
ranno | the reaction annotation |
pRGlyph | the reaction glyph |
pReactionStyle | the style of the current reaction |
References calculateAbsoluteValue(), checkLinkAnchor(), COULD_NOT_CREATE, createUniqueId(), distance(), FAIL_WITH_ERROR, getPositionPoint(), ReactionAnnotation::mBaseProducts, ReactionAnnotation::mBaseReactants, mCDBounds, ReactionAnnotation::mEditPoints, mIdMap, EditPoints::mOmittedShapeIndex, EditPoints::mPoints, EditPoints::mTShapeIndex, POSITION_UNDEFINED, setSpeciesGlyphId(), and setSpeciesReferenceId().
Referenced by convertReactionAnnotation().
|
protected |
Create style for catalysis.
|
protected |
Creates the compartment glyph from the given compartmentAliase structure.
References createCompartmentStyle(), createUniqueId(), FAIL_WITH_ERROR, CompartmentAlias::mBounds, mCDIdToLayoutElement, CompartmentAlias::mCompartment, mCompartmentAliasMap, mCompartmentNamePointMap, CompartmentAlias::mId, mIdMap, mModelIdToLayoutElement, CompartmentAlias::mNamePoint, mpLayout, and mpModel.
Referenced by createCompartmentGlyphs().
|
protected |
Creates the compartment glyphs from the given node that represents the listOfCompartmentAliases.
References createCompartmentGlyph(), FAIL_WITH_ERROR, mpLayout, and parseCompartmentAlias().
Referenced by convertCellDesignerLayout().
|
protected |
This method creates a new local style based on the passed in CompartmentAlias object. The style is associated with the object via the given id. If Creating the style fails, false is returned.
Referenced by createCompartmentGlyph().
|
protected |
Create default style for activators.
|
protected |
Create default style for inhibitors.
|
protected |
Create default style for modifiers.
|
protected |
Create default style for products.
|
protected |
Create default style for reaction glyphs.
|
protected |
TODO right now, we use default styles for species reference glyphs TODO and reaction glyphs. TODO These are created here. TODO later we have to create individual styles based on the type of reaction TODO and the color set in the CellDesigner annotation.
Referenced by convertCellDesignerLayout().
|
protected |
Create default style for substrates.
|
inlinestaticprotected |
This method takes a pointer to a curve object as well as a start iterator and an end iterator which both iterate over a data structure that contains points. For each point pair, a line segment is created and added to curve. The new curve segments are added to the end of the curve.
If no error occurs, true is returned, else false is returned.
Referenced by createProduct(), and createSubstrate().
|
staticprotected |
Creates a vector that is orthogonal to the given first vector. If there is a problem, false is returned.
Referenced by createUniUniCurve().
|
protected |
Create a primitive that corresponds to the given species specific class The primitive is created in the given group object. The complete primitive is translated by the given offset.
If creation of the primitive fails, false is returned.
References addProteinModifications(), ANTISENSE_RNA_CLASS, CHANNEL_CLASS, cleanString(), COMPLEX_CLASS, COULD_NOT_CREATE, DEGRADED_CLASS, DRUG_CLASS, FAIL_WITH_ERROR, FAIL_WITH_ERROR_AND_RETURN, GENE_CLASS, ION_CLASS, mFont, SpeciesIdentity::mHypothetical, SpeciesState::mModifications, SpeciesIdentity::mNameOrReference, mProteinInformationMap, SpeciesIdentity::mSpeciesClass, SpeciesIdentity::mState, PHENOTYPE_CLASS, PROTEIN_CLASS, RECEPTOR_CLASS, RNA_CLASS, SIMPLE_MOLECULE_CLASS, TRUNCATED_CLASS, UNDEFINED_CLASS, and UNKNOWN_CLASS.
Referenced by createSpeciesStyles().
bool CCellDesignerImporter::createProduct | ( | std::vector< Point > & | productPoints, |
ReactionGlyph * | pRGlyph, | ||
LocalStyle * | pReactionStyle, | ||
ReactionAnnotation & | ranno | ||
) |
References createLineSegments(), createUniqueId(), ReactionAnnotation::mBaseProducts, mIdMap, setProductStyle(), setSpeciesGlyphId(), and setSpeciesReferenceId().
Referenced by createUniUniCurve().
|
protected |
Takes a protein modification description and creates the corresponding primitive.
References ACETYLATED_MOD_TYPE, angle(), COULD_NOT_CREATE, DONTCARE_MOD_TYPE, GLYCOSYLATED_MOD_TYPE, HYDROXYLATED_MOD_TYPE, METHYLATED_MOD_TYPE, mFont, MYRISTOYLATED_MOD_TYPE, PALMYTOYLATED_MOD_TYPE, PHOSPHORYLATED_MOD_TYPE, PRENYLATED_MOD_TYPE, PROTONATED_MOD_TYPE, rotate(), SUFLATED_MOD_TYPE, UBIQUITINATED_MOD_TYPE, and UNKNOWN_MOD_TYPE.
Referenced by addProteinModifications().
|
protected |
Creates the species glyph from the given SpeciesAliases structure.
References addDependency(), COULD_NOT_CREATE, createUniqueId(), FAIL_WITH_ERROR, SpeciesAlias::mBounds, mCDBounds, mCDIdToLayoutElement, SpeciesAlias::mComplexSpeciesAlias, SpeciesAlias::mId, mIdMap, mModelIdToLayoutElement, mpLayout, mpModel, SpeciesAlias::mSpecies, mSpeciesAliases, and mSpeciesAliasMap.
Referenced by createSpeciesGlyphs().
|
protected |
Creates the species glyphs from the given node that represents the listOfSpeciesAliases.
References createSpeciesGlyph(), FAIL_WITH_ERROR, and parseSpeciesAlias().
Referenced by convertCellDesignerLayout().
|
protected |
Takes a node that contains a number of baseReactants or baseProducts and creates species reference glyphs for each one.
References createUniqueId(), FAIL_WITH_ERROR, findRootElementId(), getPositionPoint(), LinkTarget::mAlias, mCDBounds, mCDIdToLayoutElement, mIdMap, mpModel, LinkTarget::mPosition, LinkTarget::mSpecies, and POSITION_UNDEFINED.
|
protected |
Creates styles for all species glyphs.
References COULD_NOT_CREATE, createPrimitive(), createUniqueId(), FAIL_WITH_ERROR, FAIL_WITH_ERROR_AND_RETURN, findOrCreateColorDefinition(), CCopasiNode< _Data >::getData(), CCopasiNode< _Data >::getNext(), mComplexDependencies, mIdMap, mIncludedSpeciesNameMap, UsualView::mLineWidth, UsualView::mPaint, mpLocalRenderInfo, mpModel, SpeciesAlias::mSpecies, mSpeciesAliases, mSpeciesAliasMap, mSpeciesAnnotationMap, and SpeciesAlias::mUView.
Referenced by convertCellDesignerLayout().
|
protected |
References createUniqueId(), findOrCreateColorDefinition(), isDefaultOrEmpty(), Line::mColor, mIdMap, mpLocalRenderInfo, and Line::mWidth.
Referenced by convertReactionAnnotation().
bool CCellDesignerImporter::createSubstrate | ( | std::vector< Point > & | reactantPoints, |
ReactionGlyph * | pRGlyph, | ||
LocalStyle * | pReactionStyle, | ||
ReactionAnnotation & | ranno | ||
) |
References createLineSegments(), createUniqueId(), ReactionAnnotation::mBaseReactants, mIdMap, setSpeciesGlyphId(), and setSpeciesReferenceId().
Referenced by createUniUniCurve().
|
protected |
This method creates a new local style based on the passed in SpeciesAlias object. The style is associated with the object via the given id. If Creating the style fails, false is returned. bool createSpeciesStyle(const SpeciesAlias& sa,const std::string& objectReference); Creates a local style for a certain text glyph. The style is associated with the text glyph via the id of the text glyph.
Referenced by convertCompartmentAnnotations(), and convertSpeciesAnnotations().
bool CCellDesignerImporter::createUniBiCurve | ( | ReactionAnnotation & | ranno, |
ReactionGlyph * | pRGlyph, | ||
LocalStyle * | pReactionStyle | ||
) |
creates a curve connecting one substrate to two products
ranno | the reaction annotation |
pRGlyph | the reaction glyph |
pReactionStyle | the style of the current reaction |
Looks for CellDesigner annotation in the given reaction and ries to convert the information in that annotation into a ReactionGlyph.
References checkLinkAnchor(), COULD_NOT_CREATE, createUniqueId(), distance(), FAIL_WITH_ERROR, getPositionPoint(), ReactionAnnotation::mBaseProducts, ReactionAnnotation::mBaseReactants, mCDBounds, ReactionAnnotation::mEditPoints, mIdMap, EditPoints::mOmittedShapeIndex, EditPoints::mPoints, EditPoints::mTShapeIndex, POSITION_UNDEFINED, setSpeciesGlyphId(), and setSpeciesReferenceId().
Referenced by convertReactionAnnotation().
|
protected |
Creates a unique id with the given prefix.
References mIdMap.
Referenced by convertCellDesignerLayout(), convertCompartmentAnnotations(), convertReactionAnnotation(), convertSpeciesAnnotations(), createBiUniCurve(), createCompartmentGlyph(), createProduct(), createSpeciesGlyph(), createSpeciesReferenceGlyphs(), createSpeciesStyles(), createStyleFromLine(), createSubstrate(), createUniBiCurve(), and setProductStyle().
bool CCellDesignerImporter::createUniUniCurve | ( | ReactionAnnotation & | ranno, |
ReactionGlyph * | pRGlyph, | ||
LocalStyle * | pReactionStyle | ||
) |
creates a curve connecting one substrate to one product
ranno | the reaction annotation |
pRGlyph | the reaction glyph |
pReactionStyle | the style of the current reaction |
References calculateAbsoluteValue(), checkLinkAnchors(), createOrthogonal(), createProduct(), createSubstrate(), distance(), enforceSquare(), FAIL_WITH_ERROR, getPositionPoint(), ReactionAnnotation::mBaseProducts, ReactionAnnotation::mBaseReactants, mCDBounds, ReactionAnnotation::mConnectScheme, ReactionAnnotation::mEditPoints, EditPoints::mPoints, ConnectScheme::mRectangleIndex, and POSITION_UNDEFINED.
Referenced by convertReactionAnnotation().
|
static |
Tries to find the version number of CellDesigner that was used to write this annotation. The node should be the CellDesigner annotation of the model. If the version number is not found or could not be parsed, we return -1.
Referenced by convertCellDesignerLayout().
|
staticprotected |
Converts the given direction string to the corresponding enum. If there is no enum that corresponds to the string, DIRECTION_UNDEFINED is returned.
References DIRECTION_HORIZONTAL, DIRECTION_UNDEFINED, DIRECTION_UNKNOWN, and DIRECTION_VERTICAL.
Referenced by parseLineDirection().
|
staticprotected |
Calculate the distance between the two points.
Referenced by createBiUniCurve(), createUniBiCurve(), and createUniUniCurve().
void CCellDesignerImporter::enforceSquare | ( | const ConnectScheme & | connectScheme, |
Point & | p, | ||
const Point & | pStart, | ||
const Point & | pEnd, | ||
int & | directionCount, | ||
bool | isLast, | ||
const std::vector< Point > & | points | ||
) |
References DIRECTION_HORIZONTAL, ConnectScheme::mLineDirections, ConnectScheme::mPolicy, and POLICY_SQUARE.
Referenced by createUniUniCurve().
|
static |
Goes through the SBMLDocument and tries to find a CellDesigner annotation. If one is found, a const pointer to the corresponding XMLNode is returned. If the current SBMLDocument is NULL or if no CellDesigner annotation is found, NULL is returned.
Goes through the SBMLDocument and tries to find a CellDesigner annotation. If one is found, a const pointer to the corresponding XMLNode is returned. If the current SBMLDocument is NULL or if no CellDesigner annotation is found, ULL is returned.
References findCellDesignerNamespace().
Referenced by convertCompartmentAnnotations(), convertReactionAnnotation(), convertSpeciesAnnotations(), and setSBMLDocument().
|
static |
This method searches for the CellDesigner namespace in the annotation to the model as well as the annotation to the document. The method returns a pair of bool and string. The bool determines if the namespace was found and the string specifies the prefix for the namespace.
Referenced by findCellDesignerAnnotation().
|
staticprotected |
Goes through the children of the given node which represents a list of protein definitions and collects the names for them. These names are converted to text glyphs for the proteins. Goes through the children of the given node which represents a list of protein definitions and collects the names for them. These names are converted to text glyphs for the proteins. Goes through the children of the given node which represents a list of protein definitions and collects the names for them. These names are converted to text glyphs for the proteins. Searches for a child with a certain name and a certain prefix in the tree based on pNode. The first child that fits the name and the prefix or NULL is returned. If recursive is true, the tree is searched recursively.
Searches for a child with a certain name and a certain prefix in the tree based on pNode. The first child that fits the name and the prefix or NULL is returned. If recursive is true, the tree is searched recursively.
Referenced by convertCellDesignerLayout(), parseCompartmentAnnotation(), parseConnectScheme(), parseExtraLink(), parseLinkTarget(), parseProteins(), parseReactionAnnotation(), parseReactionModification(), parseSpeciesAnnotation(), parseSpeciesIdentity(), and parseSpeciesState().
|
protected |
|
protected |
Check if a color with the given color string already exists. If so, the id of the color is set on the given id string. If the color does not exist yet, a color definition for it is created and the id of the newly created color is returned in the id string. If color creation fails, false is returned by the method.
Referenced by createSpeciesStyles(), and createStyleFromLine().
|
protected |
Tries to find the name for the given species identity. If the name was found, it is returned in the name argument. If something goes wrong, false is returned. Goes through the dependency graph and tries to find the root element for the given species alias id.
Referenced by createSpeciesReferenceGlyphs().
|
staticprotected |
Finds the shortest connection between the given point and the object which is defined by its connection positions and its bounding box. If the method fails, e.g. because one of the vectors is empty or the bounding box contains values we can't use for calculations (inf,NAN), POSITION_UNDEFINED
|
staticprotected |
Finds the shortest connection between two objects given the potential connection positions for each object and the bounding boxes for each object. The result is returned in the original vectors as position values. If the method fails, e.g. because one of the vectors is empty or the bounding box contains values we can't use for calculations (inf,NAN), false is returned.
|
protected |
Returns the color string for the given color id or an empty string if the color id was not found.
const Layout * CCellDesignerImporter::getLayout | ( | ) | const |
Method to return the layout object. Since the layout object is owned by the importer, the caller should make a copy of the layout.
References mpLayout.
|
staticprotected |
Takes a bounding box and a position string and returns the position on the bounding box that corresponds to the given position.
Takes a bounding box and a position string and retirns the position on the bounding box that corresponds to the given position.
References POSITION_E, POSITION_ENE, POSITION_ESE, POSITION_N, POSITION_NE, POSITION_NNE, POSITION_NNW, POSITION_NW, POSITION_S, POSITION_SE, POSITION_SSE, POSITION_SSW, POSITION_SW, POSITION_W, POSITION_WNW, and POSITION_WSW.
Referenced by createBiUniCurve(), createSpeciesReferenceGlyphs(), createUniBiCurve(), and createUniUniCurve().
const SBMLDocument * CCellDesignerImporter::getSBMLDocument | ( | ) | const |
Method to return a const pointer to the SBMLDocument.
References mpDocument.
|
protected |
Creates the structures for the extra product links. If processing fails, false is returned;
Referenced by convertReactionAnnotation().
|
protected |
Tries to parse the CellDesigner species in the listOfincludedSpecies. If parsing fails, false is returned.
Referenced by convertCellDesignerLayout().
|
protected |
Creates the structures for the modification links in a reaction. If processing fails, false is returned;
Referenced by convertReactionAnnotation().
|
staticprotected |
References Line::mColor, and Line::mWidth.
Referenced by createStyleFromLine().
|
staticprotected |
Converts the given modification link type string to the corresponding enum. If there is no enum that corresponds to the string, UNDEFINED_ML_TYPE is returned.
References BOOLEAN_LOGIC_GATE_AND_ML_TYPE, BOOLEAN_LOGIC_GATE_NOT_ML_TYPE, BOOLEAN_LOGIC_GATE_OR_ML_TYPE, BOOLEAN_LOGIC_GATE_UNKNOWN_ML_TYPE, CATALYSIS_ML_TYPE, FAIL_WITH_ERROR, HETERODIMER_ASSOCIATION_ML_TYPE, INHIBITION_ML_TYPE, MODULATION_ML_TYPE, PHYSICAL_STIMULATION_ML_TYPE, TRANSCRIPTIONAL_ACTIVATION_ML_TYPE, TRANSCRIPTIONAL_INHIBITION_ML_TYPE, TRANSLATIONAL_ACTIVATION_ML_TYPE, TRANSLATIONAL_INHIBITION_ML_TYPE, TRANSPORT_ML_TYPE, TRIGGER_ML_TYPE, UNDEFINED_ML_TYPE, UNKNOWN_CATALYSIS_ML_TYPE, and UNKNOWN_INHIBITION_ML_TYPE.
Referenced by parseReactionModification().
|
staticprotected |
Converts the given modification type string to the corresponding enum. If there is no enum that corresponds to the string, UNDEFINED_MTYPE is returned.
References CATALYSIS_MTYPE, FAIL_WITH_ERROR, HETERODIMER_ASSOCIATION_MTYPE, INHIBITION_MTYPE, MODULATION_MTYPE, PHYSICAL_STIMULATION_MTYPE, TRANSCRIPTIONAL_ACTIVATION_MTYPE, TRANSCRIPTIONAL_INHIBITION_MTYPE, TRANSLATIONAL_ACTIVATION_MTYPE, TRANSLATIONAL_INHIBITION_MTYPE, TRANSPORT_MTYPE, UNDEFINED_MTYPE, UNKNOWN_CATALYSIS_MTYPE, and UNKNOWN_INHIBITION_MTYPE.
Referenced by parseReactionModification().
|
staticprotected |
Converts the given paint scheme string to the corresponding PAINT_SCHEME enum value. If no enum is found, PAINT_UNDEFINED is returned.
References PAINT_COLOR, PAINT_GRADIENT, and PAINT_UNDEFINED.
|
staticprotected |
Parse the data in the given node assuming that this is a node that represents a point and therefore contains an "x" and a "y" attribute. The data is stored in the given point object. If parsing fails, false is returned.
|
staticprotected |
Parses the given node and stored the information in the width and height attribute in the given dimensions object. If parsinf fails, false is returned.
|
staticprotected |
Parses the data in the given node which represents a compartment alias and stores it in the given CompartmentAlias structure. If parsing fails, false is returned.
Referenced by createCompartmentGlyphs().
|
staticprotected |
Tries to parse the compartment annotation in the given node and stores the data in the given CompartmentAnnotation structure. If parsing fails, false is returned.
References findChildNode(), and CompartmentAnnotation::mName.
Referenced by convertCompartmentAnnotations().
|
staticprotected |
Tries to parse the connection scheme in the given node and stores the data in the given ConnectionScheme structure. If parsing fails, false is returned.
References connectionPolicyToEnum(), FAIL_WITH_ERROR, findChildNode(), ConnectScheme::mLineDirections, ConnectScheme::mPolicy, ConnectScheme::mRectangleIndex, parseLineDirection(), and POLICY_UNDEFINED.
Referenced by parseReactionAnnotation(), and parseReactionModification().
|
staticprotected |
Parses the given XMLNode which represents a double line element. The parsed data is stored in the given DoubleLine structure. If parsing fails, false is returned.
|
staticprotected |
Tries to parse the edit points in the given node and stores the data in the given vector of Points. If parsing fails, false is returned.
References FAIL_WITH_ERROR, EditPoints::mNum0, EditPoints::mNum1, EditPoints::mNum2, EditPoints::mOmittedShapeIndex, EditPoints::mPoints, EditPoints::mTShapeIndex, and parsePointsString().
Referenced by parseReactionAnnotation().
|
staticprotected |
Tries to parse the reactant link in the given node and stores the data in the given vector of ReactionLink structure. If parsing fails, false is returned.
Tries to parse the wreactant link in the given node and stores the data in the given vector of ReactionLink structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, findChildNode(), ReactantLink::mAlias, ReactantLink::mLine, ReactantLink::mPosition, ReactantLink::mReactant, ReactantLink::mTargetLineIndex, parseLine(), POSITION_UNDEFINED, positionToEnum(), and splitString().
Referenced by parseExtraLinks().
|
staticprotected |
Tries to parse the extra reactant links in the given node and stores the data in the given vector of ReactantLinks structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, and parseExtraLink().
Referenced by parseReactionAnnotation().
|
staticprotected |
Tries to parse the line data in the given node and stores the data in the given Line structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, Line::mColor, Line::mCurve, and Line::mWidth.
Referenced by parseExtraLink(), parseReactionAnnotation(), and parseReactionModification().
|
staticprotected |
Tries to parse the line direction in the given node and stores the data in the given vector of LineDirection structure. If parsing fails, false is returned.
References DIRECTION_UNDEFINED, directionToEnum(), FAIL_WITH_ERROR, LineDirection::mArm, LineDirection::mIndex, and LineDirection::mValue.
Referenced by parseConnectScheme().
|
staticprotected |
Tries to parse the link target in the given node and stores the data in the given vector of LinkTarget structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, findChildNode(), LinkTarget::mAlias, LinkTarget::mPosition, LinkTarget::mSpecies, POSITION_UNDEFINED, and positionToEnum().
Referenced by parseReactionElements(), and parseReactionModification().
|
staticprotected |
Parses the modelDisplay data in the given XMLNode and stores the result in the given Dimensions structure. If parsing fails, false is returned.
Referenced by convertCellDesignerLayout().
|
staticprotected |
Parses the paint data in the given XMLNode and stores the result in the given Paint structure. If parsing fails, false is returned.
|
staticprotected |
Parse the data in the given node assuming that this is a node that represents a point and therefore contains an "x" and a "y" attribute. The data is stored in the given point object. If parsing fails, false is returned.
|
staticprotected |
Tries to parse the w2D points in the given string and stores the data in the given vector of Points. If parsing fails, false is returned.
Referenced by parseEditPoints(), and parseReactionModification().
|
staticprotected |
Tries to parse the protein modification in the given node and stores the data in the given ProteinModification structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, ProteinModification::mAngle, ProteinModification::mId, and ProteinModification::mName.
Referenced by parseProteins().
|
protected |
Goes through the children of the given node which represents a list of protein definitions and check the types. If the type is RECEPTOR, ION_CHANNEL or TRUNCATED, store that information.
Goes through the children of the given node which represents a list of protein definitions and collects the names for them. These names are converted to text glyphs for the proteins. bool CCellDesignerImporter::parseGeneNames(const XMLNode* pNode) { bool result=true; if(pNode != NULL && pNode->getName() == "listOfGenes") { std::string prefix=pNode->getPrefix(); unsigned int i,iMax=pNode->getNumChildren(); const XMLNode* pChild=NULL; for(i=0;i<iMax;++i) { pChild=&pNode->getChild(i); if(pChild != NULL && pChild->getPrefix() == prefix && pChild->getName() == "gene" && pChild->getAttributes().hasAttribute("id") && pChild->getAttributes().hasAttribute("name")) { std::string id=pChild->getAttributes().getValue("id"); assert(!id.empty()); std::string name=pChild->getAttributes().getValue("name"); assert(!name.empty()); this->mGeneNameMap.insert(std::pair<std::string,std::string>(id,name)); } } } return result; } Goes through the children of the given node which represents a list of protein definitions and collects the names for them. These names are converted to text glyphs for the proteins. bool CCellDesignerImporter::parseRNANames(const XMLNode* pNode) { bool result=true; if(pNode != NULL && pNode->getName() == "listOfRNAs") { std::string prefix=pNode->getPrefix(); unsigned int i,iMax=pNode->getNumChildren(); const XMLNode* pChild=NULL; for(i=0;i<iMax;++i) { pChild=&pNode->getChild(i); if(pChild != NULL && pChild->getPrefix() == prefix && pChild->getName() == "RNA" && pChild->getAttributes().hasAttribute("id") && pChild->getAttributes().hasAttribute("name")) { std::string id=pChild->getAttributes().getValue("id"); assert(!id.empty()); std::string name=pChild->getAttributes().getValue("name"); assert(!name.empty()); this->mRNANameMap.insert(std::pair<std::string,std::string>(id,name)); } } } return result; } Goes through the children of the given node which represents a list of protein definitions and collects the names for them. These names are converted to text glyphs for the proteins. bool CCellDesignerImporter::parseASRNANames(const XMLNode* pNode) { bool result=true; if(pNode != NULL && pNode->getName() == "listOfAntisenseRNAs") { std::string prefix=pNode->getPrefix(); unsigned int i,iMax=pNode->getNumChildren(); const XMLNode* pChild=NULL; for(i=0;i<iMax;++i) { pChild=&pNode->getChild(i); if(pChild != NULL && pChild->getPrefix() == prefix && pChild->getName() == "AntisenseRNA" && pChild->getAttributes().hasAttribute("id") && pChild->getAttributes().hasAttribute("name")) { std::string id=pChild->getAttributes().getValue("id"); assert(!id.empty()); std::string name=pChild->getAttributes().getValue("name"); assert(!name.empty()); this->mASRNANameMap.insert(std::pair<std::string,std::string>(id,name)); } } } return result; } Goes through the children of the given node which represents a list of protein definitions and check the types. If the type is RECEPTOR, ION_CHANNEL or TRUNCATED, store that information.
References classToEnum(), FAIL_WITH_ERROR, findChildNode(), Protein::mId, Protein::mModifications, Protein::mName, mProteinInformationMap, Protein::mType, parseProteinModification(), and UNDEFINED_CLASS.
Referenced by convertCellDesignerLayout().
|
staticprotected |
Tries to parse the reaction annotation in the given node and stores the data in the given ReactionAnnotation structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, FAIL_WITH_ERROR_AND_RETURN, findChildNode(), ReactionAnnotation::mBaseProducts, ReactionAnnotation::mBaseReactants, ReactionAnnotation::mConnectScheme, ReactionAnnotation::mEditPoints, ReactionAnnotation::mLine, ReactionAnnotation::mModifications, ReactionAnnotation::mName, ReactionAnnotation::mOffset, ReactionAnnotation::mProductLinks, ReactionAnnotation::mReactantLinks, ReactionAnnotation::mType, parseConnectScheme(), parseEditPoints(), parseExtraLinks(), parseLine(), parseReactionElements(), parseReactionModifications(), and reactionTypeToEnum().
Referenced by convertReactionAnnotation().
|
staticprotected |
Tries to parse the reaction elements (baseReactants or baseProducts) in the given node and stores the data in the given ReactionAnnotation structure. If parsing fails, false is returned.
Tries to parse the reaction elements (baseReamctants or baseProducts) in the given node and stores the data in the given ReactionAnnotation structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, and parseLinkTarget().
Referenced by parseReactionAnnotation().
|
staticprotected |
Tries to parse the reaction modification in the given node and stores the data in the given ReactionModification structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, findChildNode(), ReactionModification::mAliases, ReactionModification::mConnectScheme, ReactionModification::mEditPoints, ReactionModification::mLine, ReactionModification::mLinkTargets, ReactionModification::mModifiers, ReactionModification::mModType, ReactionModification::mNum0, ReactionModification::mNum1, ReactionModification::mNum2, modificationLinkTypeToEnum(), modificationTypeToEnum(), ReactionModification::mOffset, EditPoints::mPoints, ReactionModification::mTargetLineIndex, ReactionModification::mType, parseConnectScheme(), parseLine(), parseLinkTarget(), parsePointsString(), splitString(), UNDEFINED_ML_TYPE, and UNDEFINED_MTYPE.
Referenced by parseReactionModifications().
|
staticprotected |
Tries to parse the reaction modifications in the given node and stores the data in the given vector of ReactionModifications. If parsing fails, false is returned.
References FAIL_WITH_ERROR, and parseReactionModification().
Referenced by parseReactionAnnotation().
|
staticprotected |
Parses the data in the given node which represents a species (or ComplexSpecies) alias and stores it in the given SpeciesAlias structure. If parsing fails, false is returned.
Referenced by createSpeciesGlyphs().
|
staticprotected |
Tries to parse the species annotation in the given node and stores the data in the given SpeciesAnnotation structure. If parsing fails, false is returned.
References FAIL_WITH_ERROR, findChildNode(), SpeciesAnnotation::mIdentity, and parseSpeciesIdentity().
Referenced by convertSpeciesAnnotations().
|
staticprotected |
Parses the node which represents a speciesIdentity node and fills the given SpeciesIdentity structure with the data. If the parsing fails, false is returned.
Parses the node which represents a speciesIdentity node and fills the given SpeciesIdentity structure with the data. If the parsinf fails, false is returned.
References classToEnum(), COMPLEX_CLASS, FAIL_WITH_ERROR, findChildNode(), ION_CLASS, SpeciesIdentity::mHypothetical, SpeciesIdentity::mNameOrReference, SpeciesIdentity::mSpeciesClass, SpeciesIdentity::mState, parseSpeciesState(), PROTEIN_CLASS, and SIMPLE_MOLECULE_CLASS.
Referenced by parseSpeciesAnnotation().
|
staticprotected |
Parses the node which represents a modification ion a species node and fills the given SpeciesModification structure with the data. If the parsing fails, false is returned.
References FAIL_WITH_ERROR, SpeciesModification::mResidue, SpeciesModification::mType, speciesModificationTypeToEnum(), and UNDEFINED_MOD_TYPE.
Referenced by parseSpeciesState().
|
staticprotected |
Parses the node which represents the state in a speciesIdentity node and fills the given SpeciesState structure with the data. If the parsing fails, false is returned.
References FAIL_WITH_ERROR, findChildNode(), SpeciesState::mModifications, and parseSpeciesModification().
Referenced by parseSpeciesIdentity().
|
staticprotected |
|
staticprotected |
Converts the given position to compartment string to the corresponding enum. If there is no enum that corresponds to the string, UNDEFINED_POSITION is returned.
References INNER_SURFACE, INSIDE, INSIDE_MEMBRANE, OUTER_SURFACE, TRANSMEMBRANE, and UNDEFINED_POSITION.
|
staticprotected |
Converts the given position string to an enum.
References POSITION_E, POSITION_ENE, POSITION_ESE, POSITION_N, POSITION_NE, POSITION_NNE, POSITION_NNW, POSITION_NW, POSITION_S, POSITION_SE, POSITION_SSE, POSITION_SSW, POSITION_SW, POSITION_UNDEFINED, POSITION_W, POSITION_WNW, and POSITION_WSW.
Referenced by parseExtraLink(), and parseLinkTarget().
|
staticprotected |
Converts the given reaction type string to the corresponding enum. If there is no enum that corresponds to the string, UNDEFINED_RTYPE is returned.
References CATALYSIS_RTYPE, DISSOCIATION_RTYPE, FAIL_WITH_ERROR, HETERODIMER_ASSOCIATION_RTYPE, INHIBITION_RTYPE, KNOWN_TRANSITION_OMITTED_RTYPE, STATE_TRANSITION_RTYPE, TRANSCRIPTION_RTYPE, TRANSCRIPTIONAL_ACTIVATION_RTYPE, TRANSCRIPTIONAL_INHIBITION_RTYPE, TRANSLATION_RTYPE, TRANSLATIONAL_ACTIVATION_RTYPE, TRANSLATIONAL_INHIBITION_RTYPE, TRANSPORT_RTYPE, TRUNCATION_RTYPE, UNDEFINED_RTYPE, UNKNOWN_CATALYSIS_RTYPE, UNKNOWN_INHIBITION_RTYPE, and UNKNOWN_TRANSITION_RTYPE.
Referenced by parseReactionAnnotation().
void CCellDesignerImporter::removeCurrentLayout | ( | ) |
removes the current layout
References mpDocument, mpLayout, and mpModel.
Referenced by convertCellDesignerLayout(), and setSBMLDocument().
|
staticprotected |
|
staticprotected |
Calculates the position of point p after rotation by angle a around the origin. The angle is given in radians. The result is returned in r.
Referenced by createProteinModification().
void CCellDesignerImporter::setProductStyle | ( | const std::string & | id, |
LocalStyle * | pReactionStyle | ||
) |
References createUniqueId(), max, and mpLocalRenderInfo.
Referenced by createProduct().
void CCellDesignerImporter::setSBMLDocument | ( | SBMLDocument * | pDocument | ) |
Method to set the SBMLDocument. If the pointer is not NULL, the class will try to directly convert the CellDesigner layout if there is one.
References convertCellDesignerLayout(), findCellDesignerAnnotation(), mpDocument, mpModel, and removeCurrentLayout().
Referenced by CCellDesignerImporter().
|
protected |
Tries to set the species glyph id in the given species reference glyph.
Referenced by createBiUniCurve(), createProduct(), createSubstrate(), and createUniBiCurve().
|
protected |
Tries to set the species reference id on the given SPeciesReferenceGlyph.
Referenced by createBiUniCurve(), createProduct(), createSubstrate(), and createUniBiCurve().
|
staticprotected |
Referenced by parseSpeciesModification().
|
staticprotected |
Splits the given string at each character occurs in splitChars. The parts generated are stored in the given vector. The vector is cleared by the method. If something goes wrong false is returned.
Referenced by parseExtraLink(), and parseReactionModification().
|
protected |
|
protected |
|
protected |
Referenced by convertCellDesignerLayout().
|
protected |
Referenced by convertCellDesignerLayout(), convertCompartmentAnnotations(), and createCompartmentGlyph().
|
protected |
a map that stores the compartment annotation with each compartment.
Referenced by convertCellDesignerLayout(), and convertCompartmentAnnotations().
|
protected |
Referenced by convertCellDesignerLayout(), convertCompartmentAnnotations(), and createCompartmentGlyph().
|
protected |
Referenced by addDependency(), convertCellDesignerLayout(), and createSpeciesStyles().
|
protected |
the font to be used for text glyphs
Referenced by createPrimitive(), and createProteinModification().
|
protected |
Referenced by convertCellDesignerLayout(), convertCompartmentAnnotations(), convertReactionAnnotation(), convertSpeciesAnnotations(), createBiUniCurve(), createCompartmentGlyph(), createProduct(), createSpeciesGlyph(), createSpeciesReferenceGlyphs(), createSpeciesStyles(), createStyleFromLine(), createSubstrate(), createUniBiCurve(), and createUniqueId().
|
protected |
a map that stores the name of a CellDesigner species with its id.
Referenced by createSpeciesStyles().
|
protected |
|
protected |
a map that associated a modifier type with the corresponding style.
|
protected |
|
protected |
|
protected |
Referenced by convertCellDesignerLayout(), createSpeciesStyles(), createStyleFromLine(), and setProductStyle().
|
protected |
|
protected |
Referenced by convertCellDesignerLayout(), createPrimitive(), and parseProteins().
|
protected |
a map that associates the parsed alias data with the id of the species alias or complex species alias
Referenced by convertCellDesignerLayout(), createSpeciesGlyph(), and createSpeciesStyles().
|
protected |
Referenced by convertCellDesignerLayout(), convertSpeciesAnnotations(), createSpeciesGlyph(), and createSpeciesStyles().
|
protected |
a map that stores the species annotation with each species.
Referenced by convertCellDesignerLayout(), convertSpeciesAnnotations(), and createSpeciesStyles().