Package org.pathvisio.libgpml.model

Class GPML2013aReader

java.lang.Object

org.pathvisio.libgpml.model.GPMLFormatAbstract

org.pathvisio.libgpml.model.GPML2013aFormatAbstract

org.pathvisio.libgpml.model.GPML2013aReader

All Implemented Interfaces:

GPMLFormatReader, GPMLFormatVersion

public class GPML2013aReader
extends GPML2013aFormatAbstract
implements GPMLFormatReader

This class reads a PathwayModel from an input source (GPML 2013a).

NB:

1. In GPML2013a, there are two kinds of gpml:Biopax Element bp:openControlledVocabulary and bp:PublicationXref which correspond to Annotation and Citation respectively.
2. gpml:CommentGroup:Biopax holds references to bp:PublicationXref rdf:id.
3. All openControlledVocabulary belong to the pathway in GPML2013a.

Author:

finterly

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	GPML2013aReader.PublicationXref	Local class to help with reading gpml:Biopax:bp:PublicationXref.

Nested classes/interfaces inherited from class org.pathvisio.libgpml.model.GPML2013aFormatAbstract

GPML2013aFormatAbstract.AttributeInfo

Field Summary

Fields

Modifier and Type	Field	Description
static GPML2013aReader	GPML2013aREADER

Fields inherited from class org.pathvisio.libgpml.model.GPML2013aFormatAbstract

BINDING_LIST, BIOPAX_NAMESPACE, CATALYSIS_LIST, CELL_CMPNT_KEY, CELL_CMPNT_MAP, CONVERSION_LIST, DEPRECATED_MAP, DIRECTED_LIST, DIRECTION, DOUBLE_LINE_KEY, GPML2013A_KEY_SET, IA_PANEL_MAP, INFOBOX_CENTER_X, INFOBOX_CENTER_Y, INHIBITION_LIST, LEGEND_CENTER_X, LEGEND_CENTER_Y, OCV_ONTOLOGY_MAP, OWL_NAMESPACE, PARENT, PARENTID, PARENTID_DB, PARENTSYMBOL, PARENTSYMBOL_DB, PATHWAY_AUTHOR, PATHWAY_EMAIL, PATHWAY_LASTMODIFIED, PATHWAY_MAINTAINER, POSITION, PTM, RDF_NAMESPACE, RDF_STRING, RDFS_NAMESPACE, SHAPETYPE_TO_CAMELCASE, SITE, SITEGRPID, SITEGRPID_DB, STATE_DIRECTION_MAP, STATE_PTM_MAP, STATE_REF_LIST, STATE_ROTATION, STIMULATION_LIST, TRANSCRIPTION_TRANSLATION_LIST, TRANSLOCATION_LIST, UNDIRECTED_LIST, WP_DESCRIPTION

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	GPML2013aReader(java.lang.String xsdFile, org.jdom2.Namespace nsGPML)	readFromRoot(org.pathvisio.libgpml.model.PathwayModel, org.jdom2.Element)

Method Summary

Modifier and Type	Method	Description
protected void	convertStateCommentToRefs(DataNode.State state, java.util.Set<java.lang.String> elementIdSet)	This method is used to handle DataNode.State PathwayElement.Comment which were manually added to encode phosphosite information.
protected void	readAllElementIds(org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet)	Reads elementIds (GraphIds in GPML2013a) of root element and adds to elementIdSet.
protected void	readAnchors(LineElement lineElement, org.jdom2.Element gfx, java.util.Set<java.lang.String> elementIdSet)	Reads anchor LineElement.Anchor information for line element from element.
protected ArrowHeadType	readArrowHeadType(org.jdom2.Element pt, java.lang.String base)	Returns the arrowHead for give jdom point element.
protected void	readCommentGroup(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads comment group (comment, biopaxref/citationRef, dynamic property) for pathway element from jdom element.
protected void	readComments(PathwayElement pathwayElement, org.jdom2.Element e)	Reads comment PathwayElement.Comment information for pathway element from jdom element.
protected void	readDataNodes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads data node DataNode information for pathway model from root element.
protected void	readDynamicProperties(PathwayElement pathwayElement, org.jdom2.Element root)	Reads gpml:Attribute or dynamic property information for PathwayElement from jdom element.
protected java.lang.String	readElementId(java.lang.String tag, org.jdom2.Element e, java.util.Set<java.lang.String> elementIdSet)	Returns elementId read for given Element.
protected void	readFontProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads font property information.
void	readFromRoot(PathwayModel pathwayModel, org.jdom2.Element root)	Reads information from root element of Jdom document Document to the pathway model PathwayModel.
protected void	readGraphicalLines(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads graphical line GraphicalLine information for pathway model from root element.
protected void	readGroupGroupRef(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads groupRef property ShapedElement.setGroupRef(org.pathvisio.libgpml.model.Group) information of group pathway element.
protected void	readGroupRef(ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads and sets groupRef for given (shaped) pathway element and jdom Element.
protected void	readGroups(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<java.lang.String,Group> graphIdToGroup)	Reads group Group information for pathway model from root element.
protected void	readInfoBox(Pathway pathway, org.jdom2.Element root)	Reads the infobox x and y coordinate information.
protected void	readInteractions(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads interaction Interaction information for pathway model from root element.
protected void	readLabels(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads label Label information for pathway model from root element.
protected void	readLegend(Pathway pathway, org.jdom2.Element root)	Reads the Legend CenterX and CenterY to pathway dynamic properties PathwayElement.setDynamicProperty(java.lang.String, java.lang.String) .
protected void	readLineElement(LineElement lineElement, org.jdom2.Element ln, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads line element LineElement information for interaction or graphical line from jdom element.
protected void	readLineStyleProperty(LineElement lineElement, org.jdom2.Element gfx)	Reads line style property information.
protected void	readOpenControlledVocabulary(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet)	Reads gpml:Biopax bp:OpenControlledVocabulary information to Annotation for pathway model from root element.
protected Pathway	readPathway(Pathway pathway, org.jdom2.Element root)	Reads pathway information from root element.
protected void	readPointElementRefs(PathwayModel pathwayModel, java.util.Map<java.lang.String,Group> graphIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads LineElement.LinePoint elementRefs.
protected void	readPoints(LineElement lineElement, org.jdom2.Element ln, java.util.Set<java.lang.String> elementIdSet, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads points LineElement.LinePoint for pathway model line pathway elements.
protected java.lang.String	readPublicationXrefInfo(java.util.List<org.jdom2.Element> pubxfElements)	Reads Biopax PublicationXref information from PublicationXref children elements.
protected void	readPublicationXrefMap(org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads gpml:Biopax:bp:PublicationXref and maps "id" to GPML2013aReader.PublicationXref in idToPublicationXref.
protected void	readPublicationXrefs(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads gpml:Biopax:bp:PublicationXref and BiopaxRef information for pathway element from jdom element.
protected void	readRectProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads rect property information.
protected void	readShapedElement(ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads shaped pathway element ShapedElement information: graphics and comment group (comments, biopaxRefs (equivalent to citationRefs), and dynamic properties).
protected void	readShapes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads shape Shape information for pathway model from root element.
protected void	readShapeStyleProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads shape style property information.
protected void	readStates(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads state DataNode.State information for pathway model from root element.
protected org.bridgedb.Xref	readXref(org.jdom2.Element e)	Reads xref Xref information from element.
protected void	setGroupGraphicsProperty(Group group, GroupType type)	Reads and sets graphics properties for Group.

Methods inherited from class org.pathvisio.libgpml.model.GPML2013aFormatAbstract

fromCamelCase, getArrowHeadTypeStr, getAttr, getAttributeInfo, getInteractionPanelType, setAttr, toCamelCase

Methods inherited from class org.pathvisio.libgpml.model.GPMLFormatAbstract

getGpmlNamespace, getSchemaFile, refreshLineElements, updateGroups, validateDocument

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.pathvisio.libgpml.model.GPMLFormatVersion

getGpmlNamespace, getSchemaFile, validateDocument

Field Details

GPML2013aREADER

public static final GPML2013aReader GPML2013aREADER

Constructor Details

GPML2013aReader

protected GPML2013aReader(java.lang.String xsdFile,
org.jdom2.Namespace nsGPML)

readFromRoot(org.pathvisio.libgpml.model.PathwayModel, org.jdom2.Element)

Method Details

readFromRoot

public void readFromRoot(PathwayModel pathwayModel,
org.jdom2.Element root)
                  throws ConverterException

Reads information from root element of Jdom document Document to the pathway model PathwayModel. Referenced objects or pathway elements are read first. For example, Groups are read before other pathway element. DataNodes are read before States. And Points are read last.

NB: In GPML2013a, GraphIds (elementIds) are missing for some pathway elements, or may conflict with Biopax rdf:id or GroupId

1. elementIdSet: stores all ids for a reading session to ensure unique elementIds, readAllElementIds(org.jdom2.Element, java.util.Set<java.lang.String>)
2. idToPublicationXref: stores Biopax:PublicationXref id and element information, readPublicationXrefMap(org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>)
3. groupIdToNew: stores GroupId and newly assigned elementIds, readGroups(org.pathvisio.libgpml.model.PathwayModel, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.Group>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.Group>)
4. lineList: stores line elementIds in the order read, readGraphicalLines(org.pathvisio.libgpml.model.PathwayModel, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.Group>, java.util.Map<org.jdom2.Element, org.pathvisio.libgpml.model.LineElement.LinePoint>), readInteractions(org.pathvisio.libgpml.model.PathwayModel, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.Group>, java.util.Map<org.jdom2.Element, org.pathvisio.libgpml.model.LineElement.LinePoint>), readPoints(org.pathvisio.libgpml.model.LineElement, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<org.jdom2.Element, org.pathvisio.libgpml.model.LineElement.LinePoint>).

Specified by:

readFromRoot in interface GPMLFormatReader

Parameters:

pathwayModel - the given pathway model.

root - the root element of given Jdom document.

Throws:

ConverterException

readAllElementIds

protected void readAllElementIds(org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet)

Reads elementIds (GraphIds in GPML2013a) of root element and adds to elementIdSet. In GPML2013a, elementId (previously named GraphId) is sometimes missing. In order to assign unique new elementIds, we must first read all elementIds from the Jdom document to store in elementIdSet.

Parameters:

root - the root element.

elementIdSet - the set of all elementIds.

readPathway

protected Pathway readPathway(Pathway pathway,
org.jdom2.Element root)
                       throws ConverterException

Reads pathway information from root element. Instantiates and returns the pathway object Pathway.

Parameters:

root - the root element.

Returns:

pathway the pathway object.

Throws:

ConverterException

readInfoBox

protected void readInfoBox(Pathway pathway,
org.jdom2.Element root)

Reads the infobox x and y coordinate information. NB: Infobox is removed in GPML2021, as the info box is always located in the top left corner (0,0).

Parameters:

pathway - the pathway.

root - the root element.

readLegend

protected void readLegend(Pathway pathway,
org.jdom2.Element root)

Reads the Legend CenterX and CenterY to pathway dynamic properties PathwayElement.setDynamicProperty(java.lang.String, java.lang.String) .

Parameters:

pathway - the pathway.

root - the root element.

readOpenControlledVocabulary

protected void readOpenControlledVocabulary(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet)
                                     throws ConverterException

Reads gpml:Biopax bp:OpenControlledVocabulary information to Annotation for pathway model from root element. NB:

• In GPML2013a, all annotations are by default added to Pathway using PathwayElement.AnnotationRef.
• New unique elementIds are assigned (missing in GPML2013a).

Parameters:

pathwayModel - the pathway model.

root - the jdom root element.

elementIdSet - the set of all elementIds.

Throws:

ConverterException

readPublicationXrefMap

protected void readPublicationXrefMap(org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)
                               throws ConverterException

Reads gpml:Biopax:bp:PublicationXref and maps "id" to GPML2013aReader.PublicationXref in idToPublicationXref. PublicationXref stores jdom Element information. NB: If biopax "id" is not unique, a new unique elementId (value) is assigned, added to elementIdSet.

Parameters:

root - the jdom root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

Throws:

ConverterException

readPublicationXrefs

protected void readPublicationXrefs(PathwayElement pathwayElement,
org.jdom2.Element e,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)
                             throws ConverterException

Reads gpml:Biopax:bp:PublicationXref and BiopaxRef information for pathway element from jdom element. Creates and adds PathwayElement.CitationRef and Citation.

NB:

1. gpml:CommentGroup:BiopaxRef PathwayElement.CitationRef holds reference to gpml:Biopax:PublicationXref Citation.
2. BiopaxRef was an attribute (not the element) of many of the pathway elements in the GPML2013a schema, but was never used/implemented.
3. Biopax PublicationXref which do not have a BiopaxRef will not be read.

Parameters:

pathwayElement - the element info pathway element object.

e - the jdom element.

idToPublicationXref - the map of id to biopax jdom element.

Throws:

ConverterException

readPublicationXrefInfo

protected java.lang.String readPublicationXrefInfo(java.util.List<org.jdom2.Element> pubxfElements)
                                            throws ConverterException

Reads Biopax PublicationXref information from PublicationXref children elements. In GPML2013a there are some duplicated and/or empty gpml:Biopax PublicationXref information. This method reads the list of child elements until a valid value is obtained.

Parameters:

pubxfElements - the pubxf children elements with the same local name.

Returns:

elementText the string text value for the element.

Throws:

ConverterException

readCommentGroup

protected void readCommentGroup(PathwayElement pathwayElement,
org.jdom2.Element e,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)
                         throws ConverterException

Reads comment group (comment, biopaxref/citationRef, dynamic property) for pathway element from jdom element.

NB about CommentGroup:

1. In GPML2013a, gpml:CommentGroup:PublicationXref was not implemented.
2. The element gpml:CommentGroup:BiopaxRef acts as PathwayElement.CitationRef and holds the reference to to gpml:Biopax:PublicationXref equivalent to Citation.
3. In GPML2021, Evidence and EvidenceRef was added.
4. BiopaxRef was an attribute (not the element) of many of the pathway elements in the GPML2013a schema, but was never used/implemented.

Parameters:

pathwayElement - the pathway element.

e - the jdom element.

Throws:

ConverterException

readShapedElement

protected void readShapedElement(ShapedElement shapedElement,
org.jdom2.Element se,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)
                          throws ConverterException

Reads shaped pathway element ShapedElement information: graphics and comment group (comments, biopaxRefs (equivalent to citationRefs), and dynamic properties). NB: readGroups(org.pathvisio.libgpml.model.PathwayModel, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.Group>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.Group>) does not call this method and instead calls readCommentGroup(org.pathvisio.libgpml.model.PathwayElement, org.jdom2.Element, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>). In GPML2013a, Group graphics properties were hard coded and were not written to the gpml.

Parameters:

shapedElement - the shaped pathway element.

se - the jdom element.

idToPublicationXref - the map of id to biopax jdom element.

Throws:

ConverterException

readComments

protected void readComments(PathwayElement pathwayElement,
org.jdom2.Element e)
                     throws ConverterException

Reads comment PathwayElement.Comment information for pathway element from jdom element. NB: If pathway element is Pathway and source is WikiPathways-description, set comment as pathway description instead!

Parameters:

pathwayElement - the pathway element.

e - the jdom element.

Throws:

ConverterException

readDynamicProperties

protected void readDynamicProperties(PathwayElement pathwayElement,
org.jdom2.Element root)
                              throws ConverterException

Reads gpml:Attribute or dynamic property information for PathwayElement from jdom element.

NB:

1. For ShapedElement, if dynamic property codes for DoubleLineProperty or CellularComponentProperty, updates/overrides borderStyle or shapeType. Otherwise, sets dynamic property.
2. For LineElement, if dynamic property codes for DoubleLineProperty, updates lineStyle. Otherwise, sets dynamic property.

NB: Property (dynamic property) was named Attribute in GPML2013a.

Parameters:

pathwayElement - the pathway element.

root - the jdom root element.

Throws:

ConverterException

readGroups

protected void readGroups(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref,
java.util.Map<java.lang.String,Group> groupIdToGroup,
java.util.Map<java.lang.String,Group> graphIdToGroup)
                   throws ConverterException

Reads group Group information for pathway model from root element.

NB:

1. A group has identifier GroupId (essentially ElementId), while GraphId is optional. A group has GraphId if there is at least one LineElement.LinePoint referring to this group by GraphRef. Because GroupIds may conflict with an elementId, new unique elementIds (value) can be assigned with reference back to the original GroupIds (key) in groupIdToNew map.
2. Group type "None" (GPML2013a) is replaced with "Group" (GPML2021).
3. Group type "Group" (GPML2013a) is replaced with "Transparent" (GPML2021).
4. Rect properties (centerX, centerY, width, height) are not set but calculated when needed.

Parameters:

pathwayModel - the pathway model.

root - the root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

groupIdToGroup - the map of groupId to group.

Throws:

ConverterException

readGroupGroupRef

protected void readGroupGroupRef(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Map<java.lang.String,Group> groupIdToGroup)
                          throws ConverterException

Reads groupRef property ShapedElement.setGroupRef(org.pathvisio.libgpml.model.Group) information of group pathway element. Because a group may refer to another group not yet initialized. We read and set groupRef after reading all group elements. The groupRef is the "parent" group to which this group refers.

Parameters:

pathwayModel - the pathway model.

root - the root element.

groupIdToGroup - the map of groupId to group.

Throws:

ConverterException

setGroupGraphicsProperty

protected void setGroupGraphicsProperty(Group group,
GroupType type)
                                 throws ConverterException

Reads and sets graphics properties for Group.

Graphics depends on group type:

1. Below Group colors from Pathvisio3...
2. TRANSPARENT: transparent rectangle
3. COMPLEX: gray #b4b46419 octagon with gray #808080 solid border
4. PATHWAY: green #00ff000c rectangle with gray #808080 dashed border
5. GROUP (DEFAULT): gray #b4b46419 rectangle with gray #808080 dashed border

Parameters:

group - the group pathway element.

type - the group type.

Throws:

ConverterException

readLabels

protected void readLabels(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref,
java.util.Map<java.lang.String,Group> groupIdToGroup)
                   throws ConverterException

Reads label Label information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

groupIdToGroup - the map of groupId to group.

Throws:

ConverterException

readShapes

protected void readShapes(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref,
java.util.Map<java.lang.String,Group> groupIdToGroup)
                   throws ConverterException

Reads shape Shape information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

groupIdToGroup - the map of groupId to group.

Throws:

ConverterException

readDataNodes

protected void readDataNodes(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref,
java.util.Map<java.lang.String,Group> groupIdToGroup)
                      throws ConverterException

Reads data node DataNode information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

groupIdToGroup - the map of groupId to group.

Throws:

ConverterException

readStates

protected void readStates(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)
                   throws ConverterException

Reads state DataNode.State information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

Throws:

ConverterException

convertStateCommentToRefs

protected void convertStateCommentToRefs(DataNode.State state,
java.util.Set<java.lang.String> elementIdSet)
                                  throws ConverterException

This method is used to handle DataNode.State PathwayElement.Comment which were manually added to encode phosphosite information. This method first checks whether a comment for a state is indeed phosphosite information. The phosphosite information is parsed and stored in a LinkedHashMap annotationsMap. For each key value pair in annotationsMap, a new Xref or Annotation is created. The annotation is added to the pathway model after checking for annotations with equivalent properties. A new PathwayElement.AnnotationRef is created for the annotation and added to the state. Lastly the comment itself is removed from the state so that information is not duplicated. NB: "sitegrpid", "ptm" and "direction" are specially handled.

Parameters:

state -

elementIdSet -

Throws:

ConverterException

readInteractions

protected void readInteractions(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref,
java.util.Map<java.lang.String,Group> groupIdToGroup,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                         throws ConverterException

Reads interaction Interaction information for pathway model from root element. New unique elementIds are assigned to line pathway elements are stored in the ordered lineList so that line pathway elements can be retrieved based on previous read order. NB: points are read by readPoints(org.pathvisio.libgpml.model.LineElement, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<org.jdom2.Element, org.pathvisio.libgpml.model.LineElement.LinePoint>).

Parameters:

pathwayModel - the pathway model.

root - the root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

groupIdToGroup - the map of groupId to group.

elementToPoint - the map of jdom element to line points.

Throws:

ConverterException

readGraphicalLines

protected void readGraphicalLines(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref,
java.util.Map<java.lang.String,Group> groupIdToGroup,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                           throws ConverterException

Reads graphical line GraphicalLine information for pathway model from root element. New unique elementIds are assigned to line pathway elements are stored in the ordered lineList so that line pathway elements can be retrieved based on previous read order. NB: points are read by readPoints(org.pathvisio.libgpml.model.LineElement, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<org.jdom2.Element, org.pathvisio.libgpml.model.LineElement.LinePoint>).

Parameters:

pathwayModel - the pathway model.

root - the root element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

groupIdToGroup - the map of groupId to group.

elementToPoint - the map of jdom element to line points.

Throws:

ConverterException

readPointElementRefs

protected void readPointElementRefs(PathwayModel pathwayModel,
java.util.Map<java.lang.String,Group> graphIdToGroup,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                             throws ConverterException

Reads LineElement.LinePoint elementRefs. ElementRefs must be read after the pathway elements they refer to. Map elementToPoint stores jdom elements for Points and their corresponding LinePoint pathway element so that elementRef information can be easily added. NB: points refer to a group by its GraphId not GroupId(essentially elementId). If the pathway element referenced by a point is a group, we must search for the group by its GraphId in Map graphIdToGroup.

Parameters:

pathwayModel - the pathway model.

graphIdToGroup - the map of graphId to group.

elementToPoint - the map of jdom element to line points.

Throws:

ConverterException

readLineElement

protected void readLineElement(LineElement lineElement,
org.jdom2.Element ln,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref,
java.util.Map<java.lang.String,Group> groupIdToGroup)
                        throws ConverterException

Reads line element LineElement information for interaction or graphical line from jdom element. NB: points are read by readPoints(org.pathvisio.libgpml.model.LineElement, org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<org.jdom2.Element, org.pathvisio.libgpml.model.LineElement.LinePoint>).

Parameters:

lineElement - the line pathway element.

ln - the jdom line element.

elementIdSet - the set of all elementIds.

idToPublicationXref - the map of id to biopax jdom element.

groupIdToGroup - the map of groupId to group.

Throws:

ConverterException

readPoints

protected void readPoints(LineElement lineElement,
org.jdom2.Element ln,
java.util.Set<java.lang.String> elementIdSet,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                   throws ConverterException

Reads points LineElement.LinePoint for pathway model line pathway elements. Point elementRefs must be read after the pathway elements they refer to. Therefore points are read last in readPointElementRefs(org.pathvisio.libgpml.model.PathwayModel, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.Group>, java.util.Map<org.jdom2.Element, org.pathvisio.libgpml.model.LineElement.LinePoint>).

Parameters:

lineElement - the line pathway element.

ln - the jdom line element.

elementIdSet - the set of all elementIds.

elementToPoint - the map of jdom element to line points.

Throws:

ConverterException

readArrowHeadType

protected ArrowHeadType readArrowHeadType(org.jdom2.Element pt,
java.lang.String base)
                                   throws ConverterException

Returns the arrowHead for give jdom point element.

Parameters:

pt - the jdom point element.

base - the string for either "Interaction" or "GraphicalLine"

Returns:

the arrowhead for given jdom point element.

Throws:

ConverterException

readAnchors

protected void readAnchors(LineElement lineElement,
org.jdom2.Element gfx,
java.util.Set<java.lang.String> elementIdSet)
                    throws ConverterException

Reads anchor LineElement.Anchor information for line element from element.

Parameters:

lineElement - the line element object.

gfx - the jdom graphics element.

elementIdSet - the set of all elementIds.

Throws:

ConverterException

readXref

protected org.bridgedb.Xref readXref(org.jdom2.Element e)
                              throws ConverterException

Reads xref Xref information from element. In GPML2013a, Xref is required for DataNodes, Interactions, and optional for States.

Parameters:

e - the element.

Throws:

ConverterException

readElementId

protected java.lang.String readElementId(java.lang.String tag,
org.jdom2.Element e,
java.util.Set<java.lang.String> elementIdSet)
                                  throws ConverterException

Returns elementId read for given Element. If elementId is missing (null), generates and returns a new unique elementId. New unique elementIds are added to elementIdSet.

Parameters:

tag - the string tag for GPML2013aFormatAbstract.getAttr(java.lang.String, java.lang.String, org.jdom2.Element)

e - the jdom element.

elementIdSet - the set of all elementIds.

Returns:

elementId the elementId for given element.

Throws:

ConverterException

readGroupRef

protected void readGroupRef(ShapedElement shapedElement,
org.jdom2.Element se,
java.util.Map<java.lang.String,Group> groupIdToGroup)
                     throws ConverterException

Reads and sets groupRef for given (shaped) pathway element and jdom Element.

Parameters:

shapedElement - the (shaped) pathway element.

se - the jdom (shaped) pathway element.

groupIdToGroup - the map of groupId to group.

Throws:

ConverterException

readRectProperty

protected void readRectProperty(ShapedElement shapedElement,
org.jdom2.Element gfx)
                         throws ConverterException

Reads rect property information. Jdom handles schema default values.

Parameters:

shapedElement - the shaped pathway element.

gfx - the jdom graphics element.

Throws:

ConverterException

readFontProperty

protected void readFontProperty(ShapedElement shapedElement,
org.jdom2.Element gfx)
                         throws ConverterException

Reads font property information. Jdom handles schema default values. NB: State has no font properties in GPML2013a, set basically default values.

Parameters:

shapedElement - the shaped pathwayElement.

gfx - the jdom graphics element.

Throws:

ConverterException

readShapeStyleProperty

protected void readShapeStyleProperty(ShapedElement shapedElement,
org.jdom2.Element gfx)
                               throws ConverterException

Reads shape style property information. Jdom handles schema default values. If shape type is a key in GPML2013aFormatAbstract.DEPRECATED_MAP, replaces deprecated shape type with newer value.

NB:

1. If pathway element has dynamic property key CellularComponentProperty, shape type is again replaced, this time with the dynamic property value in readDynamicProperties(org.pathvisio.libgpml.model.PathwayElement, org.jdom2.Element).
2. If state pathway element has dynamic property key

Parameters:

shapedElement - the shaped pathway element.

gfx - the jdom graphics element.

Throws:

ConverterException

readLineStyleProperty

protected void readLineStyleProperty(LineElement lineElement,
org.jdom2.Element gfx)
                              throws ConverterException

Reads line style property information. Jdom handles schema default values.

Parameters:

lineElement - the line pathway element.

gfx - the jdom graphics element.

Throws:

ConverterException