Package org.pathvisio.libgpml.model

Class GPML2021Reader

java.lang.Object

org.pathvisio.libgpml.model.GPMLFormatAbstract

org.pathvisio.libgpml.model.GPML2021FormatAbstract

org.pathvisio.libgpml.model.GPML2021Reader

All Implemented Interfaces:

GPMLFormatReader, GPMLFormatVersion

public class GPML2021Reader
extends GPML2021FormatAbstract
implements GPMLFormatReader

This class reads a PathwayModel from an input source (GPML 2021).

Author:

finterly

Field Summary

Fields

Modifier and Type	Field	Description
static GPML2021Reader	GPML2021READER

Fields inherited from class org.pathvisio.libgpml.model.GPML2021FormatAbstract

ANCHORSHAPETYPE_DEFAULT, ANNOTATIONTYPE_DEFAULT, ARROWHEAD_DEFAULT, BACKGROUNDCOLOR_DEFAULT, BORDERCOLOR_DEFAULT, BORDERSTYLE_DEFAULT, BORDERWIDTH_DEFAULT, CONNECTORTYPE_DEFAULT, DATANODETYPE_DEFAULT, FILLCOLOR_DEFAULT, FONTDECORATION_DEFAULT, FONTNAME_DEFAULT, FONTSIZE_DEFAULT, FONTSTRIKETHRU_DEFAULT, FONTSTYLE_DEFAULT, FONTWEIGHT_DEFAULT, GROUPTYPE_DEFAULT, HALIGN_DEFAULT, LINECOLOR_DEFAULT, LINESTYLE_DEFAULT, LINEWIDTH_DEFAULT, SHAPETYPE_DEFAULT, STATETYPE_DEFAULT, TEXTCOLOR_DEFAULT, VALIGN_DEFAULT

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

BIOPAX_NAMESPACE, OWL_NAMESPACE, RDF_NAMESPACE, RDF_STRING, RDFS_NAMESPACE

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	GPML2021Reader(java.lang.String xsdFile, org.jdom2.Namespace nsGPML)	Constructor for GPML reader.

Method Summary

Modifier and Type	Method	Description
protected void	readAnchors(LineElement lineElement, org.jdom2.Element wyps)	Reads anchor LineElement.Anchor information for line element from jdom element.
protected void	readAnnotationRefs(PathwayModel pathwayModel, Referenceable.Annotatable annotatable, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads Annotation and PathwayElement.AnnotationRef information for an Referenceable.Annotatable.
protected void	readAuthors(Pathway pathway, org.jdom2.Element root)	Reads author Pathway.Author information for pathway from root element.
protected void	readCitationRefs(PathwayModel pathwayModel, Referenceable.Citable citable, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads Citation and PathwayElement.CitationRef information for a Referenceable.Citable.
protected void	readCommentGroup(PathwayModel pathwayModel, PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads comment group (comment, dynamic property, annotationRef, citationRef, evidenceRef) information for PathwayElement 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.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads data node DataNode information for pathway model from root element.
protected void	readDynamicProperties(PathwayElement pathwayElement, org.jdom2.Element e)	Reads dynamic property PathwayElement.setDynamicProperty(java.lang.String, java.lang.String) information for pathway element from jdom element.
protected void	readEvidenceRefs(PathwayModel pathwayModel, Referenceable.Evidenceable evidenceable, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads Evidence and PathwayElement.EvidenceRef information for an Referenceable.Evidenceable.
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.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads graphical line GraphicalLine information for pathway model from root element.
protected void	readGroupRef(PathwayModel pathwayModel, ShapedElement shapedElement, org.jdom2.Element e)	Reads groupRef information for DataNode, Label, and Shape.
protected void	readGroups(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads group Group information for pathway model from root element.
protected void	readInfoMap(org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads and maps ref (Annotation, Citation, and Evidence) elementId id to the corresponding jdom element in Map refIdToJdomElement, to assist other reading methods: readAnnotationRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Annotatable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>), readCitationRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Citable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>), and readEvidenceRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Evidenceable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>).
protected void	readInteractions(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement, 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.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads label Label information for pathway model from root element.
protected void	readLineElement(PathwayModel pathwayModel, LineElement lineElement, org.jdom2.Element ln, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	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 Pathway	readPathway(Pathway pathway, org.jdom2.Element root)	Reads pathway information from jdom root element.
protected void	readPointElementRefs(PathwayModel pathwayModel, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads elementRef LineElement.LinePoint.setElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo) for pathway model points.
protected void	readPoints(LineElement lineElement, org.jdom2.Element wyps, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads point LineElement.LinePoint information for line element.
protected void	readRectProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads rect property information.
protected void	readShapedElement(PathwayModel pathwayModel, ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads common properties for shaped pathway elements ShapedElement.
protected void	readShapes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	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, DataNode dataNode, org.jdom2.Element dn, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads state DataNode.State information for data node from element.
protected java.lang.String	readUrl(org.jdom2.Element e)	Reads Url link information from element.
protected org.bridgedb.Xref	readXref(org.jdom2.Element e)	Reads xref Xref information from jdom element.

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

GPML2021READER

public static final GPML2021Reader GPML2021READER

Constructor Details

GPML2021Reader

protected GPML2021Reader(java.lang.String xsdFile,
org.jdom2.Namespace nsGPML)

Constructor for GPML reader.

Parameters:

xsdFile - the schema file.

nsGPML - the GPML namespace.

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. NB: Order of reading is done in such as way that referenced elements are read first. Groups are read first as other pathway elements reference groupRef. Point and DataNode elementRef are read last to ensure the Pathway Elements referenced are already instantiated.

Specified by:

readFromRoot in interface GPMLFormatReader

Parameters:

pathwayModel - the given pathway model.

root - the root element of given Jdom document.

Throws:

ConverterException

readPathway

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

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

Parameters:

root - the jdom root element.

Throws:

ConverterException

readXref

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

Reads xref Xref information from jdom element. Xref is optional for Pathway, DataNodes, States, Interactions, Groups, Annotations, and Evidences. Citations must have either Xref or Url, or both.

Parameters:

e - the jdom element.

Returns:

xref the new xref or null if no or invalid xref information.

Throws:

ConverterException

readUrl

protected java.lang.String readUrl(org.jdom2.Element e)
                            throws ConverterException

Reads Url link information from element. Url is optional for Annotations, Citations, and Evidences. Citations must have either Xref or Url, or both.

Parameters:

e - the element.

Returns:

urlLink the link for the url.

Throws:

ConverterException

readAuthors

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

Reads author Pathway.Author information for pathway from root element.

Parameters:

pathway - the pathway.

root - the jdom root element.

Throws:

ConverterException

readInfoMap

protected void readInfoMap(org.jdom2.Element root,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)
                    throws ConverterException

Reads and maps ref (Annotation, Citation, and Evidence) elementId id to the corresponding jdom element in Map refIdToJdomElement, to assist other reading methods: readAnnotationRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Annotatable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>), readCitationRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Citable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>), and readEvidenceRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Evidenceable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>).

Parameters:

root - the jdom root element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readAnnotationRefs

protected void readAnnotationRefs(PathwayModel pathwayModel,
Referenceable.Annotatable annotatable,
org.jdom2.Element e,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)
                           throws ConverterException

Reads Annotation and PathwayElement.AnnotationRef information for an Referenceable.Annotatable.

Parameters:

pathwayModel - the pathway model.

annotatable - the pathway object which can have annotation.

e - the jdom element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readCitationRefs

protected void readCitationRefs(PathwayModel pathwayModel,
Referenceable.Citable citable,
org.jdom2.Element e,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)
                         throws ConverterException

Reads Citation and PathwayElement.CitationRef information for a Referenceable.Citable.

Parameters:

pathwayModel - the pathway model.

citable - the pathway object which can have citation.

e - the jdom element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readEvidenceRefs

protected void readEvidenceRefs(PathwayModel pathwayModel,
Referenceable.Evidenceable evidenceable,
org.jdom2.Element e,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)
                         throws ConverterException

Reads Evidence and PathwayElement.EvidenceRef information for an Referenceable.Evidenceable.

Parameters:

pathwayModel - the pathway model.

evidenceable - the pathway object which can have evidence.

e - the jdom element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readCommentGroup

protected void readCommentGroup(PathwayModel pathwayModel,
PathwayElement pathwayElement,
org.jdom2.Element e,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)
                         throws ConverterException

Reads comment group (comment, dynamic property, annotationRef, citationRef, evidenceRef) information for PathwayElement from jdom element.

Parameters:

pathwayElement - the element info pathway element object.

e - the jdom element.

refIdToJdomElement - the map of ref elementId to 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.

Parameters:

pathwayElement - the pathway element.

e - the jdom element.

Throws:

ConverterException

readDynamicProperties

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

Reads dynamic property PathwayElement.setDynamicProperty(java.lang.String, java.lang.String) information for pathway element from jdom element.

Parameters:

pathwayElement - the the pathway element.

e - the jdom element.

Throws:

ConverterException

readGroups

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

Reads group Group information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the jdom root element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readLabels

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

Reads label Label information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the jdom root element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readShapes

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

Reads shape Shape information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the root element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readDataNodes

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

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

Parameters:

pathwayModel - the pathway model.

root - the jdom root element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readStates

protected void readStates(PathwayModel pathwayModel,
DataNode dataNode,
org.jdom2.Element dn,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)
                   throws ConverterException

Reads state DataNode.State information for data node from element.

Parameters:

pathwayModel - the pathway model.

dataNode - the data node object DataNode.

dn - the jdom data node element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readShapedElement

protected void readShapedElement(PathwayModel pathwayModel,
ShapedElement shapedElement,
org.jdom2.Element se,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)
                          throws ConverterException

Reads common properties for shaped pathway elements ShapedElement.

Parameters:

pathwayModel - the pathway model.

shapedElement - the shaped pathway element.

se - the jdom (shaped) pathway element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readGroupRef

protected void readGroupRef(PathwayModel pathwayModel,
ShapedElement shapedElement,
org.jdom2.Element e)
                     throws ConverterException

Reads groupRef information for DataNode, Label, and Shape. NB: Group uses a different method.

Parameters:

pathwayModel - the pathway model.

shapedElement - the shapedElement to read groupRef for.

e - the jdom shaped element.

Throws:

ConverterException

readInteractions

protected void readInteractions(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                         throws ConverterException

Reads interaction Interaction information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the jdom root element.

refIdToJdomElement - the map of ref elementId to jdom element.

Throws:

ConverterException

readGraphicalLines

protected void readGraphicalLines(PathwayModel pathwayModel,
org.jdom2.Element root,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                           throws ConverterException

Reads graphical line GraphicalLine information for pathway model from root element.

Parameters:

pathwayModel - the pathway model.

root - the jdom root element.

refIdToJdomElement - the map of ref elementId to jdom element.

elementToPoint - the map of jdom element to line points.

Throws:

ConverterException

readPoints

protected void readPoints(LineElement lineElement,
org.jdom2.Element wyps,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                   throws ConverterException

Reads point LineElement.LinePoint information for line element.

Parameters:

lineElement - the line element object.

wyps - the jdom waypoints element.

elementToPoint - the map of jdom element to line points.

Throws:

ConverterException

readLineElement

protected void readLineElement(PathwayModel pathwayModel,
LineElement lineElement,
org.jdom2.Element ln,
java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement,
java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)
                        throws ConverterException

Reads line element LineElement information for interaction or graphical line from jdom element.

Parameters:

lineElement - the line element object.

ln - the jdom line element.

refIdToJdomElement - the map of ref elementId to jdom element.

elementToPoint - the map of jdom element to line points.

Throws:

ConverterException

readAnchors

protected void readAnchors(LineElement lineElement,
org.jdom2.Element wyps)
                    throws ConverterException

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

Parameters:

lineElement - the line element object.

wyps - the jdom waypoints element.

Throws:

ConverterException

readPointElementRefs

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

Reads elementRef LineElement.LinePoint.setElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo) for pathway model points.

Parameters:

pathwayModel - the pathway model.

elementToPoint - the map of jdom element to line points.

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.

Parameters:

shapedElement - the shaped pathway element.

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.

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