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libGPML is a library for reading, writing, manipulation, and conversion of files and data streams in the GPML (Graphical Pathway Markup Language) format.
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/*******************************************************************************
* PathVisio, a tool for data visualization and analysis using biological pathways
* Copyright 2006-2022 BiGCaT Bioinformatics, WikiPathways
*
* Licensed under the Apache License, Version 2.0 (the "License"); you may not
* use this file except in compliance with the License. You may obtain a copy
* of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
* License for the specific language governing permissions and limitations under
* the License.
******************************************************************************/
package org.pathvisio.libgpml.model;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.bridgedb.Xref;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.pathvisio.libgpml.io.ConverterException;
import org.pathvisio.libgpml.model.DataNode.State;
import org.pathvisio.libgpml.model.GraphLink.LinkableTo;
import org.pathvisio.libgpml.model.LineElement.Anchor;
import org.pathvisio.libgpml.model.LineElement.LinePoint;
import org.pathvisio.libgpml.model.Pathway.Author;
import org.pathvisio.libgpml.model.PathwayElement.AnnotationRef;
import org.pathvisio.libgpml.model.PathwayElement.CitationRef;
import org.pathvisio.libgpml.model.PathwayElement.Comment;
import org.pathvisio.libgpml.model.PathwayElement.EvidenceRef;
import org.pathvisio.libgpml.model.Referenceable.Annotatable;
import org.pathvisio.libgpml.model.Referenceable.Citable;
import org.pathvisio.libgpml.model.Referenceable.Evidenceable;
import org.pathvisio.libgpml.model.type.AnchorShapeType;
import org.pathvisio.libgpml.model.type.AnnotationType;
import org.pathvisio.libgpml.model.type.ArrowHeadType;
import org.pathvisio.libgpml.model.type.ConnectorType;
import org.pathvisio.libgpml.model.type.DataNodeType;
import org.pathvisio.libgpml.model.type.GroupType;
import org.pathvisio.libgpml.model.type.HAlignType;
import org.pathvisio.libgpml.model.type.LineStyleType;
import org.pathvisio.libgpml.model.type.ShapeType;
import org.pathvisio.libgpml.model.type.StateType;
import org.pathvisio.libgpml.model.type.VAlignType;
import org.pathvisio.libgpml.util.ColorUtils;
import org.pathvisio.libgpml.util.XrefUtils;
/**
* This class reads a PathwayModel from an input source (GPML 2021).
*
* @author finterly
*/
public class GPML2021Reader extends GPML2021FormatAbstract implements GPMLFormatReader {
public static final GPML2021Reader GPML2021READER = new GPML2021Reader("GPML2021.xsd",
Namespace.getNamespace("http://pathvisio.org/GPML/2021"));
/**
* Constructor for GPML reader.
*
* @param xsdFile the schema file.
* @param nsGPML the GPML namespace.
*/
protected GPML2021Reader(String xsdFile, Namespace nsGPML) {
super(xsdFile, nsGPML);
}
/**
* Reads information from root element of Jdom document {@link Document} to the
* pathway model {@link 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.
*
* @param pathwayModel the given pathway model.
* @param root the root element of given Jdom document.
* @throws ConverterException
*/
@Override
public void readFromRoot(PathwayModel pathwayModel, Element root) throws ConverterException {
readPathway(pathwayModel.getPathway(), root);
// reads annotation/citation/evidence ref info into a map
Map refIdToJdomElement = new HashMap();
readInfoMap(root, refIdToJdomElement);
// reads pathway info
readCommentGroup(pathwayModel, pathwayModel.getPathway(), root, refIdToJdomElement);
// reads groups first
readGroups(pathwayModel, root, refIdToJdomElement);
readLabels(pathwayModel, root, refIdToJdomElement);
readShapes(pathwayModel, root, refIdToJdomElement);
readDataNodes(pathwayModel, root, refIdToJdomElement);
// stores jdom element to point, for reading point elementRefs (last)
Map elementToPoint = new HashMap();
readInteractions(pathwayModel, root, refIdToJdomElement, elementToPoint);
readGraphicalLines(pathwayModel, root, refIdToJdomElement, elementToPoint);
readPointElementRefs(pathwayModel, elementToPoint);
// removes empty groups and updates group dimensions
updateGroups(pathwayModel);
// refreshes line elements
refreshLineElements(pathwayModel);
}
/**
* Reads pathway information from jdom root element. Instantiates and returns
* the pathway object {@link Pathway}.
*
* @param root the jdom root element.
* @throws ConverterException
*/
protected Pathway readPathway(Pathway pathway, Element root) throws ConverterException {
pathway.setTitle(root.getAttributeValue("title"));
Element gfx = root.getChild("Graphics", root.getNamespace());
pathway.setBoardWidth(Double.parseDouble(gfx.getAttributeValue("boardWidth").trim()));
pathway.setBoardHeight(Double.parseDouble(gfx.getAttributeValue("boardHeight").trim()));
pathway.setBackgroundColor(
ColorUtils.stringToColor(gfx.getAttributeValue("backgroundColor", BACKGROUNDCOLOR_DEFAULT)));
readAuthors(pathway, root);
// sets optional properties
Element desc = root.getChild("Description", root.getNamespace());
if (desc != null) {
String description = desc.getText();
pathway.setDescription(description);
}
pathway.setXref(readXref(root));
pathway.setOrganism(root.getAttributeValue("organism"));
pathway.setSource(root.getAttributeValue("source"));
pathway.setVersion(root.getAttributeValue("version"));
pathway.setLicense(root.getAttributeValue("license"));
return pathway;
}
/**
* Reads xref {@link 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.
*
* @param e the jdom element.
* @return xref the new xref or null if no or invalid xref information.
* @throws ConverterException
*/
protected Xref readXref(Element e) throws ConverterException {
Element xref = e.getChild("Xref", e.getNamespace());
if (xref != null) {
String identifier = xref.getAttributeValue("identifier");
String dataSource = xref.getAttributeValue("dataSource");
XrefUtils.createXref(identifier, dataSource);
return XrefUtils.createXref(identifier, dataSource);
}
return null;
}
/**
* Reads Url link information from element. Url is optional for Annotations,
* Citations, and Evidences. Citations must have either Xref or Url, or both.
*
* @param e the element.
* @return urlLink the link for the url.
* @throws ConverterException
*/
protected String readUrl(Element e) throws ConverterException {
Element u = e.getChild("Url", e.getNamespace());
if (u != null) {
String urlLink = u.getAttributeValue("link");
return urlLink;
}
return null;
}
/**
* Reads author {@link Author} information for pathway from root element.
*
* @param pathway the pathway.
* @param root the jdom root element.
* @throws ConverterException
*/
protected void readAuthors(Pathway pathway, Element root) throws ConverterException {
Element aus = root.getChild("Authors", root.getNamespace());
if (aus != null) {
for (Element au : aus.getChildren("Author", aus.getNamespace())) {
String name = au.getAttributeValue("name");
Author author = pathway.addAuthor(name);
// sets optional properties
String order = au.getAttributeValue("order");
if (order != null)
author.setOrder(Integer.parseInt(order.trim()));
author.setUsername(au.getAttributeValue("username"));
author.setXref(readXref(au));
}
}
}
/**
* Reads and maps ref (Annotation, Citation, and Evidence) elementId id to the
* corresponding jdom element in {@link Map} refIdToJdomElement, to assist other
* reading methods: {@link #readAnnotationRefs}, {@link #readCitationRefs}, and
* {@link #readEvidenceRefs}.
*
* @param root the jdom root element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readInfoMap(Element root, Map refIdToJdomElement) throws ConverterException {
List refType = Collections.unmodifiableList(Arrays.asList("Annotation", "Citation", "Evidence"));
for (int i = 0; i < refType.size(); i++) {
Element refs = root.getChild(refType.get(i) + "s", root.getNamespace());
if (refs != null) {
for (Element ref : refs.getChildren(refType.get(i), root.getNamespace())) {
String elementId = ref.getAttributeValue("elementId");
refIdToJdomElement.put(elementId, ref);
}
}
}
}
/**
* Reads {@link Annotation} and {@link AnnotationRef} information for an
* {@link Annotatable}.
*
* @param pathwayModel the pathway model.
* @param annotatable the pathway object which can have annotation.
* @param e the jdom element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readAnnotationRefs(PathwayModel pathwayModel, Annotatable annotatable, Element e,
Map refIdToJdomElement) throws ConverterException {
for (Element anntRef : e.getChildren("AnnotationRef", e.getNamespace())) {
String elementRef = anntRef.getAttributeValue("elementRef");
// if annotation already added, create and add annotationRef
Annotation annotation = (Annotation) pathwayModel.getPathwayObject(elementRef);
if (annotation != null) {
AnnotationRef annotationRef = annotatable.addAnnotation(annotation);
readCitationRefs(pathwayModel, annotationRef, anntRef, refIdToJdomElement);
readEvidenceRefs(pathwayModel, annotationRef, anntRef, refIdToJdomElement);
}
// else if map contains refId, create and add annotation and annotationRef
else if (refIdToJdomElement.containsKey(elementRef)) {
Element annt = refIdToJdomElement.get(elementRef);
String elementId = annt.getAttributeValue("elementId");
String value = annt.getAttributeValue("value");
AnnotationType type = AnnotationType.register(annt.getAttributeValue("type", ANNOTATIONTYPE_DEFAULT));
Xref xref = readXref(annt);
String urlLink = readUrl(annt);
// annotation must have value and type, xref and urlLink optional
if (value != null && type != null) {
AnnotationRef annotationRef = annotatable.addAnnotation(elementId, value, type, xref, urlLink);
readCitationRefs(pathwayModel, annotationRef, anntRef, refIdToJdomElement);
readEvidenceRefs(pathwayModel, annotationRef, anntRef, refIdToJdomElement);
}
}
// else invalid annotation and annotationRef
else {
throw new ConverterException("AnnotationRef refers to non-existent Annotation " + elementRef);
}
}
}
/**
* Reads {@link Citation} and {@link CitationRef} information for a
* {@link Citable}.
*
* @param pathwayModel the pathway model.
* @param citable the pathway object which can have citation.
* @param e the jdom element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readCitationRefs(PathwayModel pathwayModel, Citable citable, Element e,
Map refIdToJdomElement) throws ConverterException {
for (Element citRef : e.getChildren("CitationRef", e.getNamespace())) {
String elementRef = citRef.getAttributeValue("elementRef");
// if citation already added, create and add citationRef
Citation citation = (Citation) pathwayModel.getPathwayObject(elementRef);
if (citation != null) {
CitationRef citationRef = citable.addCitation(citation);
readAnnotationRefs(pathwayModel, citationRef, citRef, refIdToJdomElement);
}
// else if map contains refId, create and add citation and citationRef
else if (refIdToJdomElement.containsKey(elementRef)) {
Element cit = refIdToJdomElement.get(elementRef);
String elementId = cit.getAttributeValue("elementId");
Xref xref = readXref(cit);
String urlLink = readUrl(cit);
// citation must have xref or urlLink
if (xref != null || urlLink != null) {
CitationRef citationRef = citable.addCitation(elementId, xref, urlLink);
readAnnotationRefs(pathwayModel, citationRef, citRef, refIdToJdomElement);
}
}
// else invalid citation and citationRef
else {
throw new ConverterException("CitationRef refers to non-existent Citation " + elementRef);
}
}
}
/**
* Reads {@link Evidence} and {@link EvidenceRef} information for an
* {@link Evidenceable}.
*
* @param pathwayModel the pathway model.
* @param evidenceable the pathway object which can have evidence.
* @param e the jdom element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readEvidenceRefs(PathwayModel pathwayModel, Evidenceable evidenceable, Element e,
Map refIdToJdomElement) throws ConverterException {
for (Element evidRef : e.getChildren("EvidenceRef", e.getNamespace())) {
String elementRef = evidRef.getAttributeValue("elementRef");
// if evidence already added, create and add evidenceRef
Evidence evidence = (Evidence) pathwayModel.getPathwayObject(elementRef);
if (evidence != null) {
evidenceable.addEvidence(evidence);
}
// else if map contains refId, create and add evidence and evidenceRef
else if (refIdToJdomElement.containsKey(elementRef)) {
Element evid = refIdToJdomElement.get(elementRef);
String elementId = evid.getAttributeValue("elementId");
Xref xref = readXref(evid);
String urlLink = readUrl(evid);
String value = evid.getAttributeValue("value");
// evidence must have xref, value and urlLink optional
if (xref != null || urlLink != null) {
evidenceable.addEvidence(elementId, value, xref, urlLink);
}
}
// else invalid evidence and evidenceRef
else {
throw new ConverterException("EvidenceRef refers to non-existent Evidence " + elementRef);
}
}
}
/**
* Reads comment group (comment, dynamic property, annotationRef, citationRef,
* evidenceRef) information for {@link PathwayElement} from jdom element.
*
* @param pathwayElement the element info pathway element object.
* @param e the jdom element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readCommentGroup(PathwayModel pathwayModel, PathwayElement pathwayElement, Element e,
Map refIdToJdomElement) throws ConverterException {
readComments(pathwayElement, e);
readDynamicProperties(pathwayElement, e);
readAnnotationRefs(pathwayModel, pathwayElement, e, refIdToJdomElement);
readCitationRefs(pathwayModel, pathwayElement, e, refIdToJdomElement);
readEvidenceRefs(pathwayModel, pathwayElement, e, refIdToJdomElement);
}
/**
* Reads comment {@link Comment} information for pathway element from jdom
* element.
*
* @param pathwayElement the pathway element.
* @param e the jdom element.
* @throws ConverterException
*/
protected void readComments(PathwayElement pathwayElement, Element e) throws ConverterException {
for (Element cmt : e.getChildren("Comment", e.getNamespace())) {
String source = cmt.getAttributeValue("source");
String commentText = cmt.getText();
// comment must have text
if (commentText != null && !commentText.equals("")) {
pathwayElement.addComment(commentText, source);
}
}
}
/**
* Reads dynamic property {@link PathwayElement#setDynamicProperty} information
* for pathway element from jdom element.
*
* @param pathwayElement the the pathway element.
* @param e the jdom element.
* @throws ConverterException
*/
protected void readDynamicProperties(PathwayElement pathwayElement, Element e) throws ConverterException {
for (Element dp : e.getChildren("Property", e.getNamespace())) {
String key = dp.getAttributeValue("key");
String value = dp.getAttributeValue("value");
pathwayElement.setDynamicProperty(key, value);
}
}
/**
* Reads group {@link Group} information for pathway model from root element.
*
* @param pathwayModel the pathway model.
* @param root the jdom root element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readGroups(PathwayModel pathwayModel, Element root, Map refIdToJdomElement)
throws ConverterException {
Element grps = root.getChild("Groups", root.getNamespace());
if (grps != null) {
for (Element grp : grps.getChildren("Group", grps.getNamespace())) {
String elementId = grp.getAttributeValue("elementId");
GroupType type = GroupType.register(grp.getAttributeValue("type", GROUPTYPE_DEFAULT));
Group group = new Group(type);
group.setElementId(elementId);
pathwayModel.addGroup(group);
// reads graphics and comment group props
readShapedElement(pathwayModel, group, grp, refIdToJdomElement);
// sets optional properties
group.setXref(readXref(grp));
group.setTextLabel(grp.getAttributeValue("textLabel"));
}
/**
* Because a group may refer to another group not yet initialized. We read all
* group elements before setting groupRef.
*/
for (Element grp : grps.getChildren("Group", grps.getNamespace())) {
String groupRef = grp.getAttributeValue("groupRef");
if (groupRef != null && !groupRef.equals("")) {
String elementId = grp.getAttributeValue("elementId");
Group group = (Group) pathwayModel.getPathwayObject(elementId);
group.setGroupRefTo((Group) group.getPathwayModel().getPathwayObject(groupRef));
}
}
}
}
/**
* Reads label {@link Label} information for pathway model from root element.
*
* @param pathwayModel the pathway model.
* @param root the jdom root element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readLabels(PathwayModel pathwayModel, Element root, Map refIdToJdomElement)
throws ConverterException {
Element lbs = root.getChild("Labels", root.getNamespace());
if (lbs != null) {
for (Element lb : lbs.getChildren("Label", lbs.getNamespace())) {
String elementId = lb.getAttributeValue("elementId");
String textLabel = lb.getAttributeValue("textLabel");
Label label = new Label(textLabel);
label.setElementId(elementId);
pathwayModel.addLabel(label);
// reads graphics and comment group props
readShapedElement(pathwayModel, label, lb, refIdToJdomElement);
// sets optional properties
label.setHref(lb.getAttributeValue("href"));
readGroupRef(pathwayModel, label, lb);
}
}
}
/**
* Reads shape {@link Shape} information for pathway model from root element.
*
* @param pathwayModel the pathway model.
* @param root the root element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readShapes(PathwayModel pathwayModel, Element root, Map refIdToJdomElement)
throws ConverterException {
Element shps = root.getChild("Shapes", root.getNamespace());
if (shps != null) {
for (Element shp : shps.getChildren("Shape", shps.getNamespace())) {
String elementId = shp.getAttributeValue("elementId");
Shape shape = new Shape();
shape.setElementId(elementId);
pathwayModel.addShape(shape);
// reads graphics and comment group props
readShapedElement(pathwayModel, shape, shp, refIdToJdomElement);
// sets optional properties
shape.setTextLabel(shp.getAttributeValue("textLabel"));
readGroupRef(pathwayModel, shape, shp);
}
}
}
/**
* Reads data node {@link DataNode} information for pathway model from root
* element.
*
* @param pathwayModel the pathway model.
* @param root the jdom root element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readDataNodes(PathwayModel pathwayModel, Element root, Map refIdToJdomElement)
throws ConverterException {
Element dns = root.getChild("DataNodes", root.getNamespace());
if (dns != null) {
for (Element dn : dns.getChildren("DataNode", dns.getNamespace())) {
String elementId = dn.getAttributeValue("elementId");
String textLabel = dn.getAttributeValue("textLabel");
DataNodeType type = DataNodeType.register(dn.getAttributeValue("type", DATANODETYPE_DEFAULT));
DataNode dataNode = new DataNode(textLabel, type);
dataNode.setElementId(elementId);
pathwayModel.addDataNode(dataNode);
// reads graphics and comment group props
readShapedElement(pathwayModel, dataNode, dn, refIdToJdomElement);
// reads states
readStates(pathwayModel, dataNode, dn, refIdToJdomElement);
// reads optional properties
dataNode.setXref(readXref(dn));
readGroupRef(pathwayModel, dataNode, dn);
// reads aliasRef
String aliasRefStr = dn.getAttributeValue("aliasRef");
if (aliasRefStr != null) {
Group aliasRef = (Group) pathwayModel.getPathwayObject(aliasRefStr);
if (aliasRef != null) {
dataNode.setAliasRef(aliasRef);
}
}
}
}
}
/**
* Reads state {@link State} information for data node from element.
*
* @param pathwayModel the pathway model.
* @param dataNode the data node object {@link DataNode}.
* @param dn the jdom data node element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readStates(PathwayModel pathwayModel, DataNode dataNode, Element dn,
Map refIdToJdomElement) throws ConverterException {
Element sts = dn.getChild("States", dn.getNamespace());
if (sts != null) {
for (Element st : sts.getChildren("State", sts.getNamespace())) {
String elementId = st.getAttributeValue("elementId");
String textLabel = st.getAttributeValue("textLabel");
StateType type = StateType.register(st.getAttributeValue("type", STATETYPE_DEFAULT));
Element gfx = st.getChild("Graphics", st.getNamespace());
double relX = Double.parseDouble(gfx.getAttributeValue("relX").trim());
double relY = Double.parseDouble(gfx.getAttributeValue("relY").trim());
// sets zOrder based on parent data node
State state = dataNode.addState(elementId, textLabel, type, relX, relY);
// reads graphics and comment group props
readShapedElement(pathwayModel, state, st, refIdToJdomElement);
// sets optional properties
state.setXref(readXref(st));
state.setZOrder(dataNode.getZOrder() + 1);
}
}
}
/**
* Reads common properties for shaped pathway elements {@link ShapedElement}.
*
* @param pathwayModel the pathway model.
* @param shapedElement the shaped pathway element.
* @param se the jdom (shaped) pathway element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readShapedElement(PathwayModel pathwayModel, ShapedElement shapedElement, Element se,
Map refIdToJdomElement) throws ConverterException {
Element gfx = se.getChild("Graphics", se.getNamespace());
// reads graphics properties
readRectProperty(shapedElement, gfx);
readFontProperty(shapedElement, gfx);
readShapeStyleProperty(shapedElement, gfx);
// reads comment group, evidenceRefs
readCommentGroup(pathwayModel, shapedElement, se, refIdToJdomElement);
}
/**
* Reads groupRef information for {@link DataNode}, {@link Label}, and
* {@link Shape}.
*
* NB: {@link Group} uses a different method.
*
* @param pathwayModel the pathway model.
* @param shapedElement the shapedElement to read groupRef for.
* @param e the jdom shaped element.
* @throws ConverterException
*/
protected void readGroupRef(PathwayModel pathwayModel, ShapedElement shapedElement, Element e)
throws ConverterException {
String groupRef = e.getAttributeValue("groupRef");
if (groupRef != null && !groupRef.equals("")) {
shapedElement.setGroupRefTo((Group) pathwayModel.getPathwayObject(groupRef));
}
}
/**
* Reads interaction {@link Interaction} information for pathway model from root
* element.
*
* @param pathwayModel the pathway model.
* @param root the jdom root element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @throws ConverterException
*/
protected void readInteractions(PathwayModel pathwayModel, Element root, Map refIdToJdomElement,
Map elementToPoint) throws ConverterException {
Element ias = root.getChild("Interactions", root.getNamespace());
if (ias != null) {
for (Element ia : ias.getChildren("Interaction", ias.getNamespace())) {
String elementId = ia.getAttributeValue("elementId");
Interaction interaction = new Interaction();
interaction.setElementId(elementId);
Element wyps = ia.getChild("Waypoints", ia.getNamespace());
readPoints(interaction, wyps, elementToPoint);
pathwayModel.addInteraction(interaction);
// reads graphics, comment group, points, and anchors
readLineElement(pathwayModel, interaction, ia, refIdToJdomElement, elementToPoint);
// sets optional properties
interaction.setXref(readXref(ia));
}
}
}
/**
* Reads graphical line {@link GraphicalLine} information for pathway model from
* root element.
*
* @param pathwayModel the pathway model.
* @param root the jdom root element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @param elementToPoint the map of jdom element to line points.
* @throws ConverterException
*/
protected void readGraphicalLines(PathwayModel pathwayModel, Element root, Map refIdToJdomElement,
Map elementToPoint) throws ConverterException {
Element glns = root.getChild("GraphicalLines", root.getNamespace());
if (glns != null) {
for (Element gln : glns.getChildren("GraphicalLine", glns.getNamespace())) {
String elementId = gln.getAttributeValue("elementId");
GraphicalLine graphicalLine = new GraphicalLine();
graphicalLine.setElementId(elementId);
Element wyps = gln.getChild("Waypoints", gln.getNamespace());
readPoints(graphicalLine, wyps, elementToPoint);
pathwayModel.addGraphicalLine(graphicalLine);
// reads graphics, comment group, points, and anchors
readLineElement(pathwayModel, graphicalLine, gln, refIdToJdomElement, elementToPoint);
}
}
}
/**
* Reads point {@link LinePoint} information for line element.
*
* @param lineElement the line element object.
* @param wyps the jdom waypoints element.
* @param elementToPoint the map of jdom element to line points.
* @throws ConverterException
*/
protected void readPoints(LineElement lineElement, Element wyps, Map elementToPoint)
throws ConverterException {
List ptList = new ArrayList();
List pts = wyps.getChildren("Point", wyps.getNamespace());
for (int i = 0; i < pts.size(); i++) {
Element pt = pts.get(i);
String elementId = pt.getAttributeValue("elementId");
// if start or end point, set arrowhead type for parent line element
if (i == 0) {
lineElement.setStartArrowHeadType(
ArrowHeadType.register(pt.getAttributeValue("arrowHead", ARROWHEAD_DEFAULT)));
} else if (i == pts.size() - 1) {
lineElement.setEndArrowHeadType(
ArrowHeadType.register(pt.getAttributeValue("arrowHead", ARROWHEAD_DEFAULT)));
}
double x = Double.parseDouble(pt.getAttributeValue("x").trim());
double y = Double.parseDouble(pt.getAttributeValue("y").trim());
LinePoint point = lineElement.new LinePoint(x, y);
point.setElementId(elementId);
ptList.add(point);
// adds info for reading
elementToPoint.put(pt, point);
}
// adds points to line
lineElement.setLinePoints(ptList);
}
/**
* Reads line element {@link LineElement} information for interaction or
* graphical line from jdom element.
*
* @param lineElement the line element object.
* @param ln the jdom line element.
* @param refIdToJdomElement the map of ref elementId to jdom element.
* @param elementToPoint the map of jdom element to line points.
* @throws ConverterException
*/
protected void readLineElement(PathwayModel pathwayModel, LineElement lineElement, Element ln,
Map refIdToJdomElement, Map elementToPoint) throws ConverterException {
// reads graphics
Element gfx = ln.getChild("Graphics", ln.getNamespace());
readLineStyleProperty(lineElement, gfx);
// reads comment group
readCommentGroup(pathwayModel, lineElement, ln, refIdToJdomElement);
// reads anchors
Element wyps = ln.getChild("Waypoints", ln.getNamespace());
readAnchors(lineElement, wyps);
// sets optional properties
String groupRef = ln.getAttributeValue("groupRef");
if (groupRef != null && !groupRef.equals(""))
lineElement.setGroupRefTo((Group) pathwayModel.getPathwayObject(ln.getAttributeValue("groupRef")));
}
/**
* Reads anchor {@link Anchor} information for line element from jdom element.
*
* @param lineElement the line element object.
* @param wyps the jdom waypoints element.
* @throws ConverterException
*/
protected void readAnchors(LineElement lineElement, Element wyps) throws ConverterException {
for (Element an : wyps.getChildren("Anchor", wyps.getNamespace())) {
String elementId = an.getAttributeValue("elementId");
double position = Double.parseDouble(an.getAttributeValue("position"));
AnchorShapeType shapeType = AnchorShapeType
.register(an.getAttributeValue("shapeType", ANCHORSHAPETYPE_DEFAULT));
lineElement.addAnchor(elementId, position, shapeType);
}
}
/**
* Reads elementRef {@link LinePoint#setElementRef} for pathway model points.
*
* @param pathwayModel the pathway model.
* @param elementToPoint the map of jdom element to line points.
* @throws ConverterException
*/
protected void readPointElementRefs(PathwayModel pathwayModel, Map elementToPoint)
throws ConverterException {
for (Element pt : elementToPoint.keySet()) {
String elementRefStr = pt.getAttributeValue("elementRef");
if (elementRefStr != null && !elementRefStr.equals("")) {
// retrieves referenced pathway element by elementId
LinkableTo elementRef = (LinkableTo) pathwayModel.getPathwayObject(elementRefStr);
// sets elementRef, relX, and relY for point
if (elementRef != null) {
LinePoint point = elementToPoint.get(pt);
double relX = Double.parseDouble(pt.getAttributeValue("relX").trim());
double relY = Double.parseDouble(pt.getAttributeValue("relY").trim());
point.linkTo(elementRef, relX, relY);
}
}
}
}
/**
* Reads rect property information. Jdom handles schema default values.
*
* @param shapedElement the shaped pathway element.
* @param gfx the jdom graphics element.
* @throws ConverterException
*/
protected void readRectProperty(ShapedElement shapedElement, Element gfx) throws ConverterException {
if (shapedElement.getClass() != State.class) {
double centerX = Double.parseDouble(gfx.getAttributeValue("centerX").trim());
double centerY = Double.parseDouble(gfx.getAttributeValue("centerY").trim());
shapedElement.setCenterX(centerX);
shapedElement.setCenterY(centerY);
}
double width = Double.parseDouble(gfx.getAttributeValue("width").trim());
double height = Double.parseDouble(gfx.getAttributeValue("height").trim());
shapedElement.setWidth(width);
shapedElement.setHeight(height);
}
/**
* Reads font property information. Jdom handles schema default values.
*
* @param shapedElement the shaped pathway element.
* @param gfx the jdom graphics element.
* @throws ConverterException
*/
protected void readFontProperty(ShapedElement shapedElement, Element gfx) throws ConverterException {
Color textColor = ColorUtils.stringToColor(gfx.getAttributeValue("textColor", TEXTCOLOR_DEFAULT));
String fontName = gfx.getAttributeValue("fontName", FONTNAME_DEFAULT);
boolean fontWeight = gfx.getAttributeValue("fontWeight", FONTWEIGHT_DEFAULT).equalsIgnoreCase("Bold");
boolean fontStyle = gfx.getAttributeValue("fontStyle", FONTSTYLE_DEFAULT).equals("Italic");
boolean fontDecoration = gfx.getAttributeValue("fontDecoration", FONTDECORATION_DEFAULT)
.equalsIgnoreCase("Underline");
boolean fontStrikethru = gfx.getAttributeValue("fontStrikethru", FONTSTRIKETHRU_DEFAULT)
.equalsIgnoreCase("Strikethru");
int fontSize = Integer.parseInt(gfx.getAttributeValue("fontSize", FONTSIZE_DEFAULT).trim());
HAlignType hAlignType = HAlignType.fromName(gfx.getAttributeValue("hAlign", HALIGN_DEFAULT));
VAlignType vAlignType = VAlignType.fromName(gfx.getAttributeValue("vAlign", VALIGN_DEFAULT));
// set font props
shapedElement.setTextColor(textColor);
shapedElement.setFontName(fontName);
shapedElement.setFontWeight(fontWeight);
shapedElement.setFontStyle(fontStyle);
shapedElement.setFontDecoration(fontDecoration);
shapedElement.setFontStrikethru(fontStrikethru);
shapedElement.setFontSize(fontSize);
shapedElement.setHAlign(hAlignType);
shapedElement.setVAlign(vAlignType);
}
/**
* Reads shape style property information. Jdom handles schema default values.
*
* @param shapedElement the shaped pathway element.
* @param gfx the jdom graphics element.
* @throws ConverterException
*/
protected void readShapeStyleProperty(ShapedElement shapedElement, Element gfx) throws ConverterException {
Color borderColor = ColorUtils.stringToColor(gfx.getAttributeValue("borderColor", BORDERCOLOR_DEFAULT));
LineStyleType borderStyle = LineStyleType.register(gfx.getAttributeValue("borderStyle", BORDERSTYLE_DEFAULT));
double borderWidth = Double.parseDouble(gfx.getAttributeValue("borderWidth", BORDERWIDTH_DEFAULT).trim());
Color fillColor = ColorUtils.stringToColor(gfx.getAttributeValue("fillColor", FILLCOLOR_DEFAULT));
ShapeType shapeType = ShapeType.register(gfx.getAttributeValue("shapeType", SHAPETYPE_DEFAULT), null);
String zOrder = gfx.getAttributeValue("zOrder");
String rotation = gfx.getAttributeValue("rotation");
// set shape style props
shapedElement.setBorderColor(borderColor);
shapedElement.setBorderStyle(borderStyle);
shapedElement.setBorderWidth(borderWidth);
shapedElement.setFillColor(fillColor);
shapedElement.setShapeType(shapeType);
if (zOrder != null) {
shapedElement.setZOrder(Integer.parseInt(zOrder.trim()));
}
if (rotation != null) {
shapedElement.setRotation(Double.parseDouble(rotation.trim()));
}
}
/**
* Reads line style property information. Jdom handles schema default values.
*
* @param lineElement the line pathway element.
* @param gfx the jdom graphics element.
* @throws ConverterException
*/
protected void readLineStyleProperty(LineElement lineElement, Element gfx) throws ConverterException {
Color lineColor = ColorUtils.stringToColor(gfx.getAttributeValue("lineColor", LINECOLOR_DEFAULT));
LineStyleType lineStyle = LineStyleType.register(gfx.getAttributeValue("lineStyle", LINESTYLE_DEFAULT));
double lineWidth = Double.parseDouble(gfx.getAttributeValue("lineWidth", LINEWIDTH_DEFAULT).trim());
ConnectorType connectorType = ConnectorType
.register(gfx.getAttributeValue("connectorType", CONNECTORTYPE_DEFAULT));
String zOrder = gfx.getAttributeValue("zOrder");
// set line style props
lineElement.setLineColor(lineColor);
lineElement.setLineStyle(lineStyle);
lineElement.setLineWidth(lineWidth);
lineElement.setConnectorType(connectorType);
if (zOrder != null) {
lineElement.setZOrder(Integer.parseInt(zOrder.trim()));
}
}
}
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