Author: rodche
Date: 2012-06-20 08:23:43 -0700 (Wed, 20 Jun 2012)
New Revision: 29638
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
Log:
Improved BioPAX visual style (Complex node shape, size, etc.). Removed or made
private much of unused code in the BiopaxUtils.
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-06-20 13:01:46 UTC (rev 29637)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-06-20 15:23:43 UTC (rev 29638)
@@ -908,7 +908,7 @@
private static String addIHOPLinks(CyNetwork network, BioPAXElement
bpe) {
- List<String> synList = new
ArrayList<String>(BioPaxUtil.getSynonymList(bpe));
+ List<String> synList = new
ArrayList<String>(BioPaxUtil.getSynonyms(bpe));
List<ExternalLink> dbList = xrefToExternalLinks(bpe,
Xref.class);
if (!synList.isEmpty() || !dbList.isEmpty()) {
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
2012-06-20 13:01:46 UTC (rev 29637)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
2012-06-20 15:23:43 UTC (rev 29638)
@@ -9,6 +9,7 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.events.SetCurrentNetworkViewEvent;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
+import org.cytoscape.biopax.internal.BioPaxMapper;
import org.cytoscape.biopax.internal.util.BioPaxUtil;
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.biopax.internal.view.BioPaxContainer;
@@ -69,7 +70,7 @@
@Override
public void handleEvent(NetworkViewAddedEvent e) {
final CyNetworkView view = e.getNetworkView();
- if(BioPaxUtil.isBioPAXNetwork(view.getModel())) {
+ if(isBioPAXNetwork(view.getModel())) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
@@ -95,7 +96,7 @@
CyNetworkView view = e.getNetworkView();
// update bpPanel accordingly
- if (view != null &&
BioPaxUtil.isBioPAXNetwork(view.getModel())) {
+ if (view != null && isBioPAXNetwork(view.getModel())) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
@@ -108,7 +109,7 @@
@Override
public void handleEvent(NetworkViewAboutToBeDestroyedEvent e) {
- if (BioPaxUtil.isBioPAXNetwork(e.getNetworkView().getModel())) {
+ if (isBioPAXNetwork(e.getNetworkView().getModel())) {
//TODO nothing?
}
}
@@ -120,7 +121,7 @@
if(view == null) return;
final CyNetwork network = view.getModel();
- if (BioPaxUtil.isBioPAXNetwork(network)) {
+ if (isBioPAXNetwork(network)) {
if
(!network.getDefaultNodeTable().equals(e.getSource()))
return;
@@ -253,4 +254,10 @@
// dingNodeView.addCustomGraphic(rect, paint,
NodeDetails.ANCHOR_CENTER);
// }
}
+
+
+ private static boolean isBioPAXNetwork(CyNetwork cyNetwork) {
+ return Boolean.TRUE == cyNetwork.getRow(cyNetwork)
+ .get(BioPaxMapper.BIOPAX_NETWORK, Boolean.class);
+ }
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-06-20 13:01:46 UTC (rev 29637)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-06-20 15:23:43 UTC (rev 29638)
@@ -31,7 +31,6 @@
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -47,18 +46,13 @@
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.BioSource;
-import org.biopax.paxtools.model.level3.Entity;
-import org.biopax.paxtools.model.level3.EntityReference;
import org.biopax.paxtools.model.level3.Interaction;
-import org.biopax.paxtools.model.level3.Level3Element;
import org.biopax.paxtools.model.level3.Named;
import org.biopax.paxtools.model.level3.Pathway;
-import org.biopax.paxtools.model.level3.Provenance;
import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
import org.biopax.paxtools.model.level3.XReferrable;
import org.biopax.paxtools.model.level3.Xref;
import org.biopax.paxtools.util.ClassFilterSet;
-import org.cytoscape.biopax.internal.BioPaxMapper;
import org.cytoscape.model.CyNetwork;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -182,7 +176,7 @@
if (nodeName == null || nodeName.length()== 0) {
nodeName = getStandardName(bpe);
if (nodeName == null || nodeName.length() == 0) {
- Collection<String> names = getSynonymList(bpe);
+ Collection<String> names = getSynonyms(bpe);
if (!names.isEmpty())
nodeName = getTheShortestString(names);
}
@@ -194,7 +188,7 @@
// get the shortest string
- public static String getTheShortestString(Collection<String> nameList) {
+ private static String getTheShortestString(Collection<String> nameList)
{
String shortest = null;
if (nameList != null && !nameList.isEmpty()) {
int minLength = -1;
@@ -285,7 +279,7 @@
* @param bpe BioPAX element
* @return short name field, or null if not available.
*/
- public static String getShortName(BioPAXElement bpe) {
+ private static String getShortName(BioPAXElement bpe) {
String shortName = null;
if(bpe instanceof Named) {
@@ -301,7 +295,7 @@
* @param bpe BioPAX element
* @return name field, or null if not available.
*/
- public static String getStandardName(BioPAXElement bpe) {
+ private static String getStandardName(BioPAXElement bpe) {
if(bpe instanceof Named) {
return ((Named)bpe).getStandardName();
} else
@@ -309,58 +303,18 @@
}
/**
- * Gets synonym names.
+ * Gets all names, if any.
*
* @param bpe BioPAX element
- * @return Collection of Synonym String Objects.
+ * @return Collection of names.
*/
- public static Collection<String> getSynonymList(BioPAXElement bpe) {
+ public static Collection<String> getSynonyms(BioPAXElement bpe) {
Collection<String> names = new HashSet<String>();
if(bpe instanceof Named) {
names = ((Named)bpe).getName();
}
return names;
}
-
- /**
- * Gets the Organism Name.
- *
- * @param bpe BioPAX element
- * @return organism field, or null if not available.
- */
- public static String getOrganismName(CyNetwork network, BioPAXElement
bpe) {
- String organism = null;
-
- BioPAXElement bs = (BioPAXElement) getValue(bpe, "organism");
- if (bs != null) {
- organism = getNodeName(bs);
- }
-
- return organism;
- }
-
- /**
- * If exist, gets all data sources
- * (according to the BioPAX spec. there should be only one...)
- * names as "comment : name"...
- *
- * @param bpe BioPAX element
- * @return data source names
- */
- public static String getDataSource(BioPAXElement bpe) {
- StringBuffer sb = new StringBuffer();
-
- if(bpe instanceof Entity) {
- Collection<Provenance> datasources =
((Entity)bpe).getDataSource();
- for(Provenance pr : datasources) {
- if(pr.getComment() != null)
- sb.append(pr.getComment().toString());
- sb.append(" :
").append(getNodeName(pr)).append(' ');
- }
- }
-
- return sb.toString();
- }
/**
@@ -387,29 +341,6 @@
return taxonomyId;
}
-
- /**
- * Gets the Comment field.
- *
- * @param bpe a BioPAX element
- * @return comment field
- */
- public static String getComment(BioPAXElement bpe) {
- return ((Level3Element)bpe).getComment().toString();
- }
-
- /**
- * Gets the Availability Field.
- *
- * @param bpe BioPAX element
- * @return availability field or null, if not available.
- */
- public static String getAvailability(BioPAXElement bpe) {
- if(bpe instanceof Entity) {
- return ((Entity)bpe).getAvailability().toString();
- } else
- return null;
- }
public static <T extends Xref> List<T> getXRefs(BioPAXElement bpe,
Class<T> xrefClass) {
@@ -475,45 +406,9 @@
return name;
}
-
- /**
- * Gets all the objects of provided BioPAX types.
- *
- * @param model BioPAX (PaxTools) model
- * @param classes query BioPAX types - e.g. Protein.class, Complex.class
- * @return
- */
- public static Set<? extends BioPAXElement> getObjects(Model model,
Class<? extends BioPAXElement>... classes) {
- Set<BioPAXElement> coll = new HashSet<BioPAXElement>();
- if (model != null) {
- for (Class<? extends BioPAXElement> c : classes) {
- coll.addAll(model.getObjects(c));
- }
- }
- return coll;
- }
-
/**
- * Checks whether the element is of
- * any of the listed BioPAX types.
- *
- * @param e
- * @param classes
- * @return
- */
- public static boolean isOneOfBiopaxClasses(BioPAXElement e, Class<?
extends BioPAXElement>... classes) {
- for(Class<? extends BioPAXElement> c : classes) {
- if(c.isInstance(e)) {
- return true;
- }
- }
- return false;
- }
-
-
- /**
* Gets abbreviated cellular location term.
*
* @param value
@@ -544,15 +439,6 @@
}
- public static Map<String, String> getChemModificationsMap() {
- return Collections.unmodifiableMap(chemModificationsMap);
- }
-
- public static Map<String, String> getCellLocationMap() {
- return Collections.unmodifiableMap(cellLocationMap);
- }
-
-
public static String truncateLongStr(String str) {
if(str != null) {
str = str.replaceAll("[\n\r \t]+", " ");
@@ -564,12 +450,6 @@
}
- public static boolean isBioPAXNetwork(CyNetwork cyNetwork) {
- return Boolean.TRUE == cyNetwork.getRow(cyNetwork)
- .get(BioPaxMapper.BIOPAX_NETWORK, Boolean.class);
- }
-
-
public static String toOwl(final BioPAXElement bpe) {
final StringWriter writer = new StringWriter();
final SimpleIOHandler simpleExporter = new
SimpleIOHandler(BioPAXLevel.L3);
@@ -586,34 +466,4 @@
return writer.toString();
}
-
- public static void fixDisplayName(Model model) {
- if (log.isInfoEnabled())
- log.info("Trying to auto-fix 'null' displayName...");
- // where it's null, set to the shortest name if possible
- for (Named e : model.getObjects(Named.class)) {
- if (e.getDisplayName() == null) {
- if (e.getStandardName() != null) {
- e.setDisplayName(e.getStandardName());
- } else if (!e.getName().isEmpty()) {
- String dsp =
e.getName().iterator().next();
- for (String name : e.getName()) {
- if (name.length() <
dsp.length())
- dsp = name;
- }
- e.setDisplayName(dsp);
- }
- }
- }
- // if required, set PE name to (already fixed) ER's name...
- for(EntityReference er :
model.getObjects(EntityReference.class)) {
- for(SimplePhysicalEntity spe :
er.getEntityReferenceOf()) {
- if(spe.getDisplayName() == null ||
spe.getDisplayName().trim().length() == 0) {
- if(er.getDisplayName() != null &&
er.getDisplayName().trim().length() > 0) {
-
spe.setDisplayName(er.getDisplayName());
- }
- }
- }
- }
- }
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
2012-06-20 13:01:46 UTC (rev 29637)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
2012-06-20 15:23:43 UTC (rev 29638)
@@ -95,12 +95,12 @@
/**
* Size of interaction node
*/
- private static final double
BIO_PAX_VISUAL_STYLE_INTERACTION_NODE_SIZE_SCALE = 0.33;
+ private static final double
BIO_PAX_VISUAL_STYLE_INTERACTION_NODE_SIZE_SCALE = 0.67;
/**
* Size of complex node
*/
- private static final double
BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE = 0.33;
+ private static final double
BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE = 0.67;
/**
* Default color of nodes
@@ -110,18 +110,17 @@
/**
* Node border color
*/
- private static final Color DEFAULT_NODE_BORDER_COLOR = new Color(0, 102,
- 102);
+ private static final Color DEFAULT_NODE_BORDER_COLOR = new Color(0,
102, 102);
/**
* Complex node color
*/
- private static final Color COMPLEX_NODE_COLOR = new Color(0, 0, 0);
+ private static final Color COMPLEX_NODE_COLOR = DEFAULT_NODE_COLOR;
//new Color(0, 0, 0);
/**
* Complex node color
*/
- private static final Color COMPLEX_NODE_BORDER_COLOR =
COMPLEX_NODE_COLOR;
+ private static final Color COMPLEX_NODE_BORDER_COLOR =
DEFAULT_NODE_BORDER_COLOR; //COMPLEX_NODE_COLOR;
VisualStyle style;
@@ -186,7 +185,9 @@
String name = claz.getSimpleName();
shape.putMapValue(name,
NodeShapeVisualProperty.ELLIPSE);
}
-
+ // use a different shape for Complex nodes
+ shape.putMapValue("Complex", NodeShapeVisualProperty.DIAMOND);
+
// hack for phosphorylated proteins
shape.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED,
NodeShapeVisualProperty.ELLIPSE);
@@ -241,17 +242,6 @@
new
Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT
*
BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE));
- /*
- * // hack for phosphorylated proteins - make them large so
label fits
- * within node // commented out by Ethan Cerami, November 15,
2006
- *
discreteMappingWidth.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED,
- * new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH
- * BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE));
- *
discreteMappingHeight.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED,
- * new Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT
- * BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_SIZE_SCALE));
- */
-
// create and set node height calculator in node appearance
calculator
style.setDefaultValue(BasicVisualLexicon.NODE_WIDTH,
BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH);
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
2012-06-20 13:01:46 UTC (rev 29637)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
2012-06-20 15:23:43 UTC (rev 29638)
@@ -212,8 +212,8 @@
stringRef =
network.getRow(node,CyNetwork.HIDDEN_ATTRS).get(BioPaxUtil.BIOPAX_DATA,
String.class);
//stringRef = row.get(BioPaxUtil.BIOPAX_DATA, String.class);
if (stringRef != null) {
- appendHeader("BioPAX L3 (excerpt)", buf);
- buf.append("<pre>" + StringEscapeUtils.escapeXml(stringRef) +
"</pre>");
+ appendHeader("BioPAX L3 (fragment)", buf);
+ buf.append("<pre class='excerpt'>" +
StringEscapeUtils.escapeXml(stringRef) + "</pre>");
}
buf.append("</BODY></HTML>");
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
2012-06-20 13:01:46 UTC (rev 29637)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
2012-06-20 15:23:43 UTC (rev 29638)
@@ -25,13 +25,10 @@
**/
package org.cytoscape.cpath2.internal.util;
-import java.io.FileNotFoundException;
-import java.io.InputStream;
import java.io.StringWriter;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -45,7 +42,6 @@
import org.biopax.paxtools.controller.ObjectPropertyEditor;
import org.biopax.paxtools.controller.PropertyEditor;
import org.biopax.paxtools.controller.SimpleEditorMap;
-import org.biopax.paxtools.converter.OneTwoThree;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.BioPAXLevel;
@@ -53,12 +49,9 @@
import org.biopax.paxtools.model.level3.BioSource;
import org.biopax.paxtools.model.level3.CellularLocationVocabulary;
import org.biopax.paxtools.model.level3.Entity;
-import org.biopax.paxtools.model.level3.EntityReference;
import org.biopax.paxtools.model.level3.Interaction;
-import org.biopax.paxtools.model.level3.Level3Element;
import org.biopax.paxtools.model.level3.Named;
import org.biopax.paxtools.model.level3.PhysicalEntity;
-import org.biopax.paxtools.model.level3.Provenance;
import org.biopax.paxtools.model.level3.PublicationXref;
import org.biopax.paxtools.model.level3.RelationshipTypeVocabulary;
import org.biopax.paxtools.model.level3.RelationshipXref;
@@ -140,36 +133,12 @@
/**
- * Constructor.
- *
- * @param in BioPAX data file name.
- * @return BioPaxUtil new instance (containing the imported BioPAX data)
- * @throws FileNotFoundException
- */
- public static Model read(final InputStream in) throws
FileNotFoundException {
- Model model = null;
- try {
- SimpleIOHandler handler = new SimpleIOHandler();
- handler.mergeDuplicates(true); // a workaround
(illegal) BioPAX data having duplicated rdf:ID...
- model = handler.convertFromOWL(in);
- // immediately convert to BioPAX Level3 model
- if(model != null &&
BioPAXLevel.L2.equals(model.getLevel())) {
- model = new OneTwoThree().filter(model);
- }
- } catch (Throwable e) {
- log.warn("Import failed: " + e);
- }
- return model;
- }
-
-
- /**
* Gets or infers the name of the node.
*
* @param bpe BioPAX Element
* @return
*/
- public static String getNodeName(BioPAXElement bpe) {
+ private static String getNodeName(BioPAXElement bpe) {
if(bpe == null) {
return "";
@@ -179,7 +148,7 @@
if (nodeName == null || nodeName.length()== 0) {
nodeName = getStandardName(bpe);
if (nodeName == null || nodeName.length() == 0) {
- Collection<String> names = getSynonymList(bpe);
+ Collection<String> names = getSynonyms(bpe);
if (!names.isEmpty())
nodeName = getTheShortestString(names);
}
@@ -191,7 +160,7 @@
// get the shortest string
- public static String getTheShortestString(Collection<String> nameList) {
+ private static String getTheShortestString(Collection<String> nameList)
{
String shortest = null;
if (nameList != null && !nameList.isEmpty()) {
int minLength = -1;
@@ -214,7 +183,7 @@
*
* @return the value or null
*/
- public static Object getValue(BioPAXElement bpe, String... properties) {
+ private static Object getValue(BioPAXElement bpe, String... properties)
{
for (String property : properties) {
try {
Method method =
bpe.getModelInterface().getMethod(
@@ -246,7 +215,7 @@
*
* @return the set of property values or null
*/
- public static Collection<?> getValues(BioPAXElement bpe, String...
properties) {
+ private static Collection<?> getValues(BioPAXElement bpe, String...
properties) {
Collection<Object> col = new HashSet<Object>();
for (String property : properties) {
@@ -282,7 +251,7 @@
* @param bpe BioPAX element
* @return short name field, or null if not available.
*/
- public static String getShortName(BioPAXElement bpe) {
+ private static String getShortName(BioPAXElement bpe) {
String shortName = null;
if(bpe instanceof Named) {
@@ -298,7 +267,7 @@
* @param bpe BioPAX element
* @return name field, or null if not available.
*/
- public static String getStandardName(BioPAXElement bpe) {
+ private static String getStandardName(BioPAXElement bpe) {
if(bpe instanceof Named) {
return ((Named)bpe).getStandardName();
} else
@@ -306,12 +275,12 @@
}
/**
- * Gets synonym names.
+ * Gets all names, if any present.
*
* @param bpe BioPAX element
- * @return Collection of Synonym String Objects.
+ * @return Collection of names.
*/
- public static Collection<String> getSynonymList(BioPAXElement bpe) {
+ private static Collection<String> getSynonyms(BioPAXElement bpe) {
Collection<String> names = new HashSet<String>();
if(bpe instanceof Named) {
names = ((Named)bpe).getName();
@@ -319,54 +288,14 @@
return names;
}
- /**
- * Gets the Organism Name.
- *
- * @param bpe BioPAX element
- * @return organism field, or null if not available.
- */
- public static String getOrganismName(CyNetwork network, BioPAXElement
bpe) {
- String organism = null;
-
- BioPAXElement bs = (BioPAXElement) getValue(bpe, "organism");
- if (bs != null) {
- organism = getNodeName(bs);
- }
-
- return organism;
- }
-
- /**
- * If exist, gets all data sources
- * (according to the BioPAX spec. there should be only one...)
- * names as "comment : name"...
- *
- * @param bpe BioPAX element
- * @return data source names
- */
- public static String getDataSource(BioPAXElement bpe) {
- StringBuffer sb = new StringBuffer();
-
- if(bpe instanceof Entity) {
- Collection<Provenance> datasources =
((Entity)bpe).getDataSource();
- for(Provenance pr : datasources) {
- if(pr.getComment() != null)
- sb.append(pr.getComment().toString());
- sb.append(" :
").append(getNodeName(pr)).append(' ');
- }
- }
-
- return sb.toString();
- }
-
/**
* Gets the NCBI Taxonomy ID.
*
* @param bpe BioPAX element
* @return taxonomyId, or -1, if not available.
*/
- public static int getOrganismTaxonomyId(CyNetwork network,
BioPAXElement bpe) {
+ private static int getOrganismTaxonomyId(CyNetwork network,
BioPAXElement bpe) {
int taxonomyId = -1;
try {
@@ -385,31 +314,9 @@
return taxonomyId;
}
- /**
- * Gets the Comment field.
- *
- * @param bpe a BioPAX element
- * @return comment field
- */
- public static String getComment(BioPAXElement bpe) {
- return ((Level3Element)bpe).getComment().toString();
- }
-
- /**
- * Gets the Availability Field.
- *
- * @param bpe BioPAX element
- * @return availability field or null, if not available.
- */
- public static String getAvailability(BioPAXElement bpe) {
- if(bpe instanceof Entity) {
- return ((Entity)bpe).getAvailability().toString();
- } else
- return null;
- }
- public static <T extends Xref> List<T> getXRefs(BioPAXElement bpe,
Class<T> xrefClass) {
+ private static <T extends Xref> List<T> getXRefs(BioPAXElement bpe,
Class<T> xrefClass) {
if(bpe instanceof XReferrable) {
List<T> erefs = new ArrayList<T>();
erefs.addAll(new ClassFilterSet<Xref,T>(
((XReferrable)bpe).getXref(), xrefClass) );
@@ -423,67 +330,15 @@
}
return new ArrayList<T>();
}
-
- /**
- * Gets the joint set of all known subclasses of the specified BioPAX
types.
- *
- * @param classes BioPAX (PaxTools Model Interfaces) Classes
- * @return
- */
- public static Collection<Class> getSubclassNames(Class<? extends
BioPAXElement>... classes) {
- Collection<Class> subclasses = new HashSet<Class>();
-
- for (Class<? extends BioPAXElement> c : classes) {
-
subclasses.addAll(SimpleEditorMap.L3.getKnownSubClassesOf(c));
- }
-
- return subclasses;
- }
/**
- * Gets all the objects of provided BioPAX types.
- *
- * @param model BioPAX (PaxTools) model
- * @param classes query BioPAX types - e.g. Protein.class, Complex.class
- * @return
- */
- public static Set<? extends BioPAXElement> getObjects(Model model,
Class<? extends BioPAXElement>... classes) {
- Set<BioPAXElement> coll = new HashSet<BioPAXElement>();
- if (model != null) {
- for (Class<? extends BioPAXElement> c : classes) {
- coll.addAll(model.getObjects(c));
- }
- }
- return coll;
- }
-
-
- /**
- * Checks whether the element is of
- * any of the listed BioPAX types.
- *
- * @param e
- * @param classes
- * @return
- */
- public static boolean isOneOfBiopaxClasses(BioPAXElement e, Class<?
extends BioPAXElement>... classes) {
- for(Class<? extends BioPAXElement> c : classes) {
- if(c.isInstance(e)) {
- return true;
- }
- }
- return false;
- }
-
-
- /**
* Gets abbreviated cellular location term.
*
* @param value
* @return
*/
- public static String getAbbrCellLocation(String value) {
+ private static String getAbbrCellLocation(String value) {
for(String abr: cellLocationMap.keySet()) {
if(value.toLowerCase().contains(abr)) {
return cellLocationMap.get(abr);
@@ -498,7 +353,7 @@
* @param value
* @return
*/
- public static String getAbbrChemModification(String value) {
+ private static String getAbbrChemModification(String value) {
for(String abr: chemModificationsMap.keySet()) {
if(value.toLowerCase().contains(abr)) {
return chemModificationsMap.get(abr);
@@ -508,16 +363,7 @@
}
- public static Map<String, String> getChemModificationsMap() {
- return Collections.unmodifiableMap(chemModificationsMap);
- }
-
- public static Map<String, String> getCellLocationMap() {
- return Collections.unmodifiableMap(cellLocationMap);
- }
-
-
- public static String truncateLongStr(String str) {
+ private static String truncateLongStr(String str) {
if(str != null) {
str = str.replaceAll("[\n\r \t]+", " ");
if (str.length() > MAX_DISPLAY_STRING_LEN) {
@@ -528,7 +374,7 @@
}
- public static String toOwl(BioPAXElement bpe) {
+ private static String toOwl(BioPAXElement bpe) {
StringWriter writer = new StringWriter();
try {
SimpleIOHandler simpleExporter = new
SimpleIOHandler(BioPAXLevel.L3);
@@ -540,37 +386,13 @@
}
- public static void fixDisplayName(Model model) {
- if (log.isInfoEnabled())
- log.info("Trying to auto-fix 'null' displayName...");
- // where it's null, set to the shortest name if possible
- for (Named e : model.getObjects(Named.class)) {
- if (e.getDisplayName() == null) {
- if (e.getStandardName() != null) {
- e.setDisplayName(e.getStandardName());
- } else if (!e.getName().isEmpty()) {
- String dsp =
e.getName().iterator().next();
- for (String name : e.getName()) {
- if (name.length() <
dsp.length())
- dsp = name;
- }
- e.setDisplayName(dsp);
- }
- }
- }
- // if required, set PE name to (already fixed) ER's name...
- for(EntityReference er :
model.getObjects(EntityReference.class)) {
- for(SimplePhysicalEntity spe :
er.getEntityReferenceOf()) {
- if(spe.getDisplayName() == null ||
spe.getDisplayName().trim().length() == 0) {
- if(er.getDisplayName() != null &&
er.getDisplayName().trim().length() > 0) {
-
spe.setDisplayName(er.getDisplayName());
- }
- }
- }
- }
- }
-
-
+ /**
+ * Generates node attributes from BioPAX properties.
+ *
+ * @param element
+ * @param node
+ * @param network
+ */
public static void createAttributesFromProperties(final BioPAXElement
element,
final CyNode node, final CyNetwork network)
{
@@ -803,27 +625,8 @@
}
- private static String addXRefs(List<ExternalLink> xrefList) {
- if (!xrefList.isEmpty()) {
- StringBuffer temp = new StringBuffer("<ul>");
- for (ExternalLink link : xrefList) {
- // Ignore cPath Link.
- if (link.getDbName() != null &&
link.getDbName().equalsIgnoreCase("CPATH")) {
- continue;
- }
- temp.append("<li>- ");
-
temp.append(ExternalLinkUtil.createLink(link.getDbName(), link.getId()));
- temp.append("</li>");
- }
- temp.append("</ul>");
- return temp.toString();
- }
-
- return null;
- }
-
private static String addIHOPLinks(CyNetwork network, BioPAXElement
bpe) {
- List<String> synList = new
ArrayList<String>(BioPaxUtil.getSynonymList(bpe));
+ List<String> synList = new
ArrayList<String>(BioPaxUtil.getSynonyms(bpe));
List<ExternalLink> dbList = xrefToExternalLinks(bpe,
Xref.class);
if (!synList.isEmpty() || !dbList.isEmpty()) {
@@ -836,8 +639,9 @@
return null;
}
+
- public static <T extends Xref> List<ExternalLink>
xrefToExternalLinks(BioPAXElement bpe, Class<T> xrefClass) {
+ private static <T extends Xref> List<ExternalLink>
xrefToExternalLinks(BioPAXElement bpe, Class<T> xrefClass) {
if(bpe instanceof XReferrable) {
List<ExternalLink> erefs = new
ArrayList<ExternalLink>();
@@ -897,6 +701,7 @@
return dbList;
}
+
private static List<String> getXRefList(BioPAXElement bpe, String
xrefType) {
List<String> listToReturn = new ArrayList<String>();
@@ -919,6 +724,7 @@
return listToReturn;
}
+
private static NodeAttributesWrapper
getInteractionChemicalModifications(BioPAXElement participantElement)
{
@@ -976,6 +782,7 @@
return new NodeAttributesWrapper(chemicalModificationsMap,
chemicalModifications);
}
+
private static String getModificationsString(NodeAttributesWrapper
chemicalModificationsWrapper)
{
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