Author: rodche
Date: 2012-10-23 09:49:56 -0700 (Tue, 23 Oct 2012)
New Revision: 30695
Modified:
core3/impl/trunk/biopax-impl/pom.xml
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/view/BioPaxDetailsPanel.java
core3/impl/trunk/cpath2-impl/pom.xml
Log:
Updated to paxtools 4.1.5b2 (fixes a bug in the biopax level 2 to 3 converter).
Some internal re-factoring (attr. names, constants).
Modified: core3/impl/trunk/biopax-impl/pom.xml
===================================================================
--- core3/impl/trunk/biopax-impl/pom.xml 2012-10-23 16:40:59 UTC (rev
30694)
+++ core3/impl/trunk/biopax-impl/pom.xml 2012-10-23 16:49:56 UTC (rev
30695)
@@ -9,7 +9,7 @@
<properties>
<bundle.symbolicName>org.cytoscape.biopax-impl</bundle.symbolicName>
<bundle.namespace>org.cytoscape.biopax</bundle.namespace>
- <paxtools.version>4.1.5b</paxtools.version>
+ <paxtools.version>4.1.5b2</paxtools.version>
</properties>
<modelVersion>4.0.0</modelVersion>
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
2012-10-23 16:40:59 UTC (rev 30694)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-10-23 16:49:56 UTC (rev 30695)
@@ -148,12 +148,12 @@
private final Model model;
private final CyNetworkFactory networkFactory;
private final TaskMonitor taskMonitor;
- private final CyGroupFactory cyGroupFactory;
+// private final CyGroupFactory cyGroupFactory;
// BioPAX ID (URI) to CyNode map
// remark: nodes's CyTable will also have 'URI' (RDF Id) column
private final Map<BioPAXElement, CyNode>
- uriToCyNodeMap = new HashMap<BioPAXElement, CyNode>();
+ bpeToCyNodeMap = new HashMap<BioPAXElement, CyNode>();
/**
@@ -169,7 +169,7 @@
this.model = model;
this.networkFactory = cyNetworkFactory;
this.taskMonitor = taskMonitor;
- this.cyGroupFactory = cyGroupFactory;
+// this.cyGroupFactory = cyGroupFactory;
}
@@ -231,12 +231,12 @@
// List<CyNode> nodeList = new ArrayList<CyNode>();
// List<CyEdge> edgeList = new ArrayList<CyEdge>();
- CyNode cyParentNode = uriToCyNodeMap.get(par);
+ CyNode cyParentNode = bpeToCyNodeMap.get(par);
assert cyParentNode != null : "cyParentNode is NULL.";
// for each its member PE, add the directed edge
for (PhysicalEntity member : members)
{
- CyNode cyMemberNode =
uriToCyNodeMap.get(member);
+ CyNode cyMemberNode =
bpeToCyNodeMap.get(member);
CyEdge edge = network.addEdge(cyParentNode,
cyMemberNode, true);
AttributeUtil.set(network, edge,
BIOPAX_EDGE_TYPE, "member", String.class);
@@ -265,7 +265,7 @@
// Create node symbolizing the interaction
CyNode node = network.addNode();
- uriToCyNodeMap.put(bpe, node);
+ bpeToCyNodeMap.put(bpe, node);
// traverse
createAttributesFromProperties(bpe, node, network);
@@ -321,7 +321,7 @@
continue;
// get node
- CyNode complexCyNode =
uriToCyNodeMap.get(complexElement);
+ CyNode complexCyNode =
bpeToCyNodeMap.get(complexElement);
// List<CyNode> nodeList = new ArrayList<CyNode>();
// List<CyEdge> edgeList = new ArrayList<CyEdge>();
@@ -329,7 +329,7 @@
// get all components. There can be 0 or more
for (PhysicalEntity member : members)
{
- CyNode complexMemberCyNode =
uriToCyNodeMap.get(member);
+ CyNode complexMemberCyNode =
bpeToCyNodeMap.get(member);
// create edge, set attributes
CyEdge edge = network.addEdge(complexCyNode,
complexMemberCyNode, true);
AttributeUtil.set(network, edge,
BIOPAX_EDGE_TYPE, "contains", String.class);
@@ -378,14 +378,14 @@
private void linkNodes(CyNetwork network, BioPAXElement bpeA,
BioPAXElement bpeB, String type)
{
// Note: getCyNode also assigns cellular location attribute...
- CyNode nodeA = uriToCyNodeMap.get(bpeA);
+ CyNode nodeA = bpeToCyNodeMap.get(bpeA);
if(nodeA == null) {
log.debug("linkNodes: no node was created for "
+ bpeA.getModelInterface() + " " +
bpeA.getRDFId());
return; //e.g., we do not create any pathway nodes
currently...
}
- CyNode nodeB = uriToCyNodeMap.get(bpeB);
+ CyNode nodeB = bpeToCyNodeMap.get(bpeB);
if(nodeB == null) {
log.debug("linkNodes: no node was created for "
+ bpeB.getModelInterface() + " " +
bpeB.getRDFId());
@@ -435,14 +435,11 @@
}
- /**
+ /*
* Given a binding element (complex or interaction)
* and type (like left or right),
* returns chemical modification (abbreviated form).
*
- * @param physicalElement Element
- * @param type String
- * @return NodeAttributesWrapper
*/
private NodeAttributesWrapper
getInteractionChemicalModifications(BioPAXElement participantElement)
{
@@ -502,7 +499,7 @@
}
- /**
+ /*
* A helper function to get post-translational modifications string.
*/
private String getModificationsString(NodeAttributesWrapper
chemicalModificationsWrapper)
@@ -640,14 +637,13 @@
Filter<PropertyEditor> filter = new Filter<PropertyEditor>() {
@Override
// skips for entity-range properties (which map to
edges rather than attributes!),
- // and several utility classes range ones
- // (for which we do not want generate attributes or do
another way)
+ // and several utility classes ranges (for which we do
not want generate attributes or do another way)
public boolean filter(PropertyEditor editor) {
if(editor instanceof ObjectPropertyEditor) {
Class c = editor.getRange();
String prop = editor.getProperty();
if( Entity.class.isAssignableFrom(c)
- || "name".equals(prop)
//display/standard name is enough
+ || "name".equals(prop) //name
clash with the Cytoscape reserved column (display/standard name is enough)
||
Stoichiometry.class.isAssignableFrom(c)
|| "nextStep".equals(prop)
) {
@@ -662,8 +658,6 @@
@SuppressWarnings("unchecked")
AbstractTraverser bpeAutoMapper = new
AbstractTraverser(SimpleEditorMap.L3, filter)
{
- final Logger log =
LoggerFactory.getLogger(AbstractTraverser.class);
-
@SuppressWarnings("rawtypes")
@Override
protected void visit(Object obj, BioPAXElement bpe,
Model model,
@@ -711,7 +705,7 @@
}
private String getAttrName(Stack<String> props) {
- return "/" + StringUtils.join(props, "/");
+ return StringUtils.join(props, "/");
}
};
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
2012-10-23 16:40:59 UTC (rev 30694)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
2012-10-23 16:49:56 UTC (rev 30695)
@@ -204,7 +204,7 @@
for (CyNode node : network.getNodeList()) {
CyRow row = network.getRow(node);
String tip = row.get(BIOPAX_ENTITY_TYPE, String.class)
+ "\n"
- + row.get("/cellularLocation",
String.class);
+ + row.get("cellularLocation",
String.class);
View<CyNode> nodeView = networkView.getNodeView(node);
nodeView.setLockedValue(BasicVisualLexicon.NODE_TOOLTIP, tip);
}
@@ -224,6 +224,7 @@
// get chemical modifications
int count = 0;
boolean isPhosphorylated = false;
+
// TODO: MultiHashMap
// MultiHashMapDefinition mhmdef =
nodeAttributes.getMultiHashMapDefinition();
//
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
2012-10-23 16:40:59 UTC (rev 30694)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-10-23 16:49:56 UTC (rev 30695)
@@ -442,7 +442,7 @@
if(str != null) {
str = str.replaceAll("[\n\r \t]+", " ");
if (str.length() > MAX_DISPLAY_STRING_LEN) {
- str = str.substring(0, MAX_DISPLAY_STRING_LEN)
+ "...";
+ str = str.substring(0,
MAX_DISPLAY_STRING_LEN/2-1) + "..." +
str.substring(str.length()-MAX_DISPLAY_STRING_LEN/2);
}
}
return str;
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
2012-10-23 16:40:59 UTC (rev 30694)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
2012-10-23 16:49:56 UTC (rev 30695)
@@ -33,7 +33,6 @@
import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.Container;
import java.awt.Dimension;
import java.util.List;
@@ -53,7 +52,6 @@
import javax.swing.text.html.ParagraphView;
import javax.swing.text.html.StyleSheet;
-import org.apache.commons.lang.StringEscapeUtils;
import org.biopax.paxtools.model.level3.PhysicalEntity;
import org.cytoscape.application.CyApplicationManager;
@@ -150,9 +148,9 @@
*/
public void resetText(String text) {
StringBuffer temp = new StringBuffer();
- temp.append("<HTML><BODY>");
+ temp.append("<html><body>");
temp.append(text);
- temp.append("</BODY></HTML>");
+ temp.append("</body></html>");
textPane.setText(temp.toString());
}
@@ -164,7 +162,7 @@
public void showDetails(CyNetwork network, CyNode node) {
String stringRef;
- StringBuffer buf = new StringBuffer("<HTML>");
+ StringBuffer buf = new StringBuffer("<html><body>");
CyRow row = network.getRow(node);
@@ -178,9 +176,13 @@
// organism
stringRef = null;
- stringRef = row.get("/entityReference/organism/displayName",
String.class);
+ stringRef = row.get("entityReference/organism/displayName",
String.class);
if(stringRef == null)
- stringRef = row.get("/organism/displayName", String.class);
+ stringRef = row.get("entityReference/organism/standardName",
String.class);
+ if(stringRef == null)
+ stringRef = row.get("organism/displayName", String.class);
+ if(stringRef == null)
+ stringRef = row.get("organism/standardName", String.class);
if (stringRef != null) {
buf.append("<h3>" + stringRef + "</h3>");
}
@@ -190,7 +192,7 @@
// cellular location
stringRef = null;
- stringRef = row.get("/cellularLocation", String.class);
+ stringRef = row.get("cellularLocation", String.class);
if (stringRef != null) {
appendHeader("Cellular Location: " + stringRef, buf);
}
@@ -200,7 +202,7 @@
BIOPAX_CHEMICAL_MODIFICATIONS_LIST, "Chemical
Modifications:", buf);
// data source
- addAttributeList(network, node, null, "/dataSource", "Data sources:",
buf);
+ addAttributeList(network, node, null, "dataSource", "Data sources:",
buf);
// links
@@ -216,13 +218,9 @@
// buf.append("<pre class='excerpt'>" +
StringEscapeUtils.escapeXml(stringRef) + "</pre>");
// }
- buf.append("</BODY></HTML>");
+ buf.append("</body></html>");
textPane.setText(buf.toString());
textPane.setCaretPosition(0);
-
- // If the containing parent is a BioPaxDetailsWindow, show it.
- // This only applies in Cytoscape 2.1 and local testing
- Container parent = this.getTopLevelAncestor();
}
//TODO test; remove or upgrade to PC2 api (URI based)
@@ -279,21 +277,21 @@
String listItem = list.get(lc);
if ((listItem != null) && (listItem.length() > 0)) {
- displayString.append("<LI> - " + listItem);
- displayString.append("</LI>");
+ displayString.append("<li> - " + listItem);
+ displayString.append("</li>");
}
}
if (tooMany) {
- displayString.append("<LI> ...</LI>");
+ displayString.append("<li> ...</li>");
}
// do we have a string to display ?
if (displayString.length() > 0) {
if(label != null)
appendHeader(label, buf);
- buf.append ("<UL>");
+ buf.append ("<ul>");
appendData(displayString.toString(), buf, false);
- buf.append ("</UL>");
+ buf.append ("</ul>");
}
}
@@ -306,7 +304,7 @@
private void appendData(String data, StringBuffer buf, boolean
appendBr) {
buf.append(data);
if (appendBr) {
- buf.append("<BR>");
+ buf.append("<br/>");
}
}
@@ -315,9 +313,9 @@
String ihopLinks = row.get(BIOPAX_IHOP_LINKS, String.class);
if (ihopLinks != null) {
- buf.append("<UL>");
+ buf.append("<ul>");
appendData(ihopLinks, buf, false);
- buf.append("</UL>");
+ buf.append("</ul>");
}
}
}
Modified: core3/impl/trunk/cpath2-impl/pom.xml
===================================================================
--- core3/impl/trunk/cpath2-impl/pom.xml 2012-10-23 16:40:59 UTC (rev
30694)
+++ core3/impl/trunk/cpath2-impl/pom.xml 2012-10-23 16:49:56 UTC (rev
30695)
@@ -9,7 +9,7 @@
<properties>
<bundle.symbolicName>org.cytoscape.cpath2-impl</bundle.symbolicName>
<bundle.namespace>org.cytoscape.cpath2</bundle.namespace>
- <paxtools.version>4.1.5b</paxtools.version>
+ <paxtools.version>4.1.5b2</paxtools.version>
</properties>
<modelVersion>4.0.0</modelVersion>
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