Author: rodche
Date: 2012-10-18 10:35:47 -0700 (Thu, 18 Oct 2012)
New Revision: 30684
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/util/BioPaxUtil.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
Log:
Removed a feature: the hidden attribute and the results panel html section
responsible for showing a BioPAX RDF/XML fragment data for a selected node.
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
2012-10-18 15:52:25 UTC (rev 30683)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-10-18 17:35:47 UTC (rev 30684)
@@ -63,52 +63,52 @@
/**
* BioPax Node Attribute: Entity TYPE
*/
- public static final String BIOPAX_ENTITY_TYPE = "biopax_type";
+ public static final String BIOPAX_ENTITY_TYPE = "BIOPAX_TYPE";
/**
* BioPax Node Attribute: CHEMICAL_MODIFICATIONS_MAP
*/
- public static final String BIOPAX_CHEMICAL_MODIFICATIONS_MAP =
"chemical_modifications_map";
+ public static final String BIOPAX_CHEMICAL_MODIFICATIONS_MAP =
"CHEMICAL_MODIFICATIONS_MAP";
/**
* BioPax Node Attribute: CHEMICAL_MODIFICATIONS_LIST
*/
- public static final String BIOPAX_CHEMICAL_MODIFICATIONS_LIST =
"chemical_modifications";
+ public static final String BIOPAX_CHEMICAL_MODIFICATIONS_LIST =
"CHEMICAL_MODIFICATIONS";
/**
* Node Attribute: UNIFICATION_REFERENCES
*/
- public static final String BIOPAX_UNIFICATION_REFERENCES =
"unification_references";
+ public static final String BIOPAX_UNIFICATION_REFERENCES =
"UNIFICATION_REFERENCES";
/**
* Node Attribute: RELATIONSHIP_REFERENCES
*/
- public static final String BIOPAX_RELATIONSHIP_REFERENCES =
"relationship_references";
+ public static final String BIOPAX_RELATIONSHIP_REFERENCES =
"RELATIONSHIP_REFERENCES";
/**
* Node Attribute: PUBLICATION_REFERENCES
*/
- public static final String BIOPAX_PUBLICATION_REFERENCES =
"publication_references";
+ public static final String BIOPAX_PUBLICATION_REFERENCES =
"PUBLICATION_REFERENCES";
/**
* Node Attribute: XREF_IDs.
*/
- public static final String BIOPAX_XREF_IDS = "identifiers";
+ public static final String BIOPAX_XREF_IDS = "IDENTIFIERS";
/**
* Node Attribute: BIOPAX_XREF_PREFIX.
*/
- public static final String BIOPAX_XREF_PREFIX = "xref.";
+ public static final String BIOPAX_XREF_PREFIX = "XREF.";
/**
* Node Attribute: IHOP_LINKS
*/
- public static final String BIOPAX_IHOP_LINKS = "ihop_links";
+ public static final String BIOPAX_IHOP_LINKS = "IHOP_LINKS";
/**
* Node Attribute: AFFYMETRIX_REFERENCES
*/
- public static final String BIOPAX_AFFYMETRIX_REFERENCES_LIST =
"affymetrix_references";
+ public static final String BIOPAX_AFFYMETRIX_REFERENCES_LIST =
"AFFYMETRIX_REFERENCES";
public static final Logger log =
LoggerFactory.getLogger(BioPaxMapper.class);
@@ -569,7 +569,7 @@
}
// ihop links
- String stringRef = addIHOPLinks(network, resource);
+ String stringRef = ihopLinks(resource);
if (stringRef != null) {
AttributeUtil.set(network, node,
CyNetwork.HIDDEN_ATTRS, BIOPAX_IHOP_LINKS, stringRef, String.class);
}
@@ -722,11 +722,11 @@
// add a piece of the BioPAX (RDF/XML without parent|child
elements)
- //the following attr. was experimental, not so important for
users...
- if(network.getNodeCount() < 100) { //- this condition was added
for performance/memory...
- String owl = BioPaxUtil.toOwl(element); // (requires
common-lang-2.4 bundle to be started)
- AttributeUtil.set(network, node,
CyNetwork.HIDDEN_ATTRS, BioPaxUtil.BIOPAX_DATA, owl, String.class);
- }
+// //the following attr. was experimental, not so important for
users...
+// if(network.getNodeCount() < 100) { //- this condition was added
for performance/memory...
+// String owl = BioPaxUtil.toOwl(element); // (requires
common-lang-2.4 bundle to be started)
+// AttributeUtil.set(network, node,
CyNetwork.HIDDEN_ATTRS, BioPaxUtil.BIOPAX_DATA, owl, String.class);
+// }
String name =
BioPaxUtil.truncateLongStr(BioPaxUtil.getNodeName(element) + "");
@@ -941,19 +941,17 @@
}
- private static String addIHOPLinks(CyNetwork network, BioPAXElement
bpe) {
+ private static String ihopLinks(BioPAXElement bpe) {
List<String> synList = new
ArrayList<String>(BioPaxUtil.getSynonyms(bpe));
List<ExternalLink> dbList = xrefToExternalLinks(bpe,
Xref.class);
+ String htmlLink = null;
if (!synList.isEmpty() || !dbList.isEmpty()) {
- String htmlLink =
ExternalLinkUtil.createIHOPLink(bpe.getModelInterface().getSimpleName(),
- synList, dbList,
BioPaxUtil.getOrganismTaxonomyId(network, bpe));
- if (htmlLink != null) {
- return htmlLink;
- }
+ htmlLink =
ExternalLinkUtil.createIHOPLink(bpe.getModelInterface().getSimpleName(),
+ synList, dbList,
BioPaxUtil.getOrganismTaxonomyId(bpe));
}
- return null;
+ return htmlLink;
}
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
2012-10-18 15:52:25 UTC (rev 30683)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
2012-10-18 17:35:47 UTC (rev 30684)
@@ -53,7 +53,6 @@
import org.biopax.paxtools.model.level3.XReferrable;
import org.biopax.paxtools.model.level3.Xref;
import org.biopax.paxtools.util.ClassFilterSet;
-import org.cytoscape.model.CyNetwork;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -319,11 +318,11 @@
/**
* Gets the NCBI Taxonomy ID.
- *
* @param bpe BioPAX element
+ *
* @return taxonomyId, or -1, if not available.
*/
- public static int getOrganismTaxonomyId(CyNetwork network,
BioPAXElement bpe) {
+ public static int getOrganismTaxonomyId(BioPAXElement bpe) {
int taxonomyId = -1;
try {
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
2012-10-18 15:52:25 UTC (rev 30683)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
2012-10-18 17:35:47 UTC (rev 30684)
@@ -207,14 +207,14 @@
addLinks(network,node, buf);
- // excerpt from the BioPAX OWL
- stringRef = null;
- //the following attr. was experimental, not so important for
users; may be null (not generated) in large networks
- stringRef =
network.getRow(node,CyNetwork.HIDDEN_ATTRS).get(BioPaxUtil.BIOPAX_DATA,
String.class);
- if (stringRef != null) {
- appendHeader("BioPAX L3 (fragment)", buf);
- buf.append("<pre class='excerpt'>" +
StringEscapeUtils.escapeXml(stringRef) + "</pre>");
- }
+// // excerpt from the BioPAX OWL
+// stringRef = null;
+// //the following attr. was experimental, not so important for
users; may be null (not generated) in large networks
+// stringRef =
network.getRow(node,CyNetwork.HIDDEN_ATTRS).get(BioPaxUtil.BIOPAX_DATA,
String.class);
+// if (stringRef != null) {
+// appendHeader("BioPAX L3 (fragment)", buf);
+// buf.append("<pre class='excerpt'>" +
StringEscapeUtils.escapeXml(stringRef) + "</pre>");
+// }
buf.append("</BODY></HTML>");
textPane.setText(buf.toString());
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