Author: rodche
Date: 2012-07-09 15:38:38 -0700 (Mon, 09 Jul 2012)
New Revision: 29811
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/CyActivator.java
Log:
Temporarily commented out making Group nodes from Complex and PE member
nodes/edges (shelved for later)
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
2012-07-09 22:35:14 UTC (rev 29810)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-07-09 22:38:38 UTC (rev 29811)
@@ -228,8 +228,8 @@
if(members.isEmpty())
continue;
- List<CyNode> nodeList = new ArrayList<CyNode>();
- List<CyEdge> edgeList = new ArrayList<CyEdge>();
+// List<CyNode> nodeList = new ArrayList<CyNode>();
+// List<CyEdge> edgeList = new ArrayList<CyEdge>();
CyNode cyParentNode = uriToCyNodeMap.get(par);
assert cyParentNode != null : "cyParentNode is NULL.";
@@ -240,11 +240,11 @@
CyEdge edge = network.addEdge(cyParentNode,
cyMemberNode, true);
AttributeUtil.set(network, edge,
BIOPAX_EDGE_TYPE, "member", String.class);
- nodeList.add(cyMemberNode);
- edgeList.add(edge);
+// nodeList.add(cyMemberNode);
+// edgeList.add(edge);
}
- cyGroupFactory.createGroup(network, cyParentNode,
nodeList, edgeList, true);
+// cyGroupFactory.createGroup(network, cyParentNode,
nodeList, edgeList, true);
}
}
@@ -323,8 +323,8 @@
// get node
CyNode complexCyNode =
uriToCyNodeMap.get(complexElement);
- List<CyNode> nodeList = new ArrayList<CyNode>();
- List<CyEdge> edgeList = new ArrayList<CyEdge>();
+// List<CyNode> nodeList = new ArrayList<CyNode>();
+// List<CyEdge> edgeList = new ArrayList<CyEdge>();
// get all components. There can be 0 or more
for (PhysicalEntity member : members)
@@ -334,11 +334,11 @@
CyEdge edge = network.addEdge(complexCyNode,
complexMemberCyNode, true);
AttributeUtil.set(network, edge,
BIOPAX_EDGE_TYPE, "contains", String.class);
- nodeList.add(complexMemberCyNode);
- edgeList.add(edge);
+// nodeList.add(complexMemberCyNode);
+// edgeList.add(edge);
}
- cyGroupFactory.createGroup(network, complexCyNode,
nodeList, edgeList, true);
+// cyGroupFactory.createGroup(network, complexCyNode,
nodeList, edgeList, true);
}
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-07-09 22:35:14 UTC (rev 29810)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-07-09 22:38:38 UTC (rev 29811)
@@ -98,6 +98,7 @@
// t.printStackTrace();
// }
+ // TODO set paxtools logging level to ERROR
}
}
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