Author: pwang
Date: 2011-10-29 12:07:18 -0700 (Sat, 29 Oct 2011)
New Revision: 27341
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/DetailedNetworkCreator.java
Log:
Comment out some code
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/DetailedNetworkCreator.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/DetailedNetworkCreator.java
2011-10-29 19:05:06 UTC (rev 27340)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/DetailedNetworkCreator.java
2011-10-29 19:07:18 UTC (rev 27341)
@@ -75,109 +75,109 @@
//networkAttr.setUserVisible(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
false);
//networkAttr.setUserEditable(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
false);
- //Populate network
- //Nodes
- //for (int ni : selected)
- for (CyNode ni: nodes_selected2)
- {
- CyNetwork nn = ni.getNetwork();
- if (nn!=null)
- {
- for (int ni2 : nn.getNodeIndicesArray())
- detailedNetwork.addNode(ni2);
-
-// List<CyNode> nn_nodelist = nn.getNodeList();
-// for (CyNode nn_node: nn_nodelist){
-//
detailedNetwork.addNode(nn_node.getSUID());
+// //Populate network
+// //Nodes
+// //for (int ni : selected)
+// for (CyNode ni: nodes_selected2)
+// {
+// CyNetwork nn = ni.getNetwork();
+// if (nn!=null)
+// {
+// for (int ni2 : nn.getNodeIndicesArray())
+// detailedNetwork.addNode(ni2);
+//
+//// List<CyNode> nn_nodelist = nn.getNodeList();
+//// for (CyNode nn_node: nn_nodelist){
+////
detailedNetwork.addNode(nn_node.getSUID());
+//// }
+// }
+// }
+//
+// //Edges
+// final CyTable edgeAttributes = Cytoscape.getEdgeAttributes();
+//
+// List<CyNode> nodes = detailedNetwork.getNodeList();
+//
+// // Add the edges induced by "origPhysNetwork" to our new nested
network.
+// List<CyEdge> edges = (List<CyEdge>)
origPhysNetwork.getConnectingEdges(getIntersectingNodes(origPhysNetwork,
nodes));
+// for (final CyEdge edge : edges)
+// {
+// //final Double attrValue =
edgeAttributes.getDoubleAttribute(edge.getCyRow().get("name", String.class),
physEdgeAttrName);
+// final Double attrValue
=edge.getCyRow().get(physEdgeAttrName, Double.class);
+// if (attrValue != null)
+// {
+// detailedNetwork.addEdge(edge);
+//
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Physical");
+// edge.getCyRow().set("PanGIA.Interaction Type",
"Physical");
+// }
+// }
+//
+// // Add the edges induced by "origGenNetwork" to our new nested
network.
+// edges = (List<CyEdge>)
origGenNetwork.getConnectingEdges(getIntersectingNodes(origGenNetwork, nodes));
+// for (final CyEdge edge : edges)
+// {
+// //final Double attrValue =
edgeAttributes.getDoubleAttribute(edge.getCyRow().get("name", String.class),
genEdgeAttrName);
+// final Double attrValue
=edge.getCyRow().get(genEdgeAttrName, Double.class);
+// if (attrValue != null)
+// {
+// detailedNetwork.addEdge(edge);
+// //Object existingAttribute =
edgeAttributes.getAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type");
+// Object existingAttribute =
edge.getCyRow().get("PanGIA.Interaction Type", String.class);
+// if (existingAttribute==null ||
!existingAttribute.equals("Physical"))
+// {
+// if (output.isSigned())
+// {
+// if (attrValue<0) {
+//
//edgeAttributes.setAttribute(edge.getCyRow().get("name",String.class),
"PanGIA.Interaction Type", "Genetic(negative)");
+//
edge.getCyRow().set("PanGIA.Interaction Type", "Genetic(negative)");
+// }
+// else {
+//
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Genetic(positive)");
+//
edge.getCyRow().set("PanGIA.Interaction Type", "Genetic(positive)");
+// }
+// }else {
+//
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Genetic");
+//
edge.getCyRow().set("PanGIA.Interaction Type", "Genetic");
+// }
// }
- }
- }
-
- //Edges
- final CyTable edgeAttributes = Cytoscape.getEdgeAttributes();
-
- List<CyNode> nodes = detailedNetwork.getNodeList();
-
- // Add the edges induced by "origPhysNetwork" to our new nested
network.
- List<CyEdge> edges = (List<CyEdge>)
origPhysNetwork.getConnectingEdges(getIntersectingNodes(origPhysNetwork,
nodes));
- for (final CyEdge edge : edges)
- {
- //final Double attrValue =
edgeAttributes.getDoubleAttribute(edge.getCyRow().get("name", String.class),
physEdgeAttrName);
- final Double attrValue
=edge.getCyRow().get(physEdgeAttrName, Double.class);
- if (attrValue != null)
- {
- detailedNetwork.addEdge(edge);
-
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Physical");
- edge.getCyRow().set("PanGIA.Interaction Type",
"Physical");
- }
- }
-
- // Add the edges induced by "origGenNetwork" to our new nested
network.
- edges = (List<CyEdge>)
origGenNetwork.getConnectingEdges(getIntersectingNodes(origGenNetwork, nodes));
- for (final CyEdge edge : edges)
- {
- //final Double attrValue =
edgeAttributes.getDoubleAttribute(edge.getCyRow().get("name", String.class),
genEdgeAttrName);
- final Double attrValue
=edge.getCyRow().get(genEdgeAttrName, Double.class);
- if (attrValue != null)
- {
- detailedNetwork.addEdge(edge);
- //Object existingAttribute =
edgeAttributes.getAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type");
- Object existingAttribute =
edge.getCyRow().get("PanGIA.Interaction Type", String.class);
- if (existingAttribute==null ||
!existingAttribute.equals("Physical"))
- {
- if (output.isSigned())
- {
- if (attrValue<0) {
-
//edgeAttributes.setAttribute(edge.getCyRow().get("name",String.class),
"PanGIA.Interaction Type", "Genetic(negative)");
-
edge.getCyRow().set("PanGIA.Interaction Type", "Genetic(negative)");
- }
- else {
-
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Genetic(positive)");
-
edge.getCyRow().set("PanGIA.Interaction Type", "Genetic(positive)");
- }
- }else {
-
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Genetic");
-
edge.getCyRow().set("PanGIA.Interaction Type", "Genetic");
- }
- }
- else
- if (output.isSigned())
- {
- if (attrValue<0)
- {
-
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Physical&Genetic(negative)");
-
edge.getCyRow().set("PanGIA.Interaction Type", "Physical&Genetic(negative)");
- }
- else
- {
-
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Physical&Genetic(positive)");
-
edge.getCyRow().set("PanGIA.Interaction Type", "Physical&Genetic(positive)");
- }
- }else
- {
-
//edgeAttributes.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Physical&Genetic");
-
edge.getCyRow().set("PanGIA.Interaction Type", "Physical&Genetic");
- }
-
- //if (existingAttribute==null ||
!existingAttribute.equals("Physical"))
edgeAttributes.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Genetic");
- //else
edgeAttributes.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Physical&Genetic");
- }
- }
-
-
-
- CyNetworkView theView =
ServicesUtil.cyNetworkViewFactoryServiceRef.getNetworkView(detailedNetwork,
false);
-
-
- DetailedViewLayout.layout(theView, view);
-
- //theView.setVisualStyle(VisualStyleObserver.VS_MODULE_NAME);
-
-// VisualStyle vs =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VisualStyleObserver.VS_MODULE_NAME);
-// ServicesUtil.visualMappingManagerRef.setVisualStyle(vs,
theView);
- //Cytoscape.getVisualMappingManager().setVisualStyle();
-
- theView.updateView(); //.redrawGraph(false, true);
+// else
+// if (output.isSigned())
+// {
+// if (attrValue<0)
+// {
+//
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Physical&Genetic(negative)");
+//
edge.getCyRow().set("PanGIA.Interaction Type", "Physical&Genetic(negative)");
+// }
+// else
+// {
+//
//edgeAttributes.setAttribute(edge.getCyRow().get("name", String.class),
"PanGIA.Interaction Type", "Physical&Genetic(positive)");
+//
edge.getCyRow().set("PanGIA.Interaction Type", "Physical&Genetic(positive)");
+// }
+// }else
+// {
+//
//edgeAttributes.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Physical&Genetic");
+//
edge.getCyRow().set("PanGIA.Interaction Type", "Physical&Genetic");
+// }
+//
+// //if (existingAttribute==null ||
!existingAttribute.equals("Physical"))
edgeAttributes.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Genetic");
+// //else
edgeAttributes.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Physical&Genetic");
+// }
+// }
+//
+//
+//
+// CyNetworkView theView =
ServicesUtil.cyNetworkViewFactoryServiceRef.getNetworkView(detailedNetwork,
false);
+//
+//
+// DetailedViewLayout.layout(theView, view);
+//
+// //theView.setVisualStyle(VisualStyleObserver.VS_MODULE_NAME);
+//
+//// VisualStyle vs =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VisualStyleObserver.VS_MODULE_NAME);
+//// ServicesUtil.visualMappingManagerRef.setVisualStyle(vs,
theView);
+// //Cytoscape.getVisualMappingManager().setVisualStyle();
+//
+// theView.updateView(); //.redrawGraph(false, true);
}
public static void goToNestedNetwork(CyNode n)
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