Author: ruschein
Date: 2010-01-12 11:12:43 -0800 (Tue, 12 Jan 2010)
New Revision: 18875
Added:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
Log:
Work in progress.
Added:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
(rev 0)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
2010-01-12 19:12:43 UTC (rev 18875)
@@ -0,0 +1,96 @@
+package org.cytoscape.DenovoPGNetworkAlignmentPlugin;
+
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import java.util.Set;
+import networks.denovoPGNetworkAlignment.BFEdge;
+import networks.linkedNetworks.TypedLinkEdge;
+import networks.linkedNetworks.TypedLinkNetwork;
+import networks.linkedNetworks.TypedLinkNode;
+import networks.linkedNetworks.TypedLinkNodeModule;
+
+
+/** Creates an overview network for the detected complexes and nested networks
for each complex.
+ */
+class NestedNetworkCreator {
+ CyNetwork overviewNetwork = null;
+
+
+ /**
+ * Instantiates an overview network of complexes (modules) and one
nested network for each node in the overview network.
+ */
+ NestedNetworkCreator(final TypedLinkNetwork<TypedLinkNodeModule<String,
BFEdge>, BFEdge> networkOfModules) {
+ createOverviewNetwork(networkOfModules.nodes());
+ }
+
+ CyNetwork getOverviewNetwork() { return overviewNetwork; }
+
+ private void createOverviewNetwork(final
Set<TypedLinkNode<TypedLinkNodeModule<String, BFEdge>, BFEdge>> overviewNodes) {
+ overviewNetwork =
Cytoscape.createNetwork(findNextAvailableNetworkName("Complexes"), /*
create_view = */ true);
+
+ int nodeIndex = 1;
+ for (final TypedLinkNode<TypedLinkNodeModule<String, BFEdge>,
BFEdge> module : overviewNodes) {
+ final String nodeName =
findNextAvailableNodeName("Complex" + nodeIndex);
+ final CyNode newNode = Cytoscape.getCyNode(nodeName, /*
create = */ true);
+ overviewNetwork.addNode(newNode);
+
+ ++nodeIndex;
+ }
+ }
+
+
+ /**
+ * Finds an unused network name starting with a first choice. If the
first choice is not available, we will successively try to append -1
+ * -2, -3 and so on, until we indentify an unused name.
+ * @param initialPreference The network name we'd like to use, if it
is available. If not we use it as a prefix instead.
+ */
+ private String findNextAvailableNetworkName(final String
initialPreference) {
+ // Try the preferred choice first:
+ CyNetwork network = getNetworkByTitle(initialPreference);
+ if (network == null)
+ return initialPreference;
+
+ for (int suffix = 1; true; ++suffix) {
+ final String titleCandidate = initialPreference + "-" +
suffix;
+ network = getNetworkByTitle(titleCandidate);
+ if (network == null)
+ return titleCandidate;
+ }
+ }
+
+
+ /**
+ * Finds an unused node name starting with a first choice. If the
first choice is not available, we will successively try to append -1
+ * -2, -3 and so on, until we indentify an unused name.
+ * @param initialPreference The node name we'd like to use, if it is
available. If not we use it as a prefix instead.
+ */
+ private String findNextAvailableNodeName(final String
initialPreference) {
+ // Try the preferred choice first:
+ CyNode node = Cytoscape.getCyNode(initialPreference, /* create
= */ false);
+ if (node == null)
+ return initialPreference;
+
+ for (int suffix = 1; true; ++suffix) {
+ final String titleCandidate = initialPreference + "-" +
suffix;
+ node = Cytoscape.getCyNode(titleCandidate, /* create =
*/ false);
+ if (node == null)
+ return titleCandidate;
+ }
+ }
+
+
+ /** Returns the first network with title "networkTitle" or null, if
there is no network w/ this title.
+ */
+ private CyNetwork getNetworkByTitle(final String networkTitle) {
+ for (final CyNetwork network : Cytoscape.getNetworkSet()) {
+ if (network.getTitle().equals(networkTitle))
+ return network;
+ }
+
+ return null;
+ }
+}
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