Author: ruschein
Date: 2010-02-11 16:12:33 -0800 (Thu, 11 Feb 2010)
New Revision: 19306
Removed:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch_Runner.java
Log:
Not used.
Deleted:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch_Runner.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch_Runner.java
2010-02-11 23:14:13 UTC (rev 19305)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch_Runner.java
2010-02-12 00:12:33 UTC (rev 19306)
@@ -1,205 +0,0 @@
-package org.idekerlab.ModFindPlugin.networks.ModFinder;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.idekerlab.ModFindPlugin.networks.SFNetwork;
-import org.idekerlab.ModFindPlugin.networks.SNodeModule;
-import org.idekerlab.ModFindPlugin.networks.hashNetworks.FloatHashNetwork;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkEdge;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNetwork;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNode;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNodeModule;
-import org.idekerlab.ModFindPlugin.data.StringTable;
-
-
-public class HCSearch_Runner {
-
- public static void main(String args[]) {
- double time = System.currentTimeMillis();
-
- if (args.length != 5 && args.length != 6) {
- System.out.println("Error: Incorrect number of
arguments.");
- System.out.println("Searches for enriched modules and
their connections.");
- System.out.println("p1: Physical network");
- System.out.println("p2: Genetic network");
- System.out.println("p3: Output folder");
- System.out.println("p4: Alpha");
- System.out.println("p5: Alpha Multiplier");
- System.out.println("p6: Physical network filter degree
(optional)");
- System.exit(0);
- }
-
- String fpnet = args[0];
- String fgnet = args[1];
- String outputDirectory = args[2] + "/";
- float alpha = Float.valueOf(args[4]);
- float alpham = Float.valueOf(args[5]);
-
- int filter = -1;
- if (args.length == 6)
- filter = Integer.valueOf(args[6]);
-
- System.out.println("Make sure networks are unique and not
self!");
-
- // Read in networks and convert to type <String, Double>
- System.out.println("Reading networks.");
- SFNetwork pnet = new FloatHashNetwork(fpnet, false, true, 0, 1,
2);
- SFNetwork gnet = new FloatHashNetwork(fgnet, false, false, 0,
1, 2);
-
- // Trim all the nodes in the genetic network to ones found in
the
- // physical network.
- System.out.println("Trimming genetic network.");
- Set<String> pnodes = pnet.getNodes();
- Set<String> gnodes = gnet.getNodes();
- pnodes.retainAll(gnodes);
- gnet = gnet.subNetwork(pnodes);
-
- // Optionally filter physical nodes to ones near genetic nodes
- if (filter != -1) {
- System.out.println("Trimming physical network. Filter
degree "
- + filter);
- TypedLinkNetwork<String, Float> ptlnet =
pnet.asTypedLinkNetwork();
-
- pnet = new FloatHashNetwork(ptlnet.subNetwork(pnodes,
filter));
- }
-
- // System.out.println("Number of nodes remaining in the
physical network: "+pnet.numNodes());
- System.out.println("Number of edges remaining in the physical
network: " + pnet.numEdges());
- // System.out.println("Number of nodes remaining in the genetic
network: "+gnet.numNodes());
- System.out.println("Number of edges remaining in the genetic
network: " + gnet.numEdges());
-
- // Select a scoring function
- HCScoringFunction sfunc = new SouravScore(pnet, gnet, alpha,
alpham);
- System.out.println("Initializing scoring function.");
- sfunc.Initialize(pnet, gnet);
-
- // Perform network search
- System.out.println("Performing network search.");
- TypedLinkNetwork<TypedLinkNodeModule<String, BFEdge>, BFEdge>
results = HCSearch2.search(pnet, gnet, sfunc);
-
- System.out.println("Time Elapsed: " +
(System.currentTimeMillis() - time) / 1000);
-
- // Print a simple summary of the results
- HCSearch2.report(results);
-
- // Create the output directory
- File f = new File(outputDirectory);
- if (!f.exists())
- f.mkdir();
-
- // Build a table of complex properties and save it and the
complexes
- // themselves.
- System.out.println("Calculating complex properties.");
- Set<String> testedgenes = pnet.getNodes();
-
- Map<String, SNodeModule> genecomplexes = new HashMap<String,
SNodeModule>(testedgenes.size());
-
- StringTable cprops = new StringTable(results.numNodes(), 4, "");
- List<String> colnames = new ArrayList<String>(5);
- colnames.add("CID");
- colnames.add("Size");
- colnames.add("Radius");
- colnames.add("Score");
- cprops.setColNames(colnames);
-
- StringTable gprops = new StringTable(testedgenes.size(), 2, "");
- colnames = new ArrayList<String>(3);
- colnames.add("ORF");
- colnames.add("CID");
- gprops.setColNames(colnames);
-
- List<SNodeModule> clist = new
ArrayList<SNodeModule>(results.numNodes());
- Map<TypedLinkNode<TypedLinkNodeModule<String, BFEdge>, BFEdge>,
SNodeModule> cmap = new HashMap<TypedLinkNode<TypedLinkNodeModule<String,
BFEdge>, BFEdge>, SNodeModule>();
-
- int i = 0;
- for (TypedLinkNode<TypedLinkNodeModule<String, BFEdge>, BFEdge>
mod : results.nodeIterator()) {
- String id = String.valueOf(i);
- Set<String> genes = mod.value().getMemberValues();
- SNodeModule newc = new SNodeModule(id, genes);
- clist.add(newc);
- cmap.put(mod, newc);
-
- for (String gene : genes)
- genecomplexes.put(gene, newc);
-
- cprops.set(i, 0, id);
- cprops.set(i, 1, String.valueOf(genes.size()));
- cprops.set(i, 2, String.valueOf(Math.sqrt(genes.size()
/ Math.PI)));
- cprops.set(i, 3, mod.value().score());
-
- i++;
- }
- SNodeModule.saveComplexes(outputDirectory + "complexes.txt",
clist);
-
- cprops.SortRowsAsDouble(1);
- cprops.save(outputDirectory + "cprops.txt");
-
- // Save the complex network (note, this needs to be done AFTER
the
- // complex properties have completed)
- // results.saveToFile(outputDirectory+"cnet.txt");
-
- // Save gene properties
- System.out.println("Saving properties for " +
testedgenes.size() + " genes.");
- i = 0;
- for (String gene : testedgenes) {
- gprops.set(i, 0, gene);
- SNodeModule parent = genecomplexes.get(gene);
- gprops.set(i, 1, parent.getID());
- i++;
- }
-
- gprops.save(outputDirectory + "gprops.txt");
-
- // Save each edge and build the edge properties file
- System.out.println("Calculating edge properties.");
- TypedLinkNetwork<String, Float> pn = pnet.asTypedLinkNetwork();
- TypedLinkNetwork<String, Float> gn = gnet.asTypedLinkNetwork();
-
- if (results.numEdges() > 0) {
- StringTable eprops = new
StringTable(results.numEdges(), 7, "");
- colnames = new ArrayList<String>(7);
- colnames.add("CID1");
- colnames.add("CID2");
- colnames.add("Score");
- colnames.add("#Genetic");
- colnames.add("#Physical");
- colnames.add("C1Size");
- colnames.add("C2Size");
- colnames.add("Density");
- eprops.setColNames(colnames);
-
- i = 0;
- for (TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>,
BFEdge> edge : results.edgeIterator()) {
- TypedLinkNodeModule<String, BFEdge> hm1 =
edge.source().value();
- TypedLinkNodeModule<String, BFEdge> hm2 =
edge.target().value();
-
- // The modules are not built from the gn and pn
networks, so
- // their member nodes have no connectivity
information!
- int gconnectedness =
gn.getConnectedness(hm1.asStringSet(), hm2.asStringSet());
- int pconnectedness =
pn.getConnectedness(hm1.asStringSet(), hm2.asStringSet());
-
- eprops.set(i, 0,
cmap.get(edge.source()).getID());
- eprops.set(i, 1,
cmap.get(edge.target()).getID());
- eprops.set(i, 2,
String.valueOf(edge.value().link()));
- eprops.set(i, 3,
String.valueOf(gconnectedness));
- eprops.set(i, 4,
String.valueOf(pconnectedness));
- eprops.set(i, 5, String.valueOf(hm1.size()));
- eprops.set(i, 6, String.valueOf(hm2.size()));
- eprops.set(i, 7,
String.valueOf(edge.value().link() / hm1.size() / hm2.size()));
-
- i++;
- }
-
- eprops.SortRowsAsDouble(2);
-
- eprops.save(outputDirectory + "eprops.txt");
- }
-
- System.out.println("Time Elapsed: " +
(System.currentTimeMillis() - time) / 1000);
- }
-}
\ No newline at end of file
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