Initial Commit

.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="owner.project.facets" value="java"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="C:/Users/Asa/Documents/wikiimport/quinlibrary.jar"/>
+	<classpathentry kind="lib" path="C:/Users/Asa/Documents/wikiimport/GraphletCounter-1.2.jar"/>
+	<classpathentry kind="lib" path="C:/Users/Asa/Documents/wikiimport/REngine.jar"/>
+	<classpathentry kind="lib" path="C:/Users/Asa/Documents/wikiimport/RserveEngine.jar"/>
+	<classpathentry kind="output" path="build/classes"/>
+</classpath>

.gitignore

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+/build/

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>TriPOINT</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.jdt.core.prefs

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+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.8

.settings/org.eclipse.wst.common.project.facet.core.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <installed facet="java" version="1.8"/>
+</faceted-project>

src/edu/uconn/tripoint/export/CytoscapeEdge.java

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+package edu.uconn.tripoint.export;
+
+public abstract class CytoscapeEdge {
+
+	private int _id;
+	private CytoscapeNode _n1, _n2;
+
+	public CytoscapeEdge(int id, CytoscapeNode n1, CytoscapeNode n2){
+		_id = id;
+		_n1 = n1;
+		_n2 = n2;
+	}
+
+	public int getId(){
+		return _id;
+	}
+
+	public CytoscapeNode getN1(){
+		return _n1;
+	}
+
+	public CytoscapeNode getN2(){
+		return _n2;
+	}
+
+
+	public abstract String toJSON();
+
+}

src/edu/uconn/tripoint/export/CytoscapeExport.java

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+package edu.uconn.tripoint.export;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import quin.network.Location;
+import edu.uconn.tripoint.graph.Edge;
+import edu.uconn.tripoint.graph.Node;
+import edu.uconn.tripoint.pathway.Gene;
+import edu.uconn.tripoint.pathway.Pathway;
+import edu.uconn.tripoint.pathway.PathwayEdge;
+import edu.uconn.tripoint.triangulation.TriangulatedGene;
+
+/**
+ * 
+ * Exports the pathways into a cytoscape format.
+ *
+ */
+public class CytoscapeExport {
+
+	/**
+	 * 
+	 * @param p
+	 * @param genes
+	 * @param noncoding
+	 * @param outdir
+	 */
+	public void exportToCytoscapeJSON(Pathway p, Map<Gene, TriangulatedGene> genes, Map<Gene, List<Location>> noncoding, String outdir, String prefix){
+		Map<Gene, Integer> geneids = new TreeMap<Gene, Integer>();
+		int nindex = 0;
+		Map<Integer, CytoscapeNode> nl = new TreeMap<Integer, CytoscapeNode>();
+		for(Iterator<Node<Gene,PathwayEdge>> it = p.getNodes().iterator(); it.hasNext();){
+			Node<Gene,PathwayEdge> next = it.next();
+			int curnindex = nindex++;
+			Gene curgene = next.getData();
+			geneids.put(curgene, curnindex);
+			int nccount = 0;
+			if(noncoding.get(curgene) != null){
+				nccount = noncoding.get(curgene).size();
+			}
+			nl.put(curnindex,new PathwayGeneCytoscapeNode(curnindex, p.getId(), genes.get(curgene), nccount));
+		}
+
+		int eindex = 0;
+		List<CytoscapeEdge> el = new LinkedList<CytoscapeEdge>();
+		for(Iterator<Edge<Gene,PathwayEdge>> it = p.getEdges().iterator(); it.hasNext();){
+			Edge<Gene,PathwayEdge> edge = it.next();
+			Gene src = edge.getSource().getData();
+			Gene dest = edge.getDestination().getData();
+			String type = getStringType(edge.getData().getType());
+			el.add(new PathwayCytoscapeEdge(eindex, nl.get(geneids.get(src)), nl.get(geneids.get(dest)), type));
+		}
+
+		for(Iterator<Gene> git = geneids.keySet().iterator(); git.hasNext();){
+			Gene next = git.next();
+			List<Location> l = noncoding.get(next);
+			if(l != null){
+				for(Iterator<Location> lit = l.iterator(); lit.hasNext();){
+					int curnindex = nindex++;
+					CytoscapeNode n = new NonCodingCytoscapeNode(curnindex, lit.next());
+					nl.put(curnindex,n);
+					el.add(new PathwayCytoscapeEdge(eindex++, nl.get(geneids.get(next)), n, "NonCoding"));
+				}
+			}
+		}
+
+		String outdir2 = outdir;
+		if(!outdir.endsWith("/")){
+			outdir2 += "/";
+		}
+
+		String filename = p.getId();
+		filename = filename.substring(filename.indexOf(":")+1).replaceAll("[^A-Za-z0-9]", "");
+		filename = filename.substring(0, Math.min(filename.length(), 16));
+
+		try {
+			writeJSONFile(outdir2+prefix+"_"+filename+".json", p, nl, el);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+
+	private String getStringType(int type){
+		if(type == PathwayEdge.ACTIVATION){
+			return "Activation";
+		}
+		else if(type == PathwayEdge.INHIBITION){
+			return "Inhibition";
+		}
+		else{
+			return "Association";
+		}
+	}
+
+	private void writeJSONFile(String outfile, Pathway p, Map<Integer, CytoscapeNode> nodes, List<CytoscapeEdge> edges) throws IOException{
+		BufferedWriter bw  = new BufferedWriter(new FileWriter(outfile));
+		bw.write("{\n");
+		bw.write("\"data\": {\"name\": \""+p.getId()+"\"},\n");
+		bw.write("\"elements\" : {\n");
+		bw.write("\"nodes\" : [");
+		Iterator<CytoscapeNode> it = nodes.values().iterator();
+		if(it.hasNext()){
+			bw.write(it.next().toJSON()+"\n");
+		}
+		while(it.hasNext()){
+			bw.write(","+it.next().toJSON()+"\n");
+		}
+		bw.write("],\n");
+		bw.write("\"edges\" : [\n");
+		Iterator<CytoscapeEdge> ite = edges.iterator();
+		if(ite.hasNext()){
+			bw.write(ite.next().toJSON()+"\n");
+		}
+		while(ite.hasNext()){
+			bw.write(","+ite.next().toJSON()+"\n");
+		}
+		bw.write("]\n");
+		bw.write("}\n");
+		bw.write("}\n");
+		bw.flush();
+		bw.close();
+	}
+
+}

src/edu/uconn/tripoint/export/CytoscapeNode.java

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+package edu.uconn.tripoint.export;
+
+public abstract class CytoscapeNode {
+
+	private int _id;
+
+	public CytoscapeNode(int id){
+		_id = id;
+	}
+
+	public int getId(){
+		return _id;
+	}
+
+
+	public abstract String toJSON();
+
+}

src/edu/uconn/tripoint/export/NonCodingCytoscapeNode.java

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+package edu.uconn.tripoint.export;
+
+import quin.network.Location;
+
+public class NonCodingCytoscapeNode extends CytoscapeNode{
+
+	public Location _l;
+	public NonCodingCytoscapeNode(int id, Location l) {
+		super(id);
+		_l = l;
+	}
+
+	@Override
+	public String toJSON(){
+		StringBuilder sb = new StringBuilder();
+		sb.append("{\n");
+		sb.append("\"data\" : {\n");
+		sb.append("\"id\" : \""+getId()+"\",\n");
+		sb.append("\"type\" : \"NonCoding Target\",\n");
+		sb.append("\"name\" : \""+_l.getChr()+":"+_l.getStart()+"-"+_l.getEnd()+"\"\n");
+		sb.append("}\n");
+		sb.append("}\n");
+		return sb.toString();
+	}
+}

src/edu/uconn/tripoint/export/NonCodingTargetExport.java

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+package edu.uconn.tripoint.export;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import quin.network.Location;
+import edu.uconn.tripoint.pathway.Gene;
+import edu.uconn.tripoint.pathway.Pathway;
+import edu.uconn.tripoint.triangulation.TriangulatedGene;
+
+public class NonCodingTargetExport {
+
+	public void ExportNonCodingTargets(Pathway globalpathway, Pathway[] pathways, Collection<TriangulatedGene> genes, Map<Gene, List<Location>> noncoding, String outdir, String prefix) throws IOException{
+		String outdir2 = outdir;
+		if(!outdir.endsWith("/")){
+			outdir2 += "/";
+		}
+
+		BufferedWriter bw = new BufferedWriter(new FileWriter(outdir2+prefix+"_noncoding.txt"));
+		bw.write("Gene ID"+"\t"+
+				"Chr"+"\t"+"Start"+"\t"+"End"+"\n");
+		for(Iterator<TriangulatedGene> it = genes.iterator(); it.hasNext();){
+			TriangulatedGene next = it.next();
+			writeLine(bw,next, noncoding);
+		}
+
+		bw.flush();
+		bw.close();
+	}
+
+	private void writeLine(BufferedWriter bw, TriangulatedGene g, Map<Gene, List<Location>> noncoding) throws IOException{
+		Gene gene = g.getGene();
+		List<Location> nc = noncoding.get(gene);
+		if(nc.size() > 0){
+			String id = gene.getId();
+			for(Iterator<Location> it = nc.iterator(); it.hasNext();){
+				Location next = it.next();
+				bw.write(id+"\t"+
+						next.getChr()+"\t"+next.getStart()+"\t"+next.getEnd()+"\n");
+			}
+
+		}
+	}
+}

src/edu/uconn/tripoint/export/PathwayCytoscapeEdge.java

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+package edu.uconn.tripoint.export;
+
+public class PathwayCytoscapeEdge extends CytoscapeEdge{
+
+	private String _type;
+
+	public PathwayCytoscapeEdge(int id, CytoscapeNode n1, CytoscapeNode n2, String type){
+		super(id, n1, n2);
+		_type = type;
+	}
+
+	public String toJSON(){
+		StringBuilder sb = new StringBuilder();
+		sb.append("{\n");
+		sb.append("\"data\" : {\n");
+		sb.append("\"id\" : \""+getId()+"\",\n");
+		sb.append("\"source\" : \""+getN1().getId()+"\",\n");
+		sb.append("\"target\" : \""+getN2().getId()+"\",\n");
+		sb.append("\"type\" : \""+_type+"\"\n");
+		sb.append("}\n");
+		sb.append("}\n");
+		return sb.toString();
+	}
+
+}

src/edu/uconn/tripoint/export/PathwayGeneCytoscapeNode.java

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+package edu.uconn.tripoint.export;
+
+import edu.uconn.tripoint.triangulation.TriangulatedGene;
+
+public class PathwayGeneCytoscapeNode extends CytoscapeNode {
+
+	private String _pathway;
+	private TriangulatedGene _tg;
+	private int _noncodingcount;
+
+	public PathwayGeneCytoscapeNode(int id, String pathway, TriangulatedGene tg, int nccount){
+		super(id);
+		_pathway = pathway;
+		_tg = tg;
+		_noncodingcount = nccount;
+	}
+
+	@Override
+	public String toJSON(){
+		StringBuilder sb = new StringBuilder();
+		sb.append("{\n");
+		sb.append("\"data\" : {\n");
+		sb.append("\"id\" : \""+getId()+"\",\n");
+		sb.append("\"type\" : \"Pathway Gene\",\n");
+		sb.append("\"name\" : \""+_tg.getGene().getId()+"\",\n");
+		sb.append("\"pathway\" : \""+_pathway+"\",\n");
+		sb.append("\"expression\" : "+_tg.getGene().getValue()+",\n");
+		sb.append("\"inconsistency\" : "+_tg.getInconsistencyScore(_pathway)+",\n");
+		sb.append("\"inconsistency_pval\" : "+_tg.getInconsistencyPValue(_pathway)+",\n");
+		sb.append("\"inconsistency_qval\" : "+_tg.getInconsistencyFDR(_pathway)+",\n");
+		sb.append("\"support\" : "+_tg.getSupportScore(_pathway)+",\n");
+		sb.append("\"support_pval\" : "+_tg.getSupportPValue(_pathway)+",\n");
+		sb.append("\"support_qval\" : "+_tg.getSupportFDR(_pathway)+",\n");
+		sb.append("\"consistency\" : "+_tg.getConsistencyScore(_pathway)+",\n");
+		sb.append("\"consistency_pval\" : "+_tg.getConsistencyPValue(_pathway)+",\n");
+		sb.append("\"consistency_qval\" : "+_tg.getConsistencyFDR(_pathway)+",\n");
+		sb.append("\"impact\" : "+_tg.getImpactScore(_pathway)+",\n");
+		sb.append("\"impact_pval\" : "+_tg.getImpactPValue(_pathway)+",\n");
+		sb.append("\"impact_qval\" : "+_tg.getImpactFDR(_pathway)+",\n");
+		sb.append("\"noncoding_count\" : "+_noncodingcount+"\n");
+		sb.append("}\n");
+		sb.append("}\n");
+		return sb.toString();
+	}
+
+}