NESFilter now used to decide which enrichment files to load rather than

used to filter each individual gene set. Refactored enrichment parsers.
Fixes #216.

Author: mikekucera

EnrichmentMapIntegrationTest/src/test/java/org/baderlab/csplugins/enrichmentmap/integration/task/CreateEnrichmentMapTaskTest.java

@@ -65,8 +65,9 @@ public void testEnrichmentMapBuildMapTask() throws Exception {
 
 		PropertyManager pm = new PropertyManager();
 		EMCreationParameters params = 
-			new EMCreationParameters("EM1_", pm.getPvalue(), pm.getQvalue(), NESFilter.ALL, Optional.empty(), SimilarityMetric.JACCARD, 
-					                 pm.getJaccardCutoff(), pm.getCombinedConstant(), EdgeStrategy.COMPOUND);
+			new EMCreationParameters("EM1_", pm.getValue(PropertyManager.P_VALUE), pm.getValue(PropertyManager.Q_VALUE), 
+									NESFilter.ALL, Optional.empty(), SimilarityMetric.JACCARD, 
+									LegacySupport.jaccardCutOff_default, LegacySupport.combinedConstant_default, EdgeStrategy.COMPOUND);
 
 		DataSetFiles dataset1files = new DataSetFiles();
 		dataset1files.setGMTFileName(geneSetsFile);  

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/GSEAResult.java

@@ -1,3 +1,4 @@
+package org.baderlab.csplugins.enrichmentmap.model;
 /**
  **                       EnrichmentMap Cytoscape Plugin
  **
@@ -41,9 +42,6 @@
 // $LastChangedBy$
 // $HeadURL$
 
-package org.baderlab.csplugins.enrichmentmap.model;
-
-import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter;
 
 /**
  * Class representing a specialized enrichment result generated from Gene set
@@ -122,10 +120,10 @@ public GSEAResult(String[] tokens) {
 	//returns false if it doesn't pass one or both the pvalue or qvalue cut-offs
 	@Override
 	public boolean geneSetOfInterest(EnrichmentResultFilterParams params) {
-		if(params.getNESFilter() == NESFilter.POSITIVE && getNES() <= 0)
-			return false;
-		if(params.getNESFilter() == NESFilter.NEGATIVE && getNES() >= 0)
-			return false;
+//		if(params.getNESFilter() == NESFilter.POSITIVE && getNES() <= 0)
+//			return false;
+//		if(params.getNESFilter() == NESFilter.NEGATIVE && getNES() >= 0)
+//			return false;
 
 		return (getPvalue() <= params.getPvalue()) && (this.fdrqvalue <= params.getQvalue());
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/GenericResult.java

@@ -1,3 +1,4 @@
+package org.baderlab.csplugins.enrichmentmap.model;
 /**
  **                       EnrichmentMap Cytoscape Plugin
  **
@@ -35,16 +36,6 @@
  **
  **/
 
-// $Id$
-// $LastChangedDate$
-// $LastChangedRevision$
-// $LastChangedBy$
-// $HeadURL$
-
-package org.baderlab.csplugins.enrichmentmap.model;
-
-import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter;
-
 /**
  * Created by User: risserlin Date: Jan 28, 2009 Time: 3:25:51 PM
  * <p>
@@ -133,10 +124,10 @@ public GenericResult(String name, String description, double pvalue, int gssize,
 	 */
 	@Override
 	public boolean geneSetOfInterest(EnrichmentResultFilterParams params) {
-		if(params.getNESFilter() == NESFilter.POSITIVE && getNES() <= 0)
-			return false;
-		if(params.getNESFilter() == NESFilter.NEGATIVE && getNES() >= 0)
-			return false;
+//		if(params.getNESFilter() == NESFilter.POSITIVE && getNES() <= 0)
+//			return false;
+//		if(params.getNESFilter() == NESFilter.NEGATIVE && getNES() >= 0)
+//			return false;
 
 		double pvalue = params.getPvalue();
 		double fdrqvalue = params.getQvalue();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ClassFileReaderTask.java

@@ -36,7 +36,7 @@ public static String[] parseClasses(String classFile) {
 			return null;
 
 		try {
-			List<String> lines = DatasetLineParser.readLines(classFile, 4);
+			List<String> lines = LineReader.readLines(classFile, 4);
 
 			/*
 			 * GSEA class files will have 3 lines in the following format: 6 2 1

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/DatasetLineParser.java

@@ -103,7 +103,7 @@ public GeneExpressionMatrix parse(TaskMonitor taskMonitor) throws IOException {
 		EnrichmentMap map = dataset.getMap();
 
 		String expressionFileName = dataset.getExpressionSets().getFilename();
-		List<String> lines = DatasetLineParser.readLines(expressionFileName);
+		List<String> lines = LineReader.readLines(expressionFileName);
 
 		int currentProgress = 0;
 		int maxValue = lines.size();
@@ -276,7 +276,7 @@ private String[] setClasses(String classFile) throws IOException {
 		//check to see if the file was opened successfully
 
 		if(!classFile.equalsIgnoreCase(null)) {
-			List<String> lines = DatasetLineParser.readLines(classFile);
+			List<String> lines = LineReader.readLines(classFile);
 
 			//the class file can be split by a space or a tab
 			String[] classes = lines.get(2).split("\\s");

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ExpressionFileReaderTask.java

@@ -0,0 +1,38 @@
+package org.baderlab.csplugins.enrichmentmap.parsers;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+public class LineReader {
+
+	// MKTODO Its not very memory efficient to read the entire file into memory. Replace with streams.
+	
+	public static List<String> readLines(String fileName, int limit) throws IOException {
+		try(BufferedReader reader = new BufferedReader(new FileReader(fileName))) {
+			List<String> lines = new ArrayList<>();
+			int count = 0;
+            for(String line; (line = reader.readLine()) != null;) {
+                lines.add(line);
+                count++;
+                if(count >= limit) {
+                	break;
+                }
+            }
+            return lines;
+        }
+	}
+	
+	public static List<String> readLines(String fileName) throws IOException {
+		try(BufferedReader reader = new BufferedReader(new FileReader(fileName))) {
+			List<String> lines = new ArrayList<>();
+            for(String line; (line = reader.readLine()) != null;) {
+                lines.add(line);
+            }
+            return lines;
+        }
+	}
+	
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/LineReader.java

@@ -1,5 +1,6 @@
 package org.baderlab.csplugins.enrichmentmap.parsers;
 
+import java.io.IOException;
 import java.util.List;
 import java.util.Map;
 
@@ -9,22 +10,27 @@
 import org.baderlab.csplugins.enrichmentmap.model.GeneSet;
 import org.baderlab.csplugins.enrichmentmap.model.GenericResult;
 import org.baderlab.csplugins.enrichmentmap.util.NullTaskMonitor;
+import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskMonitor;
 
 import com.google.common.collect.ImmutableSet;
 
-public class ParseBingoEnrichmentResults extends DatasetLineParser {
+public class ParseBingoEnrichmentResults extends AbstractTask {
 
+	private final EMDataSet dataset;
+	
 	public ParseBingoEnrichmentResults(EMDataSet dataset) {
-		super(dataset);
+		this.dataset = dataset;
 	}
-
+	
 	@Override
-	public void parseLines(List<String> lines, EMDataSet dataset, TaskMonitor taskMonitor) {
+	public void run(TaskMonitor taskMonitor) throws IOException {
 		if(taskMonitor == null)
 			taskMonitor = new NullTaskMonitor();
 		taskMonitor.setTitle("Parsing Bingo Enrichment Result file");
-
+		
+		List<String> lines = LineReader.readLines(dataset.getEnrichments().getFilename1());
+				
 		//with Bingo results there are no genesets defined.  first pass through the file
 		// needs to parse the genesets
 
@@ -170,4 +176,6 @@ else if(!gene.isEmpty()) {
 	}
 
 
+
+	
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseBingoEnrichmentResults.java

@@ -1,5 +1,6 @@
 package org.baderlab.csplugins.enrichmentmap.parsers;
 
+import java.io.IOException;
 import java.util.List;
 import java.util.Map;
 
@@ -9,25 +10,30 @@
 import org.baderlab.csplugins.enrichmentmap.model.GeneSet;
 import org.baderlab.csplugins.enrichmentmap.model.GenericResult;
 import org.baderlab.csplugins.enrichmentmap.util.NullTaskMonitor;
+import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskMonitor;
 
 import com.google.common.collect.ImmutableSet;
 
-public class ParseDavidEnrichmentResults extends DatasetLineParser {
+public class ParseDavidEnrichmentResults extends AbstractTask {
 
+	private final EMDataSet dataset;
+	 
 	public ParseDavidEnrichmentResults(EMDataSet dataset) {
-		super(dataset);
+		this.dataset = dataset;
 	}
 
 	/**
 	 * Parse david enrichment results file
 	 */
 	@Override
-	public void parseLines(List<String> lines, EMDataSet dataset, TaskMonitor taskMonitor) {
+	public void run(TaskMonitor taskMonitor) throws IOException {
 		if(taskMonitor == null)
 			taskMonitor = new NullTaskMonitor();
 		taskMonitor.setTitle("Parsing David Enrichment Result file");
 
+		List<String> lines = LineReader.readLines(dataset.getEnrichments().getFilename1());
+		
 		//with David results there are no genesets defined.  first pass through the file
 		// needs to parse the genesets
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseDavidEnrichmentResults.java

@@ -1,32 +1,38 @@
 package org.baderlab.csplugins.enrichmentmap.parsers;
 
+import java.io.IOException;
 import java.util.List;
 import java.util.Map;
 
-import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters;
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.GreatFilter;
+import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResult;
 import org.baderlab.csplugins.enrichmentmap.model.GeneSet;
 import org.baderlab.csplugins.enrichmentmap.model.GenericResult;
 import org.baderlab.csplugins.enrichmentmap.util.NullTaskMonitor;
+import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskMonitor;
 
 import com.google.common.collect.ImmutableSet;
 
-public class ParseGREATEnrichmentResults extends DatasetLineParser {
+public class ParseGREATEnrichmentResults extends AbstractTask {
 
+	private final EMDataSet dataset;
+	
 	public ParseGREATEnrichmentResults(EMDataSet dataset) {
-		super(dataset);
+		this.dataset = dataset;
 	}
 
 	@Override
-	public void parseLines(List<String> lines, EMDataSet dataset, TaskMonitor taskMonitor) {
+	public void run(TaskMonitor taskMonitor) throws IOException {
 		if(taskMonitor == null)
 			taskMonitor = new NullTaskMonitor();
 		taskMonitor.setTitle("Parsing Enrichment Result file");
 
+		List<String> lines = LineReader.readLines(dataset.getEnrichments().getFilename1());
+		
 		boolean hasBackground = false;
 
 		EMCreationParameters params = dataset.getMap().getParams();