BasePair tracks correctly saved to and loaded from session files (use ResourceLocator).

Author: shapemapper

src/org/broad/igv/feature/basepair/BasePairFileParser.java

@@ -17,9 +17,7 @@ public class BasePairFileParser {
 
     static Logger log = Logger.getLogger(BasePairFileParser.class);
 
-    BasePairTrack track;
-
-    public BasePairTrack loadTrack(ResourceLocator locator, Genome genome) {
+    public static BasePairData loadData(ResourceLocator locator, Genome genome) {
         AsciiLineReader reader = null;
 
         List<Color> colors = new ArrayList();
@@ -106,8 +104,7 @@ public BasePairTrack loadTrack(ResourceLocator locator, Genome genome) {
         //    System.out.println(row);
         //}
 
-        track = new BasePairTrack(basePairData, locator.getTrackName());
-        return track;
+        return basePairData;
     }
 
 }

src/org/broad/igv/feature/basepair/BasePairTrack.java

@@ -1,9 +1,11 @@
 package org.broad.igv.feature.basepair;
 
 import org.apache.log4j.Logger;
+import org.broad.igv.feature.genome.*;
 import org.broad.igv.renderer.*;
 import org.broad.igv.track.AbstractTrack;
 import org.broad.igv.track.RenderContext;
+import org.broad.igv.util.ResourceLocator;
 
 import java.awt.*;
 
@@ -19,9 +21,9 @@ public class BasePairTrack extends AbstractTrack {
     private BasePairRenderer basePairRenderer = new BasePairRenderer();
     private BasePairData basePairData;
 
-    public BasePairTrack(BasePairData data, String name) {
-        super(name);
-        basePairData = data;
+    public BasePairTrack(ResourceLocator locator, String id, String name, Genome genome) {
+        super(locator, id, name);
+        basePairData = BasePairFileParser.loadData(locator, genome);
     }
 
     public void render(RenderContext context, Rectangle rect) {

src/org/broad/igv/track/TrackLoader.java

@@ -47,7 +47,7 @@
 import org.broad.igv.dev.db.SampleInfoSQLReader;
 import org.broad.igv.dev.db.SegmentedSQLReader;
 import org.broad.igv.exceptions.DataLoadException;
-import org.broad.igv.feature.basepair.BasePairFileParser;
+import org.broad.igv.feature.basepair.BasePairTrack;
 import org.broad.igv.feature.CachingFeatureSource;
 import org.broad.igv.feature.GisticFileParser;
 import org.broad.igv.feature.MutationTrackLoader;
@@ -1235,8 +1235,10 @@ private void loadTrioData(ResourceLocator locator) throws IOException {
 
 
     private void loadBasePairFile(ResourceLocator locator, List<Track> newTracks, Genome genome) throws IOException {
-        BasePairFileParser parser = new BasePairFileParser();
-        newTracks.add(parser.loadTrack(locator, genome)); // should create one track from the given file
+        String name = locator.getTrackName();
+        String path = locator.getPath();
+        String id = path + "_" + name;
+        newTracks.add(new BasePairTrack(locator, id, name, genome));
     }
 
     public static boolean isIndexed(ResourceLocator locator, Genome genome) {