Fix logic searching for features containing a position. Fixes #1541

src/main/java/org/broad/igv/feature/FeatureUtils.java

@@ -116,33 +116,6 @@ public static Feature getFeatureStartsAfter(double position, List<? extends Feat
         return null;
     }
 
-    public static Feature getFeatureEndsBefore(double position, List<? extends Feature> features) {
-
-        int index = getIndexBefore(position, features);
-        Feature prevFeature = null;
-        while (index >= 0) {
-            Feature f = features.get(index);
-            if (f.getEnd() < position) {
-                if (prevFeature == null) {
-                    prevFeature = f;
-                } else {
-                    if (f.getStart() == prevFeature.getStart()) {
-                        // Prefer smallest feature
-                        if (f.getEnd() < prevFeature.getEnd()) {
-                            prevFeature = f;
-                        }
-                    } else {
-                        // Done
-                        break;
-                    }
-                }
-            }
-            index--;
-        }
-        return prevFeature;
-
-    }
-
     /**
      * Return the first feature whose center is > the given position.  If no features satisfy the criteria
      * return null;
@@ -374,15 +347,13 @@ public static int getIndexBeforeOld(double position, List<? extends Feature> fea
      * @param features
      * @return
      */
-    public static List<Feature> getAllFeaturesAt(double position,
-                                                 double flanking,
-                                                 List<? extends htsjdk.tribble.Feature> features) {
+    public static List<Feature> getAllFeaturesContaining(double position,
+                                                         double flanking,
+                                                         List<? extends htsjdk.tribble.Feature> features) {
 
         List<Feature> returnList = null;
 
-        int startIdx = Math.max(0, getIndexBefore(position, features));
-        for (int idx = startIdx; idx < features.size(); idx++) {
-            Feature feature = features.get(idx);
+        for (Feature feature : features) {
             if (feature.getStart() > position + flanking) {
                 break;
             }

src/main/java/org/broad/igv/feature/dsi/DSITrack.java

@@ -26,7 +26,7 @@ public DSITrack(ResourceLocator locator, FeatureSource src) {
     @Override
     public String getValueStringAt(String chr, double position, int mouseX, int mouseY, ReferenceFrame frame) {
 
-        List<Feature> allFeatures = getAllFeatureAt(position, mouseY, frame);
+        List<Feature> allFeatures = getAllFeaturesContaining(position, mouseY, frame);
         if (allFeatures == null) {
             return null;
         }

src/main/java/org/broad/igv/track/FeatureTrack.java

@@ -382,7 +382,7 @@ public String getValueStringAt(String chr, double position, int mouseX, int mous
 
         if (showFeatures) {
 
-            List<Feature> allFeatures = getAllFeatureAt(position, mouseY, frame);
+            List<Feature> allFeatures = getAllFeaturesContaining(position, mouseY, frame);
             if (allFeatures == null) {
                 return null;
             }
@@ -495,7 +495,7 @@ public List<Feature> getFeatures(String chr, int start, int end) {
      * @param frame
      * @return
      */
-    protected List<Feature> getAllFeatureAt(double position, int y, ReferenceFrame frame) {
+    protected List<Feature> getAllFeaturesContaining(double position, int y, ReferenceFrame frame) {
         // Determine the level number (for expanded tracks)
         int featureRow = getFeatureRow(y);
         return getFeaturesAtPositionInFeatureRow(position, featureRow, frame);
@@ -549,19 +549,15 @@ public List<Feature> getFeaturesAtPositionInFeatureRow(double position, int feat
 
         //If features are stacked we look at only the row.
         //If they are collapsed on top of each other, we get all features in all rows
-        List<Feature> possFeatures;
-        if (getDisplayMode() == DisplayMode.COLLAPSED) {
-            possFeatures = packedFeatures.getFeatures();
-        } else {
-            possFeatures = rows.get(featureRow).getFeatures();
-        }
+        List<Feature> possFeatures = rows.get(featureRow).getFeatures();
+
 
         List<Feature> featureList = null;
         if (possFeatures != null) {
             // give a minum 2 pixel or 1/2 bp window, otherwise very narrow features will be missed.
             double bpPerPixel = frame.getScale();
             double flanking = 4 * bpPerPixel;
-            featureList = FeatureUtils.getAllFeaturesAt(position, flanking, possFeatures);
+            featureList = FeatureUtils.getAllFeaturesContaining(position, flanking, possFeatures);
         }
         return featureList;
     }
@@ -631,7 +627,7 @@ public Feature getFeatureAtMousePosition(TrackClickEvent te) {
         final ReferenceFrame referenceFrame = te.getFrame();
         if (referenceFrame != null) {
             double location = referenceFrame.getChromosomePosition(e);
-            List<Feature> features = getAllFeatureAt(location, e.getY(), referenceFrame);
+            List<Feature> features = getAllFeaturesContaining(location, e.getY(), referenceFrame);
             return (features != null && features.size() > 0) ? features.get(0) : null;
         } else {
             return null;

src/test/java/org/broad/igv/feature/FeatureUtilsTest.java

@@ -45,7 +45,6 @@
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 
 import static org.junit.Assert.*;
@@ -129,10 +128,8 @@ public void testGetFeatureClosestWithIndels(){
     public void testGetAllFeaturesAt() {
 
         int position = 56078756;
-        int maxLength = 100000;
 
-
-        List<Feature> result = FeatureUtils.getAllFeaturesAt(position, 0, featureList);
+        List<Feature> result = FeatureUtils.getAllFeaturesContaining(position, 0, featureList);
         assertEquals(21, result.size());
         for (Feature f : result) {
             assertTrue(position >= f.getStart() && position <= f.getEnd());
@@ -192,24 +189,6 @@ public void testGetFeatureCenterAfter() {
         assertNull(f);
     }
 
-    @Test
-    public void testGetFeatureBefore() {
-
-        // feature
-        // chr7	56078756	56119137
-        Feature f = FeatureUtils.getFeatureEndsBefore(56119137 + 1, featureList);
-        assertEquals(56078756, f.getStart());
-
-        // chr7	55086709	55236328
-        f = FeatureUtils.getFeatureStartsAfter(0, featureList);
-        assertEquals(55086709, f.getStart());
-
-        // last feature
-        // chr7	56182373	56184110
-        f = FeatureUtils.getFeatureStartsAfter(56182373, featureList);
-        assertNull(f);
-    }
-
     @Test
     public void testGetFeatureCenterBefore() {