improve "hit testing" for clicks over features, etc.

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

@@ -57,15 +57,15 @@ public static void sortFeatureList(List<? extends Feature> features) {
      * Return a feature from the supplied list whose extent, expanded by "buffer", contains the given position.
      *
      * @param position 0-based genomic position to which to search for feature
-     * @param buffer   search region. The first feature which contains the start position, (expanded by buffer, inclusive)
-     *                 will be accepted.
+     * @param bpPerPixel  current resolution in base pairs per pixel.
      * @param features
      * @return
      */
-    public static <T extends Feature> T getFeatureAt(double position, int buffer, List<? extends T> features) {
+    public static <T extends Feature> T getFeatureAt(double position, double bpPerPixel, List<? extends T> features) {
 
         int startIdx = 0;
         int endIdx = features.size();
+        int buffer = (int) (2 * bpPerPixel);
 
         while (startIdx != endIdx) {
             int idx = (startIdx + endIdx) / 2;
@@ -367,34 +367,33 @@ public static int getIndexBeforeOld(double position, List<? extends Feature> fea
 
 
     /**
-     * Return all features from the supplied list who's extent, expanded to "minWidth" if needed,  contains the given position
+     * Return all features from the supplied list who's extent, expanded by "flanking", intersect the position
      *
      * @param position
-     * @param maxLength -- the distance back from position at which to start search (the maximum feature length)
-     * @param minWidth  -- the minimum effective width of the feature
+     * @param flanking  -- the minimum effective width of the feature
      * @param features
      * @return
      */
     public static List<Feature> getAllFeaturesAt(double position,
-                                                 double maxLength,
-                                                 double minWidth,
+                                                 double flanking,
                                                  List<? extends htsjdk.tribble.Feature> features) {
 
         List<Feature> returnList = null;
 
-        double adjustedPosition = Math.max(0, position - maxLength);
-        int startIdx = Math.max(0, getIndexBefore(adjustedPosition, features));
+
+        int startIdx = Math.max(0, getIndexBefore(position - flanking, features));
+        double start = position - (flanking / 2);
+        double end = position + (flanking / 2);
         for (int idx = startIdx; idx < features.size(); idx++) {
             Feature feature = features.get(idx);
-            double start = feature.getStart() - (minWidth / 2);
-            if (start > position) {
-                break;
-            }
-            double end = feature.getEnd() + (minWidth / 2);
-            if (position >= start && position <= end) {
+            if(feature.getEnd() >= start && feature.getStart() <= end)  {
                 if (returnList == null) returnList = new ArrayList();
                 returnList.add(feature);
             }
+
+            if (feature.getStart() > end) {
+                break;
+            }
         }
 
         // Sort features by distance from position (features closest to position listed first)

src/main/java/org/broad/igv/sam/AlignmentTrack.java

@@ -875,8 +875,7 @@ Alignment getAlignmentAt(double position, int y, ReferenceFrame frame) {
                     List<Alignment> features = row.alignments;
 
                     // No buffer for alignments,  you must zoom in far enough for them to be visible
-                    int buffer = 0;
-                    return FeatureUtils.getFeatureAt(position, buffer, features);
+                    return FeatureUtils.getFeatureAt(position, 0, features);
                 }
             }
         }

src/main/java/org/broad/igv/sam/CoverageTrack.java

@@ -402,7 +402,7 @@ private String getPrecomputedValueString(String chr, double position, ReferenceF
         if (scores == null) {
             return "";
         } else {
-            LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, 0, scores);
+            LocusScore score = FeatureUtils.getFeatureAt(position, 0, scores);
             return score == null ? "" : "Mean count: " + score.getScore();
         }
     }

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

@@ -300,9 +300,7 @@ private LocusScore getLocusScoreAt(String chr, double position, ReferenceFrame f
             return null;
         } else {
             // give a 2 pixel window, otherwise very narrow features will be missed.
-            double bpPerPixel = frame.getScale();
-            int buffer = (int) (2 * bpPerPixel);    /* * */
-            return (LocusScore) FeatureUtils.getFeatureAt(position, buffer, scores);
+            return FeatureUtils.getFeatureAt(position, frame.getScale(), scores);
         }
     }
 

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

@@ -301,14 +301,10 @@ public String getValueString(String chr, double position, ReferenceFrame frame)
             int zoom = Math.max(0, frame.getZoom());
             List<LocusScore> scores = getSummaryScoresForRange(chr, (int) position - 10, (int) position + 10, zoom);
 
-            // give a 2 pixel window, otherwise very narrow features will be missed.
-            double bpPerPixel = frame.getScale();
-            int minWidth = (int) (2 * bpPerPixel);    /* * */
-
             if (scores == null) {
                 return "";
             } else {
-                LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, minWidth, scores);
+                LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, frame.getScale(), scores);
                 return score == null ? "" : "Mean count: " + score.getScore();
             }
         }

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

@@ -424,10 +424,7 @@ public String getValueStringAt(String chr, double position, int mouseX, int mous
             if (scores == null) {
                 return "";
             } else {
-                // give a +/- 2 pixel buffer, otherwise very narrow features will be missed.
-                double bpPerPixel = frame.getScale();
-                int minWidth = (int) (2 * bpPerPixel);    /* * */
-                LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, minWidth, scores);
+                LocusScore score = FeatureUtils.getFeatureAt(position, frame.getScale(), scores);
                 return score == null ? null : "Mean count: " + score.getScore();
             }
 
@@ -558,9 +555,8 @@ public List<Feature> getFeaturesAtPositionInFeatureRow(double position, int feat
         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 minWidth = Math.max(2, 3 * bpPerPixel);
-            int maxFeatureLength = packedFeatures.getMaxFeatureLength();
-            featureList = FeatureUtils.getAllFeaturesAt(position, maxFeatureLength, minWidth, possFeatures);
+            double minWidth = (int)  (2* bpPerPixel);
+            featureList = FeatureUtils.getAllFeaturesAt(position, minWidth, possFeatures);
         }
         return featureList;
     }

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

@@ -360,13 +360,13 @@ public String getValueStringAt(String chr, double position, int mouseX, int igno
         LocusScore amp = null;
         List<GisticScore> ampScores = ampScoreMap.get(chr);
         if (ampScores != null) {
-            amp = (LocusScore) FeatureUtils.getFeatureAt(position, 0, ampScores);
+            amp = FeatureUtils.getFeatureAt(position, 0, ampScores);
         }
 
         LocusScore del = null;
         List<GisticScore> delScores = delScoreMap.get(chr);
         if (delScores != null) {
-            del = (LocusScore) FeatureUtils.getFeatureAt(position, 0, delScores);
+            del = FeatureUtils.getFeatureAt(position, 0, delScores);
         }
 
         if ((amp == null) && (del == null)) {

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

@@ -578,14 +578,10 @@ public String getValueString(String chr, double position, ReferenceFrame frame)
                 int zoom = Math.max(0, frame.getZoom());
                 List<LocusScore> scores = getSummaryScoresForRange(chr, (int) position - 10, (int) position + 10, zoom);
 
-                // give a 2 pixel window, otherwise very narrow features will be missed.
-                double bpPerPixel = frame.getScale();
-                int minWidth = (int) (2 * bpPerPixel);    /* * */
-
                 if (scores == null) {
                     return "";
                 } else {
-                    LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, minWidth, scores);
+                    LocusScore score = FeatureUtils.getFeatureAt(position, frame.getScale(), scores);
                     return score == null ? "" : "Mean count: " + score.getScore();
                 }
             }

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

@@ -129,10 +129,8 @@ public void testGetFeatureClosestWithIndels(){
     public void testGetAllFeaturesAt() {
 
         int position = 56078756;
-        int maxLength = 100000;
-
-
-        List<Feature> result = FeatureUtils.getAllFeaturesAt(position, maxLength, 0, featureList);
+        double flanking = 0;
+        List<Feature> result = FeatureUtils.getAllFeaturesAt(position, flanking, featureList);
         assertEquals(21, result.size());
         for (Feature f : result) {
             assertTrue(position >= f.getStart() && position <= f.getEnd());