Clip splice junction arcs at junction boundaries. Fix for Bezier curv…

…e artifact that sometimes carries curve behond junction boundaries. Fixes #1535
igvteam · Aug 12, 2024 · 7663069 · 7663069
1 parent fa87234
commit 7663069
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Showing 2 changed files with 284 additions and 315 deletions.
diff --git a/src/main/java/org/broad/igv/feature/SpliceJunctionFeature.java b/src/main/java/org/broad/igv/feature/SpliceJunctionFeature.java
@@ -26,6 +26,7 @@
 
 package org.broad.igv.feature;
 
+import htsjdk.tribble.Feature;
 import org.broad.igv.track.WindowFunction;
 
 import java.util.ArrayList;
@@ -45,8 +46,8 @@ public class SpliceJunctionFeature extends BasicFeature {
     protected int junctionDepth = 0;
 
     //start and end locations of the junction
-    protected int junctionStart = 0;
-    protected int junctionEnd = 0;
+    private int junctionStart = 0;
+    private int junctionEnd = 0;
 
     int[] startFlankingRegionDepthArray, endFlankingRegionDepthArray;
 
@@ -69,11 +70,11 @@ public SpliceJunctionFeature(String chr, int start, int end, Strand strand) {
      * @param otherFeature
      * @return
      */
-    public boolean isSameJunction(SpliceJunctionFeature otherFeature) {
-        if (otherFeature.getJunctionStart() == getJunctionStart() &&
-                otherFeature.getJunctionEnd() == getJunctionEnd())
-            return true;
-        return false;
+    public boolean isSameJunction(Feature otherFeature) {
+        return (otherFeature != null &&
+                otherFeature instanceof SpliceJunctionFeature &&
+                ((SpliceJunctionFeature) otherFeature).getJunctionStart() == getJunctionStart() &&
+                    ((SpliceJunctionFeature) otherFeature).getJunctionEnd() == getJunctionEnd());
     }
 
     /**