From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Sat, 24 Jun 2017 12:06:12 +0000 (+0100)
Subject: JAL-2547 fix case of gap followed by enclosing contact feature position
X-Git-Tag: Release_2_10_3b1~190
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d8d9dadb23ea69882877e511b5fb62352bc9ed63;p=jalview.git

JAL-2547 fix case of gap followed by enclosing contact feature position
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 96a2fa1..a01d185 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1821,12 +1821,11 @@ public class Sequence extends ASequence implements SequenceI
             endPos, types);
 
     /*
-     * if the start or end column is gapped, startPos or endPos may be to the 
-     * left or right, and we may have included adjacent or enclosing features;
-     * remove any that are not enclosing features
+     * if end column is gapped, endPos may be to the right, 
+     * and we may have included adjacent or enclosing features;
+     * remove any that are not enclosing, non-contact features
      */
-    if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1])
-            || Comparison.isGap(sequence[toColumn - 1]))
+    if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
     {
       ListIterator<SequenceFeature> it = result.listIterator();
       while (it.hasNext())
@@ -1847,6 +1846,13 @@ public class Sequence extends ASequence implements SequenceI
           {
             it.remove();
           }
+          else if (featureEndColumn > toColumn && sf.isContactFeature())
+          {
+            /*
+             * remove an enclosing feature if it is a contact feature
+             */
+            it.remove();
+          }
         }
       }
     }
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index d1f4290..2f824ca 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1343,23 +1343,21 @@ public class SequenceTest
             null);
     sq.addSequenceFeature(sf0);
     // add feature on BCD
-    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 9, 11, 2f,
+    SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
             null);
-    sq.addSequenceFeature(sf1);
+    sq.addSequenceFeature(sfBCD);
     // add feature on DE
-    SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 11, 12, 2f,
+    SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
             null);
-    sq.addSequenceFeature(sf2);
+    sq.addSequenceFeature(sfDE);
     // add contact feature at [B, H]
-    SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 9,
-            15, 2f,
-            null);
-    sq.addSequenceFeature(sf3);
+    SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
+            "desc", 9, 15, 2f, null);
+    sq.addSequenceFeature(sfContactBH);
     // add contact feature at [F, G]
-    SequenceFeature sf4 = new SequenceFeature("Disulfide Bond", "desc", 13,
-            14, 2f,
-            null);
-    sq.addSequenceFeature(sf4);
+    SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
+            "desc", 13, 14, 2f, null);
+    sq.addSequenceFeature(sfContactFG);
 
     // no features in columns 1-2 (-A)
     List<SequenceFeature> found = sq.findFeatures(1, 2);
@@ -1368,20 +1366,24 @@ public class SequenceTest
     // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
     found = sq.findFeatures(1, 6);
     assertEquals(2, found.size());
-    assertTrue(found.contains(sf1));
-    assertTrue(found.contains(sf3));
+    assertTrue(found.contains(sfBCD));
+    assertTrue(found.contains(sfContactBH));
 
     // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
     found = sq.findFeatures(5, 6);
     assertEquals(1, found.size());
-    assertTrue(found.contains(sf1));
+    assertTrue(found.contains(sfBCD));
 
     // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
     found = sq.findFeatures(7, 10);
     assertEquals(3, found.size());
-    assertTrue(found.contains(sf1));
-    assertTrue(found.contains(sf2));
-    assertTrue(found.contains(sf4));
+    assertTrue(found.contains(sfBCD));
+    assertTrue(found.contains(sfDE));
+    assertTrue(found.contains(sfContactFG));
+
+    // columns 10-11 (--) should find nothing
+    found = sq.findFeatures(10, 11);
+    assertEquals(0, found.size());
   }
 
   @Test(groups = { "Functional" })