From 1b6c18d9f88fa91c284a8a671e8f242ccfef5dd5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 21 Jun 2017 12:00:04 +0100
Subject: [PATCH] JAL-2541 adjust end of contact feature spanning cut region

---
 src/jalview/commands/EditCommand.java      |   13 +++++++++++++
 test/jalview/commands/EditCommandTest.java |   29 +++++++++++++++++++++++++---
 2 files changed, 39 insertions(+), 3 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 7387295..84335c7 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1412,6 +1412,19 @@ public class EditCommand implements CommandI
               cutStartPos, cutEndPos);
   
       /*
+       * add any contact features that span the cut region
+       * (not returned by findFeatures)
+       */
+      for (SequenceFeature contact : featureStore.getContactFeatures())
+      {
+        if (contact.getBegin() < cutStartPos
+                && contact.getEnd() > cutEndPos)
+        {
+          toAmend.add(contact);
+        }
+      }
+
+      /*
        * adjust start-end of overlapping features;
        * delete features enclosed by the cut;
        * delete partially overlapping contact features
diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 9177135..326104a 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -675,26 +675,49 @@ public class EditCommandTest
     seq0.addSequenceFeature(new SequenceFeature("after", "", 8, 10, 0f,
             null));
 
+    /*
+     * add some contact features
+     */
+    SequenceFeature internalContact = new SequenceFeature("disulphide bond", "", 5,
+            6, 0f, null);
+    seq0.addSequenceFeature(internalContact); // should get deleted
+    SequenceFeature overlapLeftContact = new SequenceFeature(
+            "disulphide bond", "", 2, 6, 0f, null);
+    seq0.addSequenceFeature(overlapLeftContact); // should get deleted
+    SequenceFeature overlapRightContact = new SequenceFeature(
+            "disulphide bond", "", 5, 8, 0f, null);
+    seq0.addSequenceFeature(overlapRightContact); // should get deleted
+    SequenceFeature spanningContact = new SequenceFeature(
+            "disulphide bond", "", 2, 9, 0f, null);
+    seq0.addSequenceFeature(spanningContact); // should get shortened 3'
+
+    /*
+     * cut columns 3-6 (base 0), residues d-g 4-7
+     */
     Edit ec = testee.new Edit(Action.CUT, seqs, 3, 4, al); // cols 3-6 base 0
     EditCommand.cut(ec, new AlignmentI[] { al });
 
     List<SequenceFeature> sfs = seq0.getSequenceFeatures();
     SequenceFeatures.sortFeatures(sfs, true);
 
-    assertEquals(4, sfs.size()); // feature internal to cut has been deleted
+    assertEquals(5, sfs.size()); // features internal to cut were deleted
     SequenceFeature sf = sfs.get(0);
     assertEquals("before", sf.getType());
     assertEquals(1, sf.getBegin());
     assertEquals(3, sf.getEnd());
     sf = sfs.get(1);
+    assertEquals("disulphide bond", sf.getType());
+    assertEquals(2, sf.getBegin());
+    assertEquals(5, sf.getEnd()); // truncated by cut
+    sf = sfs.get(2);
     assertEquals("overlap left", sf.getType());
     assertEquals(2, sf.getBegin());
     assertEquals(3, sf.getEnd()); // truncated by cut
-    sf = sfs.get(2);
+    sf = sfs.get(3);
     assertEquals("after", sf.getType());
     assertEquals(4, sf.getBegin()); // shifted left by cut
     assertEquals(6, sf.getEnd()); // shifted left by cut
-    sf = sfs.get(3);
+    sf = sfs.get(4);
     assertEquals("overlap right", sf.getType());
     assertEquals(4, sf.getBegin()); // shifted left by cut
     assertEquals(4, sf.getEnd()); // truncated by cut
-- 
1.7.10.2