From be4614014839c44c1fafb3b84a71824625e5fa90 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 24 May 2017 09:17:07 +0100
Subject: [PATCH 1/1] JAL-2505 delete and readd modified feature after Cut or
 Paste

---
 src/jalview/commands/EditCommand.java |   54 ++++++++++++++++++++++-----------
 1 file changed, 36 insertions(+), 18 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 21ff841..98ac2d5 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1122,51 +1122,69 @@ public class EditCommand implements CommandI
       return;
     }
 
-    SequenceFeature[] sf = sequence.getSequenceFeatures();
+    List<SequenceFeature> sf = sequence.getFeatures()
+            .getPositionalFeatures();
 
-    if (sf == null)
+    if (sf.isEmpty())
     {
       return;
     }
 
-    SequenceFeature[] oldsf = new SequenceFeature[sf.length];
+    SequenceFeature[] oldsf = new SequenceFeature[sf.size()];
 
     int cSize = j - i;
 
-    for (int s = 0; s < sf.length; s++)
+    int s = 0;
+    for (SequenceFeature feature : sf)
     {
-      SequenceFeature copy = new SequenceFeature(sf[s]);
+      SequenceFeature copy = new SequenceFeature(feature);
 
-      oldsf[s] = copy;
+      oldsf[s++] = copy;
 
-      if (sf[s].getEnd() < i)
+      if (feature.getEnd() < i)
       {
         continue;
       }
 
-      if (sf[s].getBegin() > j)
+      if (feature.getBegin() > j)
       {
-        sf[s].setBegin(copy.getBegin() - cSize);
-        sf[s].setEnd(copy.getEnd() - cSize);
+        int newBegin = copy.getBegin() - cSize;
+        int newEnd = copy.getEnd() - cSize;
+        SequenceFeature newSf = new SequenceFeature(feature, newBegin,
+                newEnd, feature.getFeatureGroup());
+        sequence.deleteFeature(feature);
+        sequence.addSequenceFeature(newSf);
+        // feature.setBegin(newBegin);
+        // feature.setEnd(newEnd);
         continue;
       }
 
-      if (sf[s].getBegin() >= i)
+      int newBegin = feature.getBegin();
+      int newEnd = feature.getEnd();
+      if (newBegin >= i)
       {
-        sf[s].setBegin(i);
+        newBegin = i;
+        // feature.setBegin(i);
       }
 
-      if (sf[s].getEnd() < j)
+      if (newEnd < j)
       {
-        sf[s].setEnd(j - 1);
+        newEnd = j - 1;
+        // feature.setEnd(j - 1);
       }
+      newEnd = newEnd - cSize;
+      // feature.setEnd(feature.getEnd() - (cSize));
 
-      sf[s].setEnd(sf[s].getEnd() - (cSize));
-
-      if (sf[s].getBegin() > sf[s].getEnd())
+      sequence.deleteFeature(feature);
+      if (newEnd >= newBegin)
       {
-        sequence.deleteFeature(sf[s]);
+        sequence.addSequenceFeature(new SequenceFeature(feature, newBegin,
+                newEnd, feature.getFeatureGroup()));
       }
+      // if (feature.getBegin() > feature.getEnd())
+      // {
+      // sequence.deleteFeature(feature);
+      // }
     }
 
     if (command.editedFeatures == null)
-- 
1.7.10.2