X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=98ac2d5d962b6ec616f1b7f0c4e5745b28e86e14;hb=be4614014839c44c1fafb3b84a71824625e5fa90;hp=21ff841fca39214d2d3a76bac50f28f9dce79673;hpb=60e252f7e0084336b0a85620842ce3db8f63e5b0;p=jalview.git

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)