Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList

[jalview.git] / src / jalview / commands / EditCommand.java

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 21ff841..388c533 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -555,6 +555,7 @@ public class EditCommand implements CommandI
               command.oldds = new SequenceI[command.seqs.length];
             }
             command.oldds[i] = oldds;
+            // FIXME JAL-2541 JAL-2526 get correct positions if on a gap
             adjustFeatures(
                     command,
                     i,
@@ -1101,8 +1102,8 @@ public class EditCommand implements CommandI
     }
   }
 
-  final static void adjustFeatures(Edit command, int index, int i, int j,
-          boolean insert)
+  final static void adjustFeatures(Edit command, int index, final int i,
+          final int j, boolean insert)
   {
     SequenceI seq = command.seqs[index];
     SequenceI sequence = seq.getDatasetSequence();
@@ -1122,51 +1123,69 @@ 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)