From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 21 Jun 2017 12:46:50 +0000 (+0100)
Subject: JAL-2541 save/Undo only 'diffs' for features with Cut command
X-Git-Tag: Release_2_11_1_0~98^2~23^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c8e86c8d3d346840e826942470784b0fec66d439;p=jalview.git

JAL-2541 save/Undo only 'diffs' for features with Cut command

Conflicts:
	src/jalview/datamodel/features/SequenceFeatures.java
---

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index c46b36b..7dbcd6d 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -556,6 +556,10 @@ public class EditCommand implements CommandI
               command.oldds = new SequenceI[command.seqs.length];
             }
             command.oldds[i] = oldds;
+            if (oldds != sequence.getDatasetSequence())
+            {
+              oldds.getFeatures().deleteAll();
+            }
 
             if (cutPositions != null)
             {
@@ -585,22 +589,21 @@ public class EditCommand implements CommandI
    */
   static void paste(Edit command, AlignmentI[] views)
   {
-    StringBuffer tmp;
-    boolean newDSNeeded;
-    boolean newDSWasNeeded;
-    int newstart, newend;
     boolean seqWasDeleted = false;
-    int start = 0, end = 0;
 
     for (int i = 0; i < command.seqs.length; i++)
     {
-      newDSNeeded = false;
-      newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
+      int start = 0;
+      int end = 0;
+      boolean newDSNeeded = false;
+      boolean newDSWasNeeded = command.oldds != null
+              && command.oldds[i] != null;
       SequenceI sequence = command.seqs[i];
       if (sequence.getLength() < 1)
       {
-        // ie this sequence was deleted, we need to
-        // readd it to the alignment
+        /*
+         * sequence was deleted; re-add it to the alignment
+         */
         if (command.alIndex[i] < command.al.getHeight())
         {
           List<SequenceI> sequences;
@@ -618,10 +621,10 @@ public class EditCommand implements CommandI
         }
         seqWasDeleted = true;
       }
-      newstart = sequence.getStart();
-      newend = sequence.getEnd();
+      int newStart = sequence.getStart();
+      int newEnd = sequence.getEnd();
 
-      tmp = new StringBuffer();
+      StringBuilder tmp = new StringBuilder();
       tmp.append(sequence.getSequence());
       // Undo of a delete does not replace original dataset sequence on to
       // alignment sequence.
@@ -653,11 +656,11 @@ public class EditCommand implements CommandI
             }
             if (sequence.getStart() == start)
             {
-              newstart--;
+              newStart--;
             }
             else
             {
-              newend++;
+              newEnd++;
             }
           }
         }
@@ -665,8 +668,14 @@ public class EditCommand implements CommandI
       }
 
       sequence.setSequence(tmp.toString());
-      sequence.setStart(newstart);
-      sequence.setEnd(newend);
+      sequence.setStart(newStart);
+      sequence.setEnd(newEnd);
+
+      /*
+       * command and Undo share the same dataset sequence if cut was
+       * at start or end of sequence
+       */
+      boolean sameDatasetSequence = false;
       if (newDSNeeded)
       {
         if (sequence.getDatasetSequence() != null)
@@ -691,9 +700,11 @@ public class EditCommand implements CommandI
             command.oldds = new SequenceI[command.seqs.length];
           }
           command.oldds[i] = sequence.getDatasetSequence();
+          sameDatasetSequence = ds == sequence.getDatasetSequence();
+          ds.setSequenceFeatures(sequence.getSequenceFeatures());
           sequence.setDatasetSequence(ds);
         }
-        undoCutFeatures(command, i, start, end);
+        undoCutFeatures(command, i, start, end, sameDatasetSequence);
       }
     }
     adjustAnnotations(command, true, seqWasDeleted, views);
@@ -1107,7 +1118,7 @@ public class EditCommand implements CommandI
   }
 
   final static void undoCutFeatures(Edit command, int index, final int i,
-          final int j)
+          final int j, boolean sameDatasetSequence)
   {
     SequenceI seq = command.seqs[index];
     SequenceI sequence = seq.getDatasetSequence();
@@ -1117,10 +1128,13 @@ public class EditCommand implements CommandI
     }
 
     /*
-     * TODO: shift right features that lie to the right of the restored cut
-     * Currently not needed as all features restored with saved dataset sequence
-     * nor if no saved dataset sequence (as coordinates left unchanged by Cut)
+     * shift right features that lie to the right of the restored cut
+     * (but not if dataset sequence unchanged - coordinates left unchanged by Cut)
      */
+    if (!sameDatasetSequence)
+    {
+      seq.getFeatures().shiftFeatures(i + 1, j - i);
+    }
 
     /*
      * restore any features that were deleted or truncated
@@ -1476,7 +1490,6 @@ public class EditCommand implements CommandI
            * truncate left, adjust end of feature
            */
           newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
-          // newEnd = newBegin + (sfEnd - sfBegin) - overlapsBy;
           newEnd = newBegin + sfEnd - cutEndPos - 1;
           if (sf.isContactFeature())
           {
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 24f2081..217c03d 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -452,4 +452,13 @@ public class SequenceFeatures implements SequenceFeaturesI
     }
     return modified;
   }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void deleteAll()
+  {
+    featureStore.clear();
+  }
 }
diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index 40beae3..8c30dce 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -203,4 +203,9 @@ public interface SequenceFeaturesI
    * @param shiftBy
    */
   boolean shiftFeatures(int fromPosition, int shiftBy);
-}
\ No newline at end of file
+
+  /**
+   * Deletes all positional and non-positional features
+   */
+  void deleteAll();
+}