X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=0596468182f54a8f0752c3a9351e9033d117999e;hb=7c562dea24843c09b684eed45d0b71f7211166f0;hp=97f3703d5122e9aae06a61bcf509bfc72b36bb6d;hpb=5630468a241fe312a5c5ac3c323caf2df5d9d036;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 97f3703..0596468 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -246,8 +246,6 @@ public class SeqPanel
 
    void insertGapAtCursor(boolean group)
    {
-     ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                  av.alignment, HistoryItem.EDIT));
      groupEditing = group;
      startseq = seqCanvas.cursorY;
      lastres = seqCanvas.cursorX;
@@ -257,8 +255,6 @@ public class SeqPanel
 
    void deleteGapAtCursor(boolean group)
    {
-     ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                  av.alignment, HistoryItem.EDIT));
      groupEditing = group;
      startseq = seqCanvas.cursorY;
      lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
@@ -354,8 +350,6 @@ public class SeqPanel
        if(seq<0 || res<0)
          return;
 
-       ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                          av.alignment, HistoryItem.EDIT));
 
          if ((seq < av.getAlignment().getHeight()) &&
                  (res < av.getAlignment().getSequenceAt(seq).getLength()))
@@ -472,8 +466,6 @@ public class SeqPanel
 
   public void doMousePressed(MouseEvent evt)
   {
-    ap.alignFrame.addHistoryItem(new HistoryItem(
-        "Edit Sequence", av.alignment, HistoryItem.EDIT));
 
     int seq = findSeq(evt);
     int res = findRes(evt);
@@ -814,8 +806,15 @@ public class SeqPanel
       }
 
 
+
       if (groupEditing)
       {
+        Vector vseqs = sg.getSequences(true);
+        int g, groupSize = vseqs.size();
+        SequenceI[] groupSeqs = new SequenceI[groupSize];
+        for (g = 0; g < groupSeqs.length; g++)
+          groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+
         // drag to right
         if (insertGap)
         {
@@ -839,13 +838,13 @@ public class SeqPanel
                fixedRight--)
           {
             blank = true;
-            for (int s = 0; s < sg.getSize(true); s++)
+
+            for (g = 0; g < groupSize; g++)
             {
-              seq = (SequenceI)sg.getSequences(true).elementAt(s);
               for (int j = 0; j < startres - lastres; j++)
               {
                 if (!jalview.util.Comparison.isGap(
-                    seq.getCharAt(fixedRight - j)))
+                    groupSeqs[g].getCharAt(fixedRight - j)))
                 {
                   blank = false;
                   break;
@@ -894,19 +893,17 @@ public class SeqPanel
           /// Are we able to delete?
           // ie are all columns blank?
 
-          for (int s = 0; s < sg.getSize(true); s++)
+          for (g = 0; g < groupSize; g++)
           {
-            seq = (SequenceI)sg.getSequences(true).elementAt(s);
-
             for (int j = startres; j < lastres; j++)
             {
-              if (seq.getSequence().length() <= j)
+              if (groupSeqs[g].getLength() <= j)
               {
                 continue;
               }
 
               if (!jalview.util.Comparison.isGap(
-                  seq.getSequence().charAt(j)))
+                  groupSeqs[g].getCharAt(j)))
               {
                 // Not a gap, block edit not valid
                 endEditing();
@@ -917,10 +914,8 @@ public class SeqPanel
         }
 
 
-        for (int i = 0; i < sg.getSize(true); i++)
+        for (g = 0; g < groupSize; g++)
         {
-          seq = (SequenceI) sg.getSequences(true).elementAt(i);
-
           if (insertGap)
           {
             // dragging to the right
@@ -928,10 +923,10 @@ public class SeqPanel
             {
               if (fixedColumns && fixedRight != -1)
               {
-                insertChar(j, seq, fixedRight);
+                insertChar(j, groupSeqs[g], fixedRight);
               }
               else
-                insertChar(j, seq);
+                insertChar(j, groupSeqs[g]);
             }
           }
           else
@@ -941,17 +936,16 @@ public class SeqPanel
             {
               if (fixedColumns && fixedRight != -1)
               {
-                deleteChar(startres, seq, fixedRight);
+                deleteChar(startres, groupSeqs[g], fixedRight);
               }
               else
               {
-                deleteChar(startres, seq);
+                deleteChar(startres, groupSeqs[g]);
               }
             }
           }
         }
-      }
-      else /////Editing a single sequence///////////
+      }      else /////Editing a single sequence///////////
       {
         if (insertGap)
         {
@@ -1272,7 +1266,7 @@ public class SeqPanel
         y = av.alignment.getHeight() -1;
       }
 
-      if(res>av.alignment.getWidth())
+      if(res>=av.alignment.getWidth())
         res = av.alignment.getWidth()-1;
 
       if (stretchGroup.getEndRes() == res)