X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=8e596ceca355d76c01c33a364ebdb45fb6af9145;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=0b4e23677df8f5f5a195c6785109e2d4598568a6;hpb=659d52531c89150f901f7b12cb4c681bf73bf8c8;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 0b4e236..8e596ce 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -107,7 +107,7 @@ public class AlignmentView
     {
       Vector sel = selection.getSequences(null);
       this.selected = new Vector();
-      selseqs = selection.getSequencesInOrder(alignment, false);
+      selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
     }
     else
     {
@@ -115,7 +115,13 @@ public class AlignmentView
     }
 
     // get the alignment's group list and make a copy
-    Vector grps = new Vector(alignment.getGroups());
+    Vector grps = new Vector();
+    Vector gg = alignment.getGroups();
+    Enumeration gge = gg.elements();
+    while (gge.hasMoreElements())
+    {
+      grps.addElement(gge.nextElement());
+    }
     ScGroup[] sgrps = null;
     boolean addedgps[] = null;
     if (grps != null)
@@ -128,7 +134,7 @@ public class AlignmentView
         // visible and selected region
         int ssel = selection.getStartRes(), esel = selection.getEndRes();
         Vector isg = new Vector();
-        Enumeration<?> en = grps.elements();
+        Enumeration en = grps.elements();
         while (en.hasMoreElements())
         {
           sg = (SequenceGroup) en.nextElement();
@@ -144,6 +150,9 @@ public class AlignmentView
             {
               sg.setEndRes(esel);
             }
+            sg.setStartRes(sg.getStartRes()-ssel+1);
+            sg.setEndRes(sg.getEndRes()-ssel+1);
+            
             isg.addElement(sg);
           }
         }
@@ -177,7 +186,7 @@ public class AlignmentView
         {
           for (int sg = 0; sg < sgrps.length; sg++)
           {
-            if (((Vector) grps.get(sg)).contains(selseqs[i]))
+            if (((Vector) grps.elementAt(sg)).contains(selseqs[i]))
             {
               sequences[csi].setGroupMembership(sgrps[sg]);
               sgrps[sg].sg.deleteSequence(selseqs[i], false);
@@ -326,7 +335,7 @@ public class AlignmentView
        * prune any groups to the visible coordinates of the alignment.
        */
       {
-        int nvg = scGroups != null ? scGroups.size() : 0;
+        int nvg = (scGroups != null) ? scGroups.size() : 0;
         if (nvg > 0)
         {
           SequenceGroup[] nsg = new SequenceGroup[nvg];
@@ -342,9 +351,14 @@ public class AlignmentView
                 continue;
               }
             }
+
+            // clone group properties
+            nsg[g] = new SequenceGroup(sg);
+
             // may need to shift/trim start and end ?
             if (r && !viscontigs)
             {
+              // Not fully tested code - routine not yet called with viscontigs==false
               if (nsg[g].getStartRes() < gstart)
               {
                 nsg[g].setStartRes(0);
@@ -354,14 +368,11 @@ public class AlignmentView
                 nsg[g].setStartRes(nsg[g].getStartRes() - gstart);
                 nsg[g].setEndRes(nsg[g].getEndRes() - gstart);
               }
-              if (nsg[g].getEndRes() > gend)
+              if (nsg[g].getEndRes() > (gend-gstart))
               {
-                nsg[g].setEndRes(gend);
+                nsg[g].setEndRes(gend-gstart);
               }
             }
-
-            // clone group properties
-            nsg[g] = new SequenceGroup(sg);
           }
           if (viscontigs)
           {
@@ -983,9 +994,13 @@ public class AlignmentView
   public static void summariseAlignmentView(AlignmentView view,
           PrintStream os)
   {
-    os.println("View has " + view.sequences.length + " of which "
-            + (view.selected == null ? "None" : view.selected.size())
-            + " are selected.");
+    os.print("View has " + view.sequences.length + " of which ");
+    if (view.selected == null) {
+      os.print("None");
+    } else {
+      os.print(" "+view.selected.size());
+    }
+    os.println(" are selected.");
     os.print("View is " + view.getWidth() + " columns wide");
     int viswid = 0;
     int[] contigs = view.getContigs();