X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=a23aad5e837e04ad8d4e19a8feacadb76b2aba0b;hb=27d1490bba5753b3f9c8fac0647cfe8148c53310;hp=21b5e7f26963750eadc951a5ac7b8ec52965ec21;hpb=1f5616e7db919162a5cc3b25b09ccf95845f03ee;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 21b5e7f..a23aad5 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.
  * 
@@ -21,6 +21,7 @@ import jalview.util.ShiftList;
 
 import java.io.PrintStream;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Vector;
 
 /**
@@ -105,9 +106,9 @@ public class AlignmentView
     SequenceI[] selseqs;
     if (selection != null)
     {
-      Vector sel = selection.getSequences(null);
+      List<SequenceI> sel = selection.getSequences(null);
       this.selected = new Vector();
-      selseqs = selection.getSequencesInOrder(alignment, false);
+      selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
     }
     else
     {
@@ -116,12 +117,8 @@ public class AlignmentView
 
     // get the alignment's group list and make a copy
     Vector grps = new Vector();
-    Vector gg = alignment.getGroups();
-    Enumeration gge = gg.elements();
-    while (gge.hasMoreElements())
-    {
-      grps.addElement(gge.nextElement());
-    }
+    List<SequenceGroup> gg = alignment.getGroups();
+    grps.addAll(gg);
     ScGroup[] sgrps = null;
     boolean addedgps[] = null;
     if (grps != null)
@@ -351,9 +348,14 @@ 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);
@@ -363,14 +365,11 @@ 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)
           {
@@ -1045,12 +1044,10 @@ public class AlignmentView
                 + " wide and has " + visal.getHeight() + " seqs.");
         if (visal.getGroups() != null && visal.getGroups().size() > 0)
         {
-          SequenceGroup sg;
-          Enumeration en = visal.getGroups().elements();
+          
           int i = 1;
-          while (en.hasMoreElements())
+          for (SequenceGroup sg:visal.getGroups())
           {
-            sg = (SequenceGroup) en.nextElement();
             os.println("Group " + (i++) + " begins at column "
                     + sg.getStartRes() + " and ends at " + sg.getEndRes());
           }