X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=ebe8301551f10aa01a7ddc099ed07af13b6a6984;hb=e549be446ec3ed7f7b1bc8b348c409bcffca901b;hp=e0d8d4478606f7c9af7f200278de925eaf626698;hpb=ea1129578da8007d62c540724d0856165181f8ec;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index e0d8d44..ebe8301 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -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
     {
@@ -150,6 +150,9 @@ public class AlignmentView
             {
               sg.setEndRes(esel);
             }
+            sg.setStartRes(sg.getStartRes()-ssel+1);
+            sg.setEndRes(sg.getEndRes()-ssel+1);
+            
             isg.addElement(sg);
           }
         }
@@ -348,9 +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);
@@ -360,14 +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)
           {
@@ -989,9 +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();