update author list in license for (JAL-826)

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 2da7c80..8e596ce 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
  * \r
  * This file is part of Jalview.\r
  * \r
@@ -107,7 +107,7 @@ public class AlignmentView
     {\r
       Vector sel = selection.getSequences(null);\r
       this.selected = new Vector();\r
-      selseqs = selection.getSequencesInOrder(alignment, false);\r
+      selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);\r
     }\r
     else\r
     {\r
@@ -150,6 +150,9 @@ public class AlignmentView
             {\r
               sg.setEndRes(esel);\r
             }\r
+            sg.setStartRes(sg.getStartRes()-ssel+1);\r
+            sg.setEndRes(sg.getEndRes()-ssel+1);\r
+            \r
             isg.addElement(sg);\r
           }\r
         }\r
@@ -348,9 +351,14 @@ public class AlignmentView
                 continue;\r
               }\r
             }\r
+\r
+            // clone group properties\r
+            nsg[g] = new SequenceGroup(sg);\r
+\r
             // may need to shift/trim start and end ?\r
             if (r && !viscontigs)\r
             {\r
+              // Not fully tested code - routine not yet called with viscontigs==false\r
               if (nsg[g].getStartRes() < gstart)\r
               {\r
                 nsg[g].setStartRes(0);\r
@@ -360,14 +368,11 @@ public class AlignmentView
                 nsg[g].setStartRes(nsg[g].getStartRes() - gstart);\r
                 nsg[g].setEndRes(nsg[g].getEndRes() - gstart);\r
               }\r
-              if (nsg[g].getEndRes() > gend)\r
+              if (nsg[g].getEndRes() > (gend-gstart))\r
               {\r
-                nsg[g].setEndRes(gend);\r
+                nsg[g].setEndRes(gend-gstart);\r
               }\r
             }\r
-\r
-            // clone group properties\r
-            nsg[g] = new SequenceGroup(sg);\r
           }\r
           if (viscontigs)\r
           {\r