historyItem.restore

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b714aea..a4f5e4d 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -450,42 +450,8 @@ public class AlignFrame
   // used by undo and redo\r
   void restoreHistoryItem(HistoryItem hi)\r
   {\r
-    if (hi.getType() == HistoryItem.SORT)\r
-    {\r
-      for (int i = 0; i < hi.getSequences().size(); i++)\r
-      {\r
-        viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
-            .elementAt(i),\r
-            i);\r
-      }\r
-    }\r
-    else\r
-    {\r
-      for (int i = 0; i < hi.getSequences().size(); i++)\r
-      {\r
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 \r
-        if (restore.getLength() == 0)\r
-        {\r
-          restore.setSequence(hi.getHidden().elementAt(i).toString());\r
-          viewport.alignment.getSequences().insertElementAt(restore,\r
-              hi.getAlignIndex(i));\r
-        }\r
-        else\r
-        {\r
-          restore.setSequence(hi.getHidden().elementAt(i).toString());\r
-        }\r
-      }\r
-\r
-      if (hi.getType() == HistoryItem.PASTE)\r
-      {\r
-        for (int i = viewport.alignment.getHeight() - 1;\r
-             i > (hi.getSequences().size() - 1); i--)\r
-        {\r
-          viewport.alignment.deleteSequence(i);\r
-        }\r
-      }\r
-    }\r
+    hi.restore();\r
 \r
     updateEditMenuBar();\r
 \r
@@ -2575,11 +2541,12 @@ public void showTranslation_actionPerformed(ActionEvent e)
  */\r
 public boolean parseGroupsFile(String file)\r
 {\r
+    String line = null;\r
     try\r
     {\r
       BufferedReader in = new BufferedReader(new FileReader(file));\r
       SequenceI seq = null;\r
-      String line, type, desc, token;\r
+      String type, desc, token;\r
 \r
       int index, start, end;\r
       StringTokenizer st;\r
@@ -2650,8 +2617,9 @@ public boolean parseGroupsFile(String file)
     }\r
     catch (Exception ex)\r
     {\r
+      System.out.println(line);\r
       ex.printStackTrace();\r
-      System.out.println("Error parsing groups file: " + ex);\r
+      System.out.println("Error parsing groups file: " + ex +"\n"+line);\r
       return false;\r
     }\r
 \r