Updated with latest from mchmmer branch

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index fe6b8d9..28aabe1 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -234,6 +234,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
+    viewport.initInformationWorker(alignPanel);
 
     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
     followMouseOverFlag.setState(viewport.isFollowHighlight());
@@ -1906,7 +1907,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   static StringBuffer copiedSequences;
 
-  static Vector<int[]> copiedHiddenColumns;
+  static HiddenColumns copiedHiddenColumns;
 
   protected void copy_actionPerformed()
   {
@@ -1930,14 +1931,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
     {
-      copiedHiddenColumns = new Vector<>(viewport.getAlignment()
-              .getHiddenColumns().getHiddenColumnsCopy());
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int[] region : copiedHiddenColumns)
-      {
-        region[0] = region[0] - hiddenOffset;
-        region[1] = region[1] - hiddenOffset;
-      }
+      int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+
+      // create new HiddenColumns object with copy of hidden regions
+      // between startRes and endRes, offset by startRes
+      copiedHiddenColumns = new HiddenColumns(
+              viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+              hiddenCutoff, hiddenOffset);
     }
     else
     {
@@ -2006,13 +2007,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     try
     {
-
       if (copiedSequences == null)
       {
         return;
       }
 
-      StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+      StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+              "\t");
       Vector seqs = new Vector();
       while (st.hasMoreElements())
       {
@@ -2044,14 +2045,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
                 viewport.applet, newtitle, false);
-        if (copiedHiddenColumns != null)
-        {
-          for (int i = 0; i < copiedHiddenColumns.size(); i++)
-          {
-            int[] region = copiedHiddenColumns.elementAt(i);
-            af.viewport.hideColumns(region[0], region[1]);
-          }
-        }
+        af.viewport.setHiddenColumns(copiedHiddenColumns);
 
         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
                 frameHeight);