From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 9 Aug 2006 15:53:22 +0000 (+0000)
Subject: Copy hidden cols to new alignment
X-Git-Tag: Release_2_1~137
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9970c99badd3ff277a19e6880cc83dc04ded23da;p=jalview.git

Copy hidden cols to new alignment
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e1d8ce8..6a8645e 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -521,6 +521,12 @@ public void itemStateChanged(ItemEvent evt)
       url.append( appendProtocol( viewport.applet.getParameter("features") ) );
     }
 
+    if(viewport.applet.getParameter("annotations")!=null)
+    {
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
+    }
+
     if(viewport.applet.getParameter("defaultColour")!=null)
     {
       url.append("&colour=" +
@@ -689,7 +695,8 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
-  StringBuffer copiedSequences;
+  static StringBuffer copiedSequences;
+  static Vector copiedHiddenColumns;
   protected void copy_actionPerformed()
   {
     if (viewport.getSelectionGroup() == null)
@@ -710,6 +717,25 @@ public void itemStateChanged(ItemEvent evt)
     int index = 0, startRes, endRes;
     char ch;
 
+    if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
+    {
+      copiedHiddenColumns = new Vector();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
+           i++)
+      {
+        int[] region = (int[])
+            viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+
+        copiedHiddenColumns.addElement(new int[]
+                                 {region[0] - hiddenOffset,
+                                 region[1] - hiddenOffset});
+      }
+    }
+    else
+      copiedHiddenColumns = null;
+
+
     for (int i = 0; i < sg.getSize(false); i++)
     {
         SequenceI seq = null;
@@ -821,6 +847,15 @@ public void itemStateChanged(ItemEvent evt)
                                        viewport.applet,
                                        newtitle,
                                        false);
+        if (copiedHiddenColumns != null)
+        {
+          for (int i = 0; i < copiedHiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+            af.viewport.hideColumns(region[0], region[1]);
+          }
+        }
+
 
         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
                                          NEW_WINDOW_HEIGHT);