From: jprocter <Jim Procter>
Date: Tue, 8 Jun 2010 14:27:25 +0000 (+0000)
Subject: trim hidden regions outside selection when copying selected region to clipboard ... 
X-Git-Tag: Release_2_5_1~21
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6ef8b014737c1dac4f2e566e27cf4b34b68af9c0;p=jalview.git

trim hidden regions outside selection when copying selected region to clipboard * JAL-573
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 22647a3..0e607c7 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1530,15 +1530,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.hasHiddenColumns)
     {
       hiddenColumns = new Vector();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes(),hiddenCutoff=viewport.getSelectionGroup().getEndRes();
       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
               .size(); i++)
       {
         int[] region = (int[]) viewport.getColumnSelection()
                 .getHiddenColumns().elementAt(i);
-
-        hiddenColumns.addElement(new int[]
+        if (region[0]>=hiddenOffset && region[1]<=hiddenCutoff)
+        {
+          hiddenColumns.addElement(new int[]
         { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        }
       }
     }