From 2fd908578cc00b0315504af557adf1366e4ac34a Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 4 Oct 2007 16:32:06 +0000
Subject: [PATCH] refactored invertColumnSelection as an object method

---
 src/jalview/datamodel/ColumnSelection.java |   38 +++++++++++++++++++++++++---
 src/jalview/gui/AlignViewport.java         |   18 +++----------
 2 files changed, 38 insertions(+), 18 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 73b7899..6cba6b3 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -962,10 +962,15 @@ public class ColumnSelection
           blockEnd = end;
         }
 
-        if (end > blockStart)
+        if (end >= blockStart)
         {
-          annels.addElement(els = new Annotation[end-blockStart]);
-          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
+          annels.addElement(els = new Annotation[end-blockStart+1]);
+          if (end-blockStart+1<=alignmentAnnotation.annotations.length)
+          {
+            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
+          } else {
+            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, (end-blockStart+1));
+          }
           w+=els.length;
         }
         if (w==0)
@@ -979,6 +984,33 @@ public class ColumnSelection
           System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);
           w+=chnk.length;
         }
+    } else {
+      alignmentAnnotation.restrict(start, end);
+    }
+  }
+
+  /**
+   * Invert the column selection from first to end-1.
+   * leaves hiddenColumns untouched (and unselected)
+   * @param first
+   * @param end
+   */
+  public void invertColumnSelection(int first, int width)
+  {
+    boolean hasHidden = hiddenColumns!=null && hiddenColumns.size()>0;
+    for(int i=first; i<width; i++)
+    {
+      if(contains(i))
+    {
+        removeElement(i);
     }
+      else
+      {
+        if (!hasHidden || isVisible(i))
+        {
+          addElement(i);
+        }
+      }
+    }    
   }
 }
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 41341d0..afdfd69 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1453,20 +1453,7 @@ public class AlignViewport
 
     public void invertColumnSelection()
     {
-      for(int i=0; i<alignment.getWidth(); i++)
-      {
-        if(colSel.contains(i))
-      {
-          colSel.removeElement(i);
-      }
-        else
-        {
-          if (!hasHiddenColumns || colSel.isVisible(i))
-          {
-            colSel.addElement(i);
-          }
-        }
-      }
+      colSel.invertColumnSelection(0,alignment.getWidth());
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1479,7 +1466,7 @@ public class AlignViewport
      * derived from the whole alignment or just the current
      * selection with start and end points adjusted
      * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
-     * @return String[]
+     * @return selection as new sequenceI objects
      */
     public SequenceI[] getSelectionAsNewSequence()
     {
@@ -1501,6 +1488,7 @@ public class AlignViewport
 
       return sequences;
     }
+    
     /**
      * get the currently selected sequence objects or all the sequences in the alignment.
      * @return array of references to sequence objects
-- 
1.7.10.2