From ab2005eb4fd46c5d9f2df238f2cf20bcb35bf1f3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:29:55 +0000
Subject: [PATCH] isVisible and hiddenboundary added

---
 src/jalview/gui/ColumnSelection.java |   39 +++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index c9e232a..26dba83 100755
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -20,7 +20,6 @@ package jalview.gui;
 
 import java.util.*;
 
-
 /**
  * NOTE: Columns are zero based.
  */
@@ -262,6 +261,31 @@ public class ColumnSelection
       return result;
     }
 
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenRegionBoundary(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos < region[0])
+            return region[0];
+
+          index++;
+        }
+        while(index < hiddenColumns.size());
+      }
+
+      return alPos;
+
+    }
 
 
     public void hideColumns(int res, AlignViewport av)
@@ -322,4 +346,17 @@ public class ColumnSelection
         av.hasHiddenColumns = false;
     }
 
+    public boolean isVisible(int column)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( column >= region[0] && column <= region[1])
+        {
+          return false;
+        }
+      }
+      return true;
+    }
+
 }
-- 
1.7.10.2