X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FColumnSelection.java;h=55c055c46d5546a5613ca18c7e5352ba8fbe0974;hb=a1a0288d696c1dedef111a4edab027d95c89ed25;hp=a7fd83a211c26d4f97f96534d512ea006f421bad;hpb=3cd503affe392c274ebf2df5ca869af3c4961bfa;p=jalview.git

diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index a7fd83a..55c055c 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.
  */
@@ -28,6 +27,9 @@ public class ColumnSelection
 {
     Vector selected = new Vector();
 
+    //Vector of int [] {startCol, endCol}
+    Vector hiddenColumns;
+
     /**
      * DOCUMENT ME!
      *
@@ -151,15 +153,6 @@ public class ColumnSelection
         return min;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector asVector()
-    {
-        return selected;
-    }
 
     /**
      * DOCUMENT ME!
@@ -179,4 +172,216 @@ public class ColumnSelection
             }
         }
     }
+
+    /**
+     * This Method is used to return all the HiddenColumn regions
+     * less than the given index.
+     * @param end int
+     * @return Vector
+     */
+    public Vector getHiddenColumns()
+    {
+      return hiddenColumns;
+    }
+
+    public int adjustForHiddenColumns(int column)
+    {
+      int result = column;
+      if (hiddenColumns != null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          if (result >= region[0])
+          {
+            result += region[1] - region[0] + 1;
+          }
+        }
+      }
+      return result;
+    }
+
+    /**
+     * Use this method to find out where a visible column is in the alignment
+     * when hidden columns exist
+     * @param hiddenColumn int
+     * @return int
+     */
+    public int findColumnPosition(int hiddenColumn)
+    {
+      int result = hiddenColumn;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if (hiddenColumn > region[1])
+          {
+            result -= region[1]+1-region[0];
+          }
+          index++;
+        }
+        while (index < hiddenColumns.size());
+
+        result -= gaps;
+      }
+
+      return result;
+    }
+
+    /**
+     * Use this method to determine where the next hiddenRegion starts
+    */
+    public int findHiddenRegionPosition(int hiddenRegion)
+    {
+      int result = 0;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(hiddenRegion==0)
+          {
+            return region[0];
+          }
+
+            gaps +=  region[1] +1 - region[0];
+            result = region[1] +1;
+            index++;
+        }
+        while(index < hiddenRegion+1);
+
+        result -= gaps;
+      }
+
+      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 getHiddenBoundaryRight(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;
+
+    }
+    /**
+     * 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 getHiddenBoundaryLeft(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = hiddenColumns.size()-1;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos > region[1])
+            return region[1];
+
+          index--;
+        }
+        while(index >-1);
+      }
+
+      return alPos;
+
+    }
+
+
+    public void hideColumns(int res, AlignViewport av)
+    {
+      if(hiddenColumns==null)
+        hiddenColumns = new Vector();
+
+      // First find out range of columns to hide
+      int min = res, max = res+1;
+      while( contains(min) )
+      {  removeElement(min); min --;  }
+
+      while( contains(max) )
+      { removeElement(max);  max ++;  }
+
+      min++; max--;
+
+      boolean added = false;
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( max < region[0])
+        {
+          hiddenColumns.insertElementAt(new int[]{min, max}, i);
+          added = true;
+          break;
+        }
+      }
+
+      if(!added)
+        hiddenColumns.addElement(new int[]{min, max});
+
+
+      av.setSelectionGroup(null);
+      av.hasHiddenColumns = true;
+    }
+
+    public void revealAllHiddenColumns(AlignViewport av)
+    {
+      av.hasHiddenColumns = false;
+      hiddenColumns = null;
+    }
+
+    public void revealHiddenColumns(int res, AlignViewport av)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( res == region[0])
+        {
+          hiddenColumns.remove(region);
+          break;
+        }
+      }
+
+
+      if(hiddenColumns.size()<1)
+        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;
+    }
+
 }