From 72baa5e02d3f71f1c0259072fdbd0b2bf8250e6c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 25 Jul 2006 15:49:14 +0000
Subject: [PATCH] Moved to datamodel

---
 src/jalview/appletgui/ColumnSelection.java |  124 ---------
 src/jalview/gui/ColumnSelection.java       |  418 ----------------------------
 2 files changed, 542 deletions(-)
 delete mode 100755 src/jalview/appletgui/ColumnSelection.java
 delete mode 100755 src/jalview/gui/ColumnSelection.java

diff --git a/src/jalview/appletgui/ColumnSelection.java b/src/jalview/appletgui/ColumnSelection.java
deleted file mode 100755
index 33c4604..0000000
--- a/src/jalview/appletgui/ColumnSelection.java
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-/**
- * NOTE: Columns are zero based.
- */
-public class ColumnSelection
-{
-  Vector selected = new Vector();
-
-  public void addElement(int col)
-  {
-    if(!selected.contains(new Integer(col)))
-      selected.addElement(new Integer(col));
-  }
-
-  public void clear()
-  {
-    selected.removeAllElements();
-  }
-
-  public void removeElement(int col)
-  {
-    Integer colInt = new Integer(col);
-    if (selected.contains(colInt))
-    {
-      selected.removeElement(colInt);
-    }
-  }
-
-  public void removeElements(int start, int end)
-  {
-    Integer colInt;
-    for(int i=start; i<end; i++)
-    {
-      colInt = new Integer(i);
-      if (selected.contains(colInt))
-      {
-          selected.removeElement(colInt);
-      }
-    }
-    }
-
-  public boolean contains(int col)
-  {
-    return selected.contains(new Integer(col));
-  }
-
-  public int columnAt(int i)
-  {
-    return ( (Integer) selected.elementAt(i)).intValue();
-  }
-
-  public int size()
-  {
-    return selected.size();
-  }
-
-  public int getMax()
-  {
-    int max = -1;
-
-    for (int i = 0; i < selected.size(); i++)
-    {
-      if (columnAt(i) > max)
-      {
-        max = columnAt(i);
-      }
-    }
-    return max;
-  }
-
-  public int getMin()
-  {
-    int min = 1000000000;
-
-    for (int i = 0; i < selected.size(); i++)
-    {
-      if (columnAt(i) < min)
-      {
-        min = columnAt(i);
-      }
-    }
-    return min;
-  }
-
-  public Vector asVector()
-  {
-    return selected;
-  }
-
-  public void compensateForEdit(int start, int change)
-  {
-    for (int i = 0; i < size(); i++)
-    {
-      int temp = columnAt(i);
-
-      if (temp >= start)
-      {
-        selected.setElementAt(new Integer(temp - change), i);
-      }
-    }
-  }
-}
diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
deleted file mode 100755
index 94e2642..0000000
--- a/src/jalview/gui/ColumnSelection.java
+++ /dev/null
@@ -1,418 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-/**
- * NOTE: Columns are zero based.
- */
-public class ColumnSelection
-{
-    Vector selected = new Vector();
-
-    //Vector of int [] {startCol, endCol}
-    Vector hiddenColumns;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     */
-    public void addElement(int col)
-    {
-        if (!selected.contains(new Integer(col)))
-        {
-            selected.addElement(new Integer(col));
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void clear()
-    {
-        selected.removeAllElements();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     */
-    public void removeElement(int col)
-    {
-        Integer colInt = new Integer(col);
-
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
-    }
-
-    public void removeElements(int start, int end)
-    {
-      Integer colInt;
-      for(int i=start; i<end; i++)
-      {
-        colInt = new Integer(i);
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean contains(int col)
-    {
-        return selected.contains(new Integer(col));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int columnAt(int i)
-    {
-        return ((Integer) selected.elementAt(i)).intValue();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int size()
-    {
-        return selected.size();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMax()
-    {
-        int max = -1;
-
-        for (int i = 0; i < selected.size(); i++)
-        {
-            if (columnAt(i) > max)
-            {
-                max = columnAt(i);
-            }
-        }
-
-        return max;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMin()
-    {
-        int min = 1000000000;
-
-        for (int i = 0; i < selected.size(); i++)
-        {
-            if (columnAt(i) < min)
-            {
-                min = columnAt(i);
-            }
-        }
-
-        return min;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     * @param change DOCUMENT ME!
-     */
-    public void compensateForEdit(int start, int change)
-    {
-        for (int i = 0; i < size(); i++)
-        {
-            int temp = columnAt(i);
-
-            if (temp >= start)
-            {
-                selected.setElementAt(new Integer(temp - change), i);
-            }
-        }
-
-        if(hiddenColumns!=null)
-        {
-          for(int i=0; i<hiddenColumns.size(); i++)
-          {
-            int[] region = (int[]) hiddenColumns.elementAt(i);
-            if(region[0] > start)
-            {
-              region[0] -= change;
-              region[1] -= change;
-            }
-            if(region[0]<0)
-              region[0] = 0;
-            if(region[1] <0)
-             region[1] = 0;
-          }
-        }
-    }
-
-    /**
-     * 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)
-    {
-      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});
-
-    }
-
-    public void revealAllHiddenColumns(AlignViewport av)
-    {
-      if(hiddenColumns!=null)
-      {
-        for (int i = 0; i < hiddenColumns.size(); i++)
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          for (int j = region[0]; j < region[1]; j++)
-          {
-            addElement(j);
-          }
-        }
-      }
-      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])
-        {
-          for (int j = region[0]; j < region[1]; j++)
-          {
-            addElement(j);
-          }
-
-          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;
-    }
-
-}
-- 
1.7.10.2