Moved to datamodel

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

diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
deleted file mode 100755 (executable)
index 94e2642..0000000
--- a/src/jalview/gui/ColumnSelection.java
+++ /dev/null
@@ -1,418 +0,0 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-\r
-/**\r
- * NOTE: Columns are zero based.\r
- */\r
-public class ColumnSelection\r
-{\r
-    Vector selected = new Vector();\r
-\r
-    //Vector of int [] {startCol, endCol}\r
-    Vector hiddenColumns;\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param col DOCUMENT ME!\r
-     */\r
-    public void addElement(int col)\r
-    {\r
-        if (!selected.contains(new Integer(col)))\r
-        {\r
-            selected.addElement(new Integer(col));\r
-        }\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void clear()\r
-    {\r
-        selected.removeAllElements();\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param col DOCUMENT ME!\r
-     */\r
-    public void removeElement(int col)\r
-    {\r
-        Integer colInt = new Integer(col);\r
-\r
-        if (selected.contains(colInt))\r
-        {\r
-            selected.removeElement(colInt);\r
-        }\r
-    }\r
-\r
-    public void removeElements(int start, int end)\r
-    {\r
-      Integer colInt;\r
-      for(int i=start; i<end; i++)\r
-      {\r
-        colInt = new Integer(i);\r
-        if (selected.contains(colInt))\r
-        {\r
-            selected.removeElement(colInt);\r
-        }\r
-      }\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param col DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public boolean contains(int col)\r
-    {\r
-        return selected.contains(new Integer(col));\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int columnAt(int i)\r
-    {\r
-        return ((Integer) selected.elementAt(i)).intValue();\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int size()\r
-    {\r
-        return selected.size();\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getMax()\r
-    {\r
-        int max = -1;\r
-\r
-        for (int i = 0; i < selected.size(); i++)\r
-        {\r
-            if (columnAt(i) > max)\r
-            {\r
-                max = columnAt(i);\r
-            }\r
-        }\r
-\r
-        return max;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getMin()\r
-    {\r
-        int min = 1000000000;\r
-\r
-        for (int i = 0; i < selected.size(); i++)\r
-        {\r
-            if (columnAt(i) < min)\r
-            {\r
-                min = columnAt(i);\r
-            }\r
-        }\r
-\r
-        return min;\r
-    }\r
-\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param start DOCUMENT ME!\r
-     * @param change DOCUMENT ME!\r
-     */\r
-    public void compensateForEdit(int start, int change)\r
-    {\r
-        for (int i = 0; i < size(); i++)\r
-        {\r
-            int temp = columnAt(i);\r
-\r
-            if (temp >= start)\r
-            {\r
-                selected.setElementAt(new Integer(temp - change), i);\r
-            }\r
-        }\r
-\r
-        if(hiddenColumns!=null)\r
-        {\r
-          for(int i=0; i<hiddenColumns.size(); i++)\r
-          {\r
-            int[] region = (int[]) hiddenColumns.elementAt(i);\r
-            if(region[0] > start)\r
-            {\r
-              region[0] -= change;\r
-              region[1] -= change;\r
-            }\r
-            if(region[0]<0)\r
-              region[0] = 0;\r
-            if(region[1] <0)\r
-             region[1] = 0;\r
-          }\r
-        }\r
-    }\r
-\r
-    /**\r
-     * This Method is used to return all the HiddenColumn regions\r
-     * less than the given index.\r
-     * @param end int\r
-     * @return Vector\r
-     */\r
-    public Vector getHiddenColumns()\r
-    {\r
-      return hiddenColumns;\r
-    }\r
-\r
-    public int adjustForHiddenColumns(int column)\r
-    {\r
-      int result = column;\r
-      if (hiddenColumns != null)\r
-      {\r
-        for (int i = 0; i < hiddenColumns.size(); i++)\r
-        {\r
-          int[] region = (int[]) hiddenColumns.elementAt(i);\r
-          if (result >= region[0])\r
-          {\r
-            result += region[1] - region[0] + 1;\r
-          }\r
-        }\r
-      }\r
-      return result;\r
-    }\r
-\r
-    /**\r
-     * Use this method to find out where a visible column is in the alignment\r
-     * when hidden columns exist\r
-     * @param hiddenColumn int\r
-     * @return int\r
-     */\r
-    public int findColumnPosition(int hiddenColumn)\r
-    {\r
-      int result = hiddenColumn;\r
-      if (hiddenColumns != null)\r
-      {\r
-        int index = 0;\r
-        int gaps = 0;\r
-        do\r
-        {\r
-          int[] region = (int[]) hiddenColumns.elementAt(index);\r
-          if (hiddenColumn > region[1])\r
-          {\r
-            result -= region[1]+1-region[0];\r
-          }\r
-          index++;\r
-        }\r
-        while (index < hiddenColumns.size());\r
-\r
-        result -= gaps;\r
-      }\r
-\r
-      return result;\r
-    }\r
-\r
-    /**\r
-     * Use this method to determine where the next hiddenRegion starts\r
-    */\r
-    public int findHiddenRegionPosition(int hiddenRegion)\r
-    {\r
-      int result = 0;\r
-      if (hiddenColumns != null)\r
-      {\r
-        int index = 0;\r
-        int gaps = 0;\r
-        do\r
-        {\r
-          int[] region = (int[]) hiddenColumns.elementAt(index);\r
-          if(hiddenRegion==0)\r
-          {\r
-            return region[0];\r
-          }\r
-\r
-            gaps +=  region[1] +1 - region[0];\r
-            result = region[1] +1;\r
-            index++;\r
-        }\r
-        while(index < hiddenRegion+1);\r
-\r
-        result -= gaps;\r
-      }\r
-\r
-      return result;\r
-    }\r
-\r
-    /**\r
-     * THis method returns the rightmost limit of a\r
-     * region of an alignment with hidden columns.\r
-     * In otherwords, the next hidden column.\r
-     * @param index int\r
-     */\r
-    public int getHiddenBoundaryRight(int alPos)\r
-    {\r
-      if (hiddenColumns != null)\r
-      {\r
-        int index = 0;\r
-        do\r
-        {\r
-          int[] region = (int[]) hiddenColumns.elementAt(index);\r
-          if(alPos < region[0])\r
-            return region[0];\r
-\r
-          index++;\r
-        }\r
-        while(index < hiddenColumns.size());\r
-      }\r
-\r
-      return alPos;\r
-\r
-    }\r
-    /**\r
-     * THis method returns the rightmost limit of a\r
-     * region of an alignment with hidden columns.\r
-     * In otherwords, the next hidden column.\r
-     * @param index int\r
-     */\r
-    public int getHiddenBoundaryLeft(int alPos)\r
-    {\r
-      if (hiddenColumns != null)\r
-      {\r
-        int index = hiddenColumns.size()-1;\r
-        do\r
-        {\r
-          int[] region = (int[]) hiddenColumns.elementAt(index);\r
-          if(alPos > region[1])\r
-            return region[1];\r
-\r
-          index--;\r
-        }\r
-        while(index >-1);\r
-      }\r
-\r
-      return alPos;\r
-\r
-    }\r
-\r
-\r
-\r
-    public void hideColumns(int res)\r
-    {\r
-      if(hiddenColumns==null)\r
-        hiddenColumns = new Vector();\r
-\r
-      // First find out range of columns to hide\r
-      int min = res, max = res+1;\r
-      while( contains(min) )\r
-      {  removeElement(min); min --;  }\r
-\r
-      while( contains(max) )\r
-      { removeElement(max);  max ++;  }\r
-\r
-      min++; max--;\r
-\r
-      boolean added = false;\r
-      for(int i=0; i<hiddenColumns.size(); i++)\r
-      {\r
-        int [] region = (int[])hiddenColumns.elementAt(i);\r
-        if( max < region[0])\r
-        {\r
-          hiddenColumns.insertElementAt(new int[]{min, max}, i);\r
-          added = true;\r
-          break;\r
-        }\r
-      }\r
-\r
-      if(!added)\r
-        hiddenColumns.addElement(new int[]{min, max});\r
-\r
-    }\r
-\r
-    public void revealAllHiddenColumns(AlignViewport av)\r
-    {\r
-      if(hiddenColumns!=null)\r
-      {\r
-        for (int i = 0; i < hiddenColumns.size(); i++)\r
-        {\r
-          int[] region = (int[]) hiddenColumns.elementAt(i);\r
-          for (int j = region[0]; j < region[1]; j++)\r
-          {\r
-            addElement(j);\r
-          }\r
-        }\r
-      }\r
-      av.hasHiddenColumns = false;\r
-      hiddenColumns = null;\r
-    }\r
-\r
-    public void revealHiddenColumns(int res, AlignViewport av)\r
-    {\r
-      for(int i=0; i<hiddenColumns.size(); i++)\r
-      {\r
-        int [] region = (int[])hiddenColumns.elementAt(i);\r
-        if( res == region[0])\r
-        {\r
-          for (int j = region[0]; j < region[1]; j++)\r
-          {\r
-            addElement(j);\r
-          }\r
-\r
-          hiddenColumns.remove(region);\r
-          break;\r
-        }\r
-      }\r
-\r
-\r
-      if(hiddenColumns.size()<1)\r
-        av.hasHiddenColumns = false;\r
-    }\r
-\r
-    public boolean isVisible(int column)\r
-    {\r
-      for(int i=0; i<hiddenColumns.size(); i++)\r
-      {\r
-        int [] region = (int[])hiddenColumns.elementAt(i);\r
-        if( column >= region[0] && column <= region[1])\r
-        {\r
-          return false;\r
-        }\r
-      }\r
-      return true;\r
-    }\r
-\r
-}\r