1.1 compatible

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
new file mode 100644 (file)
index 0000000..1dafcf0
--- /dev/null
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -0,0 +1,419 @@
+/*\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.datamodel;\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
+    public Vector getSelected()\r
+    {\r
+      return selected;\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()\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
+\r
+      hiddenColumns = null;\r
+    }\r
+\r
+    public void revealHiddenColumns(int res)\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.removeElement(region);\r
+          break;\r
+        }\r
+      }\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