This commit was manufactured by cvs2svn to create branch 'VamJalview'.

[jalview.git] / src / jalview / gui / ColumnSelection.java

diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index 356dd1c..26dba83 100755 (executable)
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -20,7 +20,6 @@ package jalview.gui;
 \r
 import java.util.*;\r
 \r
-\r
 /**\r
  * NOTE: Columns are zero based.\r
  */\r
@@ -28,6 +27,9 @@ public class ColumnSelection
 {\r
     Vector selected = new Vector();\r
 \r
+    //Vector of int [] {startCol, endCol}\r
+    Vector hiddenColumns;\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -64,6 +66,19 @@ public class ColumnSelection
         }\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
@@ -138,15 +153,6 @@ public class ColumnSelection
         return min;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Vector asVector()\r
-    {\r
-        return selected;\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -166,4 +172,191 @@ public class ColumnSelection
             }\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 getHiddenRegionBoundary(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
+\r
+    public void hideColumns(int res, AlignViewport av)\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
+      av.setSelectionGroup(null);\r
+      av.hasHiddenColumns = true;\r
+    }\r
+\r
+    public void revealAllHiddenColumns(AlignViewport av)\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
+          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