+\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
+ 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
+ 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
+ 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