setting and merging selected columns from another selection object

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6bba5d2..afa2e07 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -36,7 +36,7 @@ public class ColumnSelection
    * Add a column to the selection\r
    * \r
    * @param col\r
-   *                index of column\r
+   *          index of column\r
    */\r
   public void addElement(int col)\r
   {\r
@@ -59,7 +59,7 @@ public class ColumnSelection
    * removes col from selection\r
    * \r
    * @param col\r
-   *                index of column to be removed\r
+   *          index of column to be removed\r
    */\r
   public void removeElement(int col)\r
   {\r
@@ -75,9 +75,9 @@ public class ColumnSelection
    * removes a range of columns from the selection\r
    * \r
    * @param start\r
-   *                int - first column in range to be removed\r
+   *          int - first column in range to be removed\r
    * @param end\r
-   *                int - last col\r
+   *          int - last col\r
    */\r
   public void removeElements(int start, int end)\r
   {\r
@@ -104,7 +104,7 @@ public class ColumnSelection
   /**\r
    * \r
    * @param col\r
-   *                index to search for in column selection\r
+   *          index to search for in column selection\r
    * \r
    * @return true if Integer(col) is in selection.\r
    */\r
@@ -117,7 +117,7 @@ public class ColumnSelection
    * Column number at position i in selection\r
    * \r
    * @param i\r
-   *                index into selected columns\r
+   *          index into selected columns\r
    * \r
    * @return column number in alignment\r
    */\r
@@ -180,9 +180,9 @@ public class ColumnSelection
    * propagate shift in alignment columns to column selection\r
    * \r
    * @param start\r
-   *                beginning of edit\r
+   *          beginning of edit\r
    * @param left\r
-   *                shift in edit (+ve for removal, or -ve for inserts)\r
+   *          shift in edit (+ve for removal, or -ve for inserts)\r
    */\r
   public Vector compensateForEdit(int start, int change)\r
   {\r
@@ -238,9 +238,9 @@ public class ColumnSelection
    * compensateForEdit - allowing for edits within hidden regions\r
    * \r
    * @param start\r
-   *                beginning of edit\r
+   *          beginning of edit\r
    * @param left\r
-   *                shift in edit (+ve for removal, or -ve for inserts)\r
+   *          shift in edit (+ve for removal, or -ve for inserts)\r
    */\r
   private void compensateForDelEdits(int start, int change)\r
   {\r
@@ -403,7 +403,7 @@ public class ColumnSelection
       }\r
     }\r
     return pruned; // true if any interval was removed or modified by\r
-                    // operations.\r
+    // operations.\r
   }\r
 \r
   private boolean pruneColumnList(Vector deletion, Vector list)\r
@@ -476,7 +476,7 @@ public class ColumnSelection
    * given index.\r
    * \r
    * @param end\r
-   *                int\r
+   *          int\r
    * @return Vector\r
    */\r
   public Vector getHiddenColumns()\r
@@ -488,7 +488,7 @@ public class ColumnSelection
    * Return absolute column index for a visible column index\r
    * \r
    * @param column\r
-   *                int column index in alignment view\r
+   *          int column index in alignment view\r
    * @return alignment column index for column\r
    */\r
   public int adjustForHiddenColumns(int column)\r
@@ -513,7 +513,7 @@ public class ColumnSelection
    * hidden columns exist\r
    * \r
    * @param hiddenColumn\r
-   *                int\r
+   *          int\r
    * @return int\r
    */\r
   public int findColumnPosition(int hiddenColumn)\r
@@ -573,7 +573,7 @@ public class ColumnSelection
    * hidden columns. In otherwords, the next hidden column.\r
    * \r
    * @param index\r
-   *                int\r
+   *          int\r
    */\r
   public int getHiddenBoundaryRight(int alPos)\r
   {\r
@@ -601,7 +601,7 @@ public class ColumnSelection
    * hidden columns. In otherwords, the previous hidden column.\r
    * \r
    * @param index\r
-   *                int\r
+   *          int\r
    */\r
   public int getHiddenBoundaryLeft(int alPos)\r
   {\r
@@ -679,7 +679,7 @@ public class ColumnSelection
    * specified\r
    * \r
    * @param res\r
-   *                int\r
+   *          int\r
    */\r
   public void hideColumns(int col)\r
   {\r
@@ -867,10 +867,11 @@ public class ColumnSelection
    * return all visible segments between the given start and end boundaries\r
    * \r
    * @param start\r
-   *                (first column inclusive from 0)\r
+   *          (first column inclusive from 0)\r
    * @param end\r
-   *                (last column - not inclusive)\r
-   * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end<end\r
+   *          (last column - not inclusive)\r
+   * @return int[] {i_start, i_end, ..} where intervals lie in\r
+   *         start<=i_start<=i_end<end\r
    */\r
   public int[] getVisibleContigs(int start, int end)\r
   {\r
@@ -940,11 +941,11 @@ public class ColumnSelection
    * sequence associated annotation).\r
    * \r
    * @param start\r
-   *                remove any annotation to the right of this column\r
+   *          remove any annotation to the right of this column\r
    * @param end\r
-   *                remove any annotation to the left of this column\r
+   *          remove any annotation to the left of this column\r
    * @param alignmentAnnotation\r
-   *                the annotation to operate on\r
+   *          the annotation to operate on\r
    */\r
   public void makeVisibleAnnotation(int start, int end,\r
           AlignmentAnnotation alignmentAnnotation)\r
@@ -998,7 +999,7 @@ public class ColumnSelection
       if (end > blockStart)\r
       {\r
         annels.addElement(els = new Annotation[end - blockStart + 1]);\r
-        if ((els.length+blockStart)<= alignmentAnnotation.annotations.length)\r
+        if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)\r
         {\r
           // copy just the visible segment of the annotation row\r
           System.arraycopy(alignmentAnnotation.annotations, blockStart,\r
@@ -1008,7 +1009,8 @@ public class ColumnSelection
         {\r
           // copy to the end of the annotation row\r
           System.arraycopy(alignmentAnnotation.annotations, blockStart,\r
-                  els, 0, (alignmentAnnotation.annotations.length - blockStart));\r
+                  els, 0,\r
+                  (alignmentAnnotation.annotations.length - blockStart));\r
         }\r
         w += els.length;\r
       }\r
@@ -1056,4 +1058,49 @@ public class ColumnSelection
       }\r
     }\r
   }\r
+\r
+  /**\r
+   * add in any unselected columns from the given column selection, excluding any that are hidden.\r
+   * @param colsel\r
+   */\r
+  public void addElementsFrom(ColumnSelection colsel)\r
+  {\r
+    if (colsel != null && colsel.size() > 0)\r
+    {\r
+      Enumeration e = colsel.getSelected().elements();\r
+      while (e.hasMoreElements())\r
+      {\r
+        Object eo = e.nextElement();\r
+        if (hiddenColumns!=null && isVisible(((Integer) eo).intValue())) {\r
+          if (!selected.contains(eo))\r
+          {\r
+            selected.addElement(eo);\r
+          }\r
+        }\r
+      }\r
+    }\r
+  }\r
+/**\r
+ * set the selected columns the given column selection, excluding any columns that are hidden. \r
+ * @param colsel\r
+ */\r
+  public void setElementsFrom(ColumnSelection colsel)\r
+  {\r
+    if (colsel.selected != null && colsel.selected.size() > 0)\r
+    {\r
+      if (hiddenColumns!=null && hiddenColumns.size()>0)\r
+      {\r
+        // only select visible columns in this columns selection\r
+        selected = new Vector();\r
+        addElementsFrom(colsel);\r
+      } else {\r
+        // be quick\r
+        selected = new Vector(colsel.selected);\r
+      }\r
+    }\r
+    else\r
+    {\r
+      selected = new Vector();\r
+    }\r
+  }\r
 }\r