X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=5c1707fb9b79b910b1b82fe63377de4914acaf74;hb=c16c1633e1a5acc9f44e4de40b9abbb8a59b99b4;hp=6bba5d202ed6cdfc6b1cba45896346ab50ccb75c;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6bba5d2..5c1707f 100644
--- 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
    * 
    * @param col
-   *                index of column
+   *          index of column
    */
   public void addElement(int col)
   {
@@ -59,7 +59,7 @@ public class ColumnSelection
    * removes col from selection
    * 
    * @param col
-   *                index of column to be removed
+   *          index of column to be removed
    */
   public void removeElement(int col)
   {
@@ -75,9 +75,9 @@ public class ColumnSelection
    * removes a range of columns from the selection
    * 
    * @param start
-   *                int - first column in range to be removed
+   *          int - first column in range to be removed
    * @param end
-   *                int - last col
+   *          int - last col
    */
   public void removeElements(int start, int end)
   {
@@ -104,7 +104,7 @@ public class ColumnSelection
   /**
    * 
    * @param col
-   *                index to search for in column selection
+   *          index to search for in column selection
    * 
    * @return true if Integer(col) is in selection.
    */
@@ -117,7 +117,7 @@ public class ColumnSelection
    * Column number at position i in selection
    * 
    * @param i
-   *                index into selected columns
+   *          index into selected columns
    * 
    * @return column number in alignment
    */
@@ -180,9 +180,9 @@ public class ColumnSelection
    * propagate shift in alignment columns to column selection
    * 
    * @param start
-   *                beginning of edit
+   *          beginning of edit
    * @param left
-   *                shift in edit (+ve for removal, or -ve for inserts)
+   *          shift in edit (+ve for removal, or -ve for inserts)
    */
   public Vector compensateForEdit(int start, int change)
   {
@@ -238,9 +238,9 @@ public class ColumnSelection
    * compensateForEdit - allowing for edits within hidden regions
    * 
    * @param start
-   *                beginning of edit
+   *          beginning of edit
    * @param left
-   *                shift in edit (+ve for removal, or -ve for inserts)
+   *          shift in edit (+ve for removal, or -ve for inserts)
    */
   private void compensateForDelEdits(int start, int change)
   {
@@ -403,7 +403,7 @@ public class ColumnSelection
       }
     }
     return pruned; // true if any interval was removed or modified by
-                    // operations.
+    // operations.
   }
 
   private boolean pruneColumnList(Vector deletion, Vector list)
@@ -476,7 +476,7 @@ public class ColumnSelection
    * given index.
    * 
    * @param end
-   *                int
+   *          int
    * @return Vector
    */
   public Vector getHiddenColumns()
@@ -488,7 +488,7 @@ public class ColumnSelection
    * Return absolute column index for a visible column index
    * 
    * @param column
-   *                int column index in alignment view
+   *          int column index in alignment view
    * @return alignment column index for column
    */
   public int adjustForHiddenColumns(int column)
@@ -513,7 +513,7 @@ public class ColumnSelection
    * hidden columns exist
    * 
    * @param hiddenColumn
-   *                int
+   *          int
    * @return int
    */
   public int findColumnPosition(int hiddenColumn)
@@ -573,7 +573,7 @@ public class ColumnSelection
    * hidden columns. In otherwords, the next hidden column.
    * 
    * @param index
-   *                int
+   *          int
    */
   public int getHiddenBoundaryRight(int alPos)
   {
@@ -601,7 +601,7 @@ public class ColumnSelection
    * hidden columns. In otherwords, the previous hidden column.
    * 
    * @param index
-   *                int
+   *          int
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
@@ -679,7 +679,7 @@ public class ColumnSelection
    * specified
    * 
    * @param res
-   *                int
+   *          int
    */
   public void hideColumns(int col)
   {
@@ -867,10 +867,11 @@ public class ColumnSelection
    * return all visible segments between the given start and end boundaries
    * 
    * @param start
-   *                (first column inclusive from 0)
+   *          (first column inclusive from 0)
    * @param end
-   *                (last column - not inclusive)
-   * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end<end
+   *          (last column - not inclusive)
+   * @return int[] {i_start, i_end, ..} where intervals lie in
+   *         start<=i_start<=i_end<end
    */
   public int[] getVisibleContigs(int start, int end)
   {
@@ -940,11 +941,11 @@ public class ColumnSelection
    * sequence associated annotation).
    * 
    * @param start
-   *                remove any annotation to the right of this column
+   *          remove any annotation to the right of this column
    * @param end
-   *                remove any annotation to the left of this column
+   *          remove any annotation to the left of this column
    * @param alignmentAnnotation
-   *                the annotation to operate on
+   *          the annotation to operate on
    */
   public void makeVisibleAnnotation(int start, int end,
           AlignmentAnnotation alignmentAnnotation)
@@ -998,7 +999,7 @@ public class ColumnSelection
       if (end > blockStart)
       {
         annels.addElement(els = new Annotation[end - blockStart + 1]);
-        if ((els.length+blockStart)<= alignmentAnnotation.annotations.length)
+        if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
         {
           // copy just the visible segment of the annotation row
           System.arraycopy(alignmentAnnotation.annotations, blockStart,
@@ -1008,7 +1009,8 @@ public class ColumnSelection
         {
           // copy to the end of the annotation row
           System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                  els, 0, (alignmentAnnotation.annotations.length - blockStart));
+                  els, 0,
+                  (alignmentAnnotation.annotations.length - blockStart));
         }
         w += els.length;
       }
@@ -1056,4 +1058,50 @@ public class ColumnSelection
       }
     }
   }
+
+  /**
+   * add in any unselected columns from the given column selection, excluding any that are hidden.
+   * @param colsel
+   */
+  public void addElementsFrom(ColumnSelection colsel)
+  {
+    if (colsel != null && colsel.size() > 0)
+    {
+      Enumeration e = colsel.getSelected().elements();
+      while (e.hasMoreElements())
+      {
+        Object eo = e.nextElement();
+        if (hiddenColumns!=null && isVisible(((Integer) eo).intValue())) {
+          if (!selected.contains(eo))
+          {
+            selected.addElement(eo);
+          }
+        }
+      }
+    }
+  }
+/**
+ * set the selected columns the given column selection, excluding any columns that are hidden. 
+ * @param colsel
+ */
+  public void setElementsFrom(ColumnSelection colsel)
+  {
+    selected = new Vector();
+    if (colsel.selected != null && colsel.selected.size() > 0)
+    {
+      if (hiddenColumns!=null && hiddenColumns.size()>0)
+      {
+        // only select visible columns in this columns selection
+        selected = new Vector();
+        addElementsFrom(colsel);
+      } else {
+        // add everything regardless
+        Enumeration en = colsel.selected.elements();
+        while (en.hasMoreElements())
+        {
+          selected.addElement(en.nextElement());
+        }
+      }
+    }
+  }
 }