X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=4371994e0d3593a5594b07d2bd89e86895aee9a9;hb=5f7810e6c809dbc218fed92b811999807dec148a;hp=ca54570a09085a98f06ad0b90425e43b7b4ec8f9;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index ca54570..4371994 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -36,7 +35,7 @@ public class ColumnSelection
    * Add a column to the selection
    * 
    * @param col
-   *                index of column
+   *          index of column
    */
   public void addElement(int col)
   {
@@ -59,7 +58,7 @@ 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 +74,9 @@ 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 +103,7 @@ 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 +116,7 @@ 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 +179,9 @@ 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 +237,9 @@ 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 +402,7 @@ 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 +475,7 @@ public class ColumnSelection
    * given index.
    * 
    * @param end
-   *                int
+   *          int
    * @return Vector
    */
   public Vector getHiddenColumns()
@@ -488,7 +487,7 @@ 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 +512,7 @@ public class ColumnSelection
    * hidden columns exist
    * 
    * @param hiddenColumn
-   *                int
+   *          int
    * @return int
    */
   public int findColumnPosition(int hiddenColumn)
@@ -573,7 +572,7 @@ public class ColumnSelection
    * hidden columns. In otherwords, the next hidden column.
    * 
    * @param index
-   *                int
+   *          int
    */
   public int getHiddenBoundaryRight(int alPos)
   {
@@ -601,7 +600,7 @@ public class ColumnSelection
    * hidden columns. In otherwords, the previous hidden column.
    * 
    * @param index
-   *                int
+   *          int
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
@@ -679,7 +678,7 @@ public class ColumnSelection
    * specified
    * 
    * @param res
-   *                int
+   *          int
    */
   public void hideColumns(int col)
   {
@@ -867,10 +866,11 @@ 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 +940,11 @@ 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)
@@ -998,15 +998,18 @@ public class ColumnSelection
       if (end > blockStart)
       {
         annels.addElement(els = new Annotation[end - blockStart + 1]);
-        if (end - blockStart + 1 <= alignmentAnnotation.annotations.length)
+        if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
         {
+          // copy just the visible segment of the annotation row
           System.arraycopy(alignmentAnnotation.annotations, blockStart,
                   els, 0, els.length);
         }
         else
         {
+          // copy to the end of the annotation row
           System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                  els, 0, (end - blockStart + 1));
+                  els, 0,
+                  (alignmentAnnotation.annotations.length - blockStart));
         }
         w += els.length;
       }
@@ -1054,4 +1057,58 @@ 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());
+        }
+      }
+    }
+  }
 }