applied copyright 2008

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

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 73b7899..9ec4270 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,17 +1,17 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
  * as published by the Free Software Foundation; either version 2\r
  * of the License, or (at your option) any later version.\r
- *\r
+ * \r
  * This program is distributed in the hope that it will be useful,\r
  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  * GNU General Public License for more details.\r
- *\r
+ * \r
  * You should have received a copy of the GNU General Public License\r
  * along with this program; if not, write to the Free Software\r
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
@@ -964,8 +964,13 @@ public class ColumnSelection
 \r
         if (end > blockStart)\r
         {\r
-          annels.addElement(els = new Annotation[end-blockStart]);\r
-          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);\r
+          annels.addElement(els = new Annotation[end-blockStart+1]);\r
+          if (end-blockStart+1<=alignmentAnnotation.annotations.length)\r
+          {\r
+            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);\r
+          } else {\r
+            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, (end-blockStart+1));\r
+          }\r
           w+=els.length;\r
         }\r
         if (w==0)\r
@@ -979,6 +984,33 @@ public class ColumnSelection
           System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);\r
           w+=chnk.length;\r
         }\r
+    } else {\r
+      alignmentAnnotation.restrict(start, end);\r
     }\r
   }\r
+\r
+  /**\r
+   * Invert the column selection from first to end-1.\r
+   * leaves hiddenColumns untouched (and unselected)\r
+   * @param first\r
+   * @param end\r
+   */\r
+  public void invertColumnSelection(int first, int width)\r
+  {\r
+    boolean hasHidden = hiddenColumns!=null && hiddenColumns.size()>0;\r
+    for(int i=first; i<width; i++)\r
+    {\r
+      if(contains(i))\r
+    {\r
+        removeElement(i);\r
+    }\r
+      else\r
+      {\r
+        if (!hasHidden || isVisible(i))\r
+        {\r
+          addElement(i);\r
+        }\r
+      }\r
+    }    \r
+  }\r
 }\r