JAL-1620 version bump and release notes

[jalview.git] / src / jalview / structure / StructureListener.java

diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index 0f7bf30..2698d9d 100644 (file)
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -1,34 +1,84 @@
 /*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.structure;
 
 public interface StructureListener
 {
-  public String getPdbFile();
+  /**
+   * 
+   * @return list of structure files (unique IDs/filenames) that this listener
+   *         handles messages for, or null if generic listener (only used by
+   *         removeListener method)
+   */
+  public String[] getPdbFile();
 
+  /**
+   * NOT A LISTENER METHOD! called by structure viewer when the given
+   * atom/structure has been moused over. Typically, implementors call
+   * StructureSelectionManager.mouseOverStructure
+   * 
+   * @param atomIndex
+   * @param strInfo
+   */
   public void mouseOverStructure(int atomIndex, String strInfo);
 
+  /**
+   * called by StructureSelectionManager to inform viewer to highlight given
+   * atomspec
+   * 
+   * @param atomIndex
+   * @param pdbResNum
+   * @param chain
+   * @param pdbId
+   */
   public void highlightAtom(int atomIndex, int pdbResNum, String chain,
           String pdbId);
 
+  /**
+   * called by StructureSelectionManager when the colours of a sequence
+   * associated with a structure have changed.
+   * 
+   * @param source
+   *          (untyped) usually an alignPanel
+   */
   public void updateColours(Object source);
 
+  /**
+   * called by Jalview to get the colour for the given atomspec
+   * 
+   * @param atomIndex
+   * @param pdbResNum
+   * @param chain
+   * @param pdbId
+   * @return
+   */
   public java.awt.Color getColour(int atomIndex, int pdbResNum,
           String chain, String pdbId);
+
+  /**
+   * called by structureSelectionManager to instruct implementor to release any
+   * direct references it may hold to the given object (typically, these are
+   * Jalview alignment panels).
+   * 
+   * @param svl
+   */
+  public void releaseReferences(Object svl);
 }