JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index 4ad4405..755fd0c 100644 (file)
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -1,62 +1,69 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.structure;
 
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
 public interface StructureListener
 {
   /**
-   * 
-   * @return list of structure files (unique IDs/filenames) that this listener handles messages for, or null if generic listener (only used by removeListener method)
+   * Returns a 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
+   * Called by StructureSelectionManager to inform viewer to highlight given
+   * atom positions
+   * 
+   * @param atoms
    */
-  public void mouseOverStructure(int atomIndex, String strInfo);
+  public void highlightAtoms(List<AtomSpec> atoms);
 
   /**
-   * called by StructureSelectionManager to inform viewer to highlight given atomspec
-   * @param atomIndex
-   * @param pdbResNum
-   * @param chain
-   * @param pdbId
+   * Called by StructureSelectionManager when the colours of a sequence
+   * associated with a structure have changed.
+   * 
+   * @param source
+   *          (untyped) usually an alignPanel
    */
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbId);
+  public void updateColours(Object source);
 
   /**
-   * called by StructureSelectionManager when the colours of a sequence associated with a structure have changed.
-   * @param source (untyped) usually an alignPanel
+   * 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 updateColours(Object source);
+  public void releaseReferences(Object svl);
 
   /**
-   * called by Jalview to get the colour for the given atomspec
-   * @param atomIndex
-   * @param pdbResNum
-   * @param chain
-   * @param pdbId
+   * Answers true if this listener is interested in the given sequence
+   * 
+   * @param seq
    * @return
    */
-  public java.awt.Color getColour(int atomIndex, int pdbResNum,
-          String chain, String pdbId);
+  public boolean isListeningFor(SequenceI seq);
 }