JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index eef46a7..e5c5d04 100644 (file)
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -1,57 +1,48 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+   * Called by StructureSelectionManager to inform viewer to highlight given
+   * atom positions
    * 
-   * @param atomIndex
-   * @param strInfo
+   * @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
-   */
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbId);
-
-  /**
-   * called by StructureSelectionManager when the colours of a sequence
+   * Called by StructureSelectionManager when the colours of a sequence
    * associated with a structure have changed.
    * 
    * @param source
@@ -60,23 +51,19 @@ public interface StructureListener
   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
+   * 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);
+
+  /**
+   * Answers true if this listener is interested in the given sequence
+   * 
+   * @param seq
+   * @return
+   */
+  public boolean isListeningFor(SequenceI seq);
 }