JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

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

diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java
index 5370e12..f8c5bea 100644 (file)
--- a/src/jalview/structure/SequenceListener.java
+++ b/src/jalview/structure/SequenceListener.java
@@ -1,30 +1,46 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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
+ * 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.
- *
- * 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 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;
 
-import jalview.datamodel.*;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceI;
 
 public interface SequenceListener
 {
+  // TODO remove this? never called on SequenceListener type
   public void mouseOverSequence(SequenceI sequence, int index, int pos);
 
-  public void highlightSequence(jalview.datamodel.SearchResults results);
+  /**
+   * Highlights any position(s) represented by the search results and
+   * (optionally) returns an informative message about the position(s)
+   * higlighted
+   * 
+   * @param results
+   * @return
+   */
+  public String highlightSequence(SearchResultsI results);
 
+  // TODO remove this? never called
   public void updateColours(SequenceI sequence, int index);
+
+  public VamsasSource getVamsasSource();
+
 }