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

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

diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index ff365a9..0c159b3 100644 (file)
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,14 +1,46 @@
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 public interface AnnotatedCollectionI extends SequenceCollectionI
 {
 
   /**
-   * TODO: decide if null is a valid response if there is no annotation on the object
+   * TODO: decide if null is a valid response if there is no annotation on the
+   * object
+   * 
    * @return null
    */
   AlignmentAnnotation[] getAlignmentAnnotation();
 
   Iterable<AlignmentAnnotation> findAnnotation(String calcId);
 
+  Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+          String calcId, String label);
+
+  /**
+   * context for this annotated collection
+   * 
+   * @return null or the collection upon which this collection is defined (e.g.
+   *         alignment, parent group).
+   */
+  AnnotatedCollectionI getContext();
 }