X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotatedCollectionI.java;h=17c29ef2d31fce584b9d19d254817ffe6a30e364;hb=HEAD;hp=0b4c1178d214a199f1b634557b3980b8f2cdb043;hpb=a4c795966bb5dd6dc504129aa5e07b8e962293c9;p=jalview.git

diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index 0b4c117..17c29ef 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -20,7 +20,8 @@
  */
 package jalview.datamodel;
 
-public interface AnnotatedCollectionI extends SequenceCollectionI
+public interface AnnotatedCollectionI
+        extends SequenceCollectionI, ContactMapHolderI
 {
 
   /**
@@ -31,9 +32,30 @@ public interface AnnotatedCollectionI extends SequenceCollectionI
    */
   AlignmentAnnotation[] getAlignmentAnnotation();
 
+  /**
+   * Returns a list of annotations matching the given calc id, or an empty list
+   * if calcId is null
+   * 
+   * @param calcId
+   * @return
+   */
   Iterable<AlignmentAnnotation> findAnnotation(String calcId);
 
   /**
+   * Returns an iterable collection of any annotations that match on given
+   * sequence ref, calcId and label (ignoring null values).
+   * 
+   * @param seq
+   *          null or reference sequence to select annotation for
+   * @param calcId
+   *          null or the calcId to select annotation for
+   * @param label
+   *          null or the label to select annotation for
+   */
+  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.