X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotatedCollectionI.java;h=17c29ef2d31fce584b9d19d254817ffe6a30e364;hb=a81e74154d35e10958b58c3c9411aa9ee21880a6;hp=b882123bf4b83d48159fe3427c7a330284b44b1f;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index b882123..17c29ef 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,6 +1,27 @@
+/*
+ * 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.
+ *  
+ * 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
+public interface AnnotatedCollectionI
+        extends SequenceCollectionI, ContactMapHolderI
 {
 
   /**
@@ -11,6 +32,34 @@ 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.
+   *         alignment, parent group).
+   */
+  AnnotatedCollectionI getContext();
 }