X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotatedCollectionI.java;h=2963fd5eabbd0665edb3f104d223036409326e50;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=d7a0339b8c5215ff1cd8022cfd716ad2e24042ca;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git

diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index d7a0339..2963fd5 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,14 +1,64 @@
+/*
+ * 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;
 
-import java.util.List;
-
-public interface AnnotatedCollectionI
+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();
 
+  /**
+   * 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();
 }