X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotatedCollectionI.java;h=878f22abb5ea689598f3620cf492901b9b1d7c8b;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=0f856ee6efbc64b348414a0a53762e20ccb2a0a0;hpb=fb27f86492eb06fc39b0578e1c31de8b4c26491a;p=jalview.git
diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index 0f856ee..878f22a 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
@@ -29,11 +31,36 @@ 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 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 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).
+ *
+ * @return null or the collection upon which this collection is defined (e.g.
+ * alignment, parent group).
*/
AnnotatedCollectionI getContext();
+
+
}