X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotatedCollectionI.java;h=3f6c515bd9f79975919a618cdc7c12d2ceef81fe;hb=aa2c6fc3fbfa5a5a60ffd3bfeb6321f1d5e4a2f2;hp=ff365a99dfb3a7e4c4f52ccc38e4f14b8f9736e7;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index ff365a9..3f6c515 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,14 +1,53 @@
+/*
+ * 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 .
+ * 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();
+ /**
+ * 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);
+ 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).
+ */
+ AnnotatedCollectionI getContext();
}