X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAnnotatedCollectionI.java;h=2963fd5eabbd0665edb3f104d223036409326e50;hb=c6584ae5dccdd8166a863a29f265973aab82e784;hp=b882123bf4b83d48159fe3427c7a330284b44b1f;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index b882123..2963fd5 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,3 +1,23 @@
+/*
+ * 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
@@ -11,6 +31,34 @@ 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 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).
+ */
+ AnnotatedCollectionI getContext();
}