X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=7777dce8a7ba5939c05d0624f92af5750088c27b;hb=7aef14d879f7bfb8af464a6b7700a99413eab0c6;hp=73cf03fa0c969e3647c4849028d7b4038f62616c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 73cf03f..7777dce 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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;
@@ -27,14 +29,28 @@ public interface SequenceCollectionI
List getSequences(
Map hiddenReps);
-
int getWidth();
+ /**
+ *
+ * @return true if getSeqrep doesn't return null
+ */
+ boolean hasSeqrep();
+ /**
+ * get the reference or representative sequence within this collection
+ * @return null or the current reference sequence
+ */
+ SequenceI getSeqrep();
+ /**
+ * set the reference or representative sequence for this collection.
+ * Reference is assumed to be present within the collection.
+ * @return
+ */
+ void setSeqrep(SequenceI refseq);
- /**
- * @return the first column included in this collection. Runs from 0<=i