X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=f681f11df6839222e8add6df30c46572b6402f7b;hb=refs%2Fheads%2Ffeatures%2FJAL-2465_No-mapping_Jmol-structures-loaded-via-url;hp=95afb3d675605506e6c62440ff2d1c7c37b395c3;hpb=d5a24269526ff4dcaa3d246a23a0904065565f92;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 95afb3d..f681f11 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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;
@@ -26,21 +29,45 @@ 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.
+ * 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