X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=aa15d1f5fc231fc9b1b9b29ce2e059c3cdaf89fb;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=73cf03fa0c969e3647c4849028d7b4038f62616c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 73cf03f..aa15d1f 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;
@@ -23,18 +25,51 @@ import java.util.Map;
public interface SequenceCollectionI
{
+ /**
+ *
+ * @return (visible) sequences in this collection. This may be a direct
+ * reference to the collection so not thread safe
+ */
List getSequences();
+ /**
+ * FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
+ * contract!
+ *
+ * @param hiddenReps
+ * @return the full set of sequences in this collection, including any
+ * sequences represented by sequences in the collection.
+ */
List getSequences(
Map hiddenReps);
int getWidth();
- /**
- * @return the first column included in this collection. Runs from 0<=i getHmmSequences();
}