X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCollectionI.java;h=aca79c83f37394812b583491465308e931ac0132;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=db79b4da4d5bf6f33592dd4887232a3f51069944;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index db79b4d..aca79c8 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.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;
import java.util.List;
@@ -6,7 +26,42 @@ import java.util.Map;
public interface SequenceCollectionI
{
List getSequences();
- List getSequences(Map hiddenReps);
+
+ 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