/*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
public interface SequenceCollectionI
{
+ /**
+ *
+ * @return (visible) sequences in this collection. This may be a direct
+ * reference to the collection so not thread safe
+ */
List<SequenceI> 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<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps);
int getWidth();
- /**
- * @return the first column included in this collection. Runs from 0<=i<N_cols
- */
+ /**
+ *
+ * @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<N_cols
+ */
int getStartRes();
-
/**
*
*/
int getEndRes();
+ /**
+ * Answers true if sequence data is nucleotide (according to some heuristic)
+ *
+ * @return
+ */
+ boolean isNucleotide();
}