/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
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 getEndRes();
+ /**
+ * Answers true if sequence data is nucleotide (according to some heuristic)
+ *
+ * @return
+ */
+ boolean isNucleotide();
}