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JAL-2788 possible adjustments to sequence accesses
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceCollectionI.java
diff --git
a/src/jalview/datamodel/SequenceCollectionI.java
b/src/jalview/datamodel/SequenceCollectionI.java
index
ee216a4
..
f681f11
100644
(file)
--- a/
src/jalview/datamodel/SequenceCollectionI.java
+++ b/
src/jalview/datamodel/SequenceCollectionI.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
*
* This file is part of Jalview.
*
@@
-29,20
+29,26
@@
public interface SequenceCollectionI
List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps);
List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps);
+
int getWidth();
int getWidth();
+
/**
*
* @return true if getSeqrep doesn't return null
*/
boolean hasSeqrep();
/**
*
* @return true if getSeqrep doesn't return null
*/
boolean hasSeqrep();
+
/**
* get the reference or representative sequence within this collection
/**
* get the reference or representative sequence within this collection
+ *
* @return null or the current reference sequence
*/
SequenceI getSeqrep();
* @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
*/
void setSeqrep(SequenceI refseq);
@@
-58,4
+64,10
@@
public interface SequenceCollectionI
*/
int getEndRes();
*/
int getEndRes();
+ /**
+ * Answers true if sequence data is nucleotide (according to some heuristic)
+ *
+ * @return
+ */
+ boolean isNucleotide();
}
}