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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceCollectionI.java
diff --git
a/src/jalview/datamodel/SequenceCollectionI.java
b/src/jalview/datamodel/SequenceCollectionI.java
index
7777dce
..
f681f11
100644
(file)
--- a/
src/jalview/datamodel/SequenceCollectionI.java
+++ b/
src/jalview/datamodel/SequenceCollectionI.java
@@
-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();
}
}