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JAL-3081 new method to get alignment sequence order lookup
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
93a2456
..
34457fc
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-624,4
+624,12
@@
public interface AlignmentI extends AnnotatedCollectionI
public HiddenColumns propagateInsertions(SequenceI profileseq,
AlignmentView input);
public HiddenColumns propagateInsertions(SequenceI profileseq,
AlignmentView input);
+ /**
+ * Returns a map whose key is a sequence in the alignment, and value the
+ * position (0, 1, 2...) of the sequence
+ *
+ * @return
+ */
+ Map<SequenceI, Integer> getSequencePositions();
+
}
}