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JAL-2629 update spikes/mungo to latest
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
5b3d782
..
6d34d07
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-499,10
+499,6
@@
public interface SequenceI extends ASequenceI
*/
public List<DBRefEntry> getPrimaryDBRefs();
*/
public List<DBRefEntry> getPrimaryDBRefs();
- boolean isHMMConsensusSequence();
-
- void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
-
/**
* Answers true if the sequence has annotation for Hidden Markov Model
* information content, else false
/**
* Answers true if the sequence has annotation for Hidden Markov Model
* information content, else false
@@
-576,7
+572,7
@@
public interface SequenceI extends ASequenceI
* the iterator to use
* @return a String corresponding to the sequence
*/
* the iterator to use
* @return a String corresponding to the sequence
*/
- public String getSequenceStringFromIterator(Iterator<int[]> it);
+ String getSequenceStringFromIterator(Iterator<int[]> it);
/**
* Locate the first position in this sequence which is not contained in an
/**
* Locate the first position in this sequence which is not contained in an
@@
-586,5
+582,12
@@
public interface SequenceI extends ASequenceI
* iterator over regions
* @return first residue not contained in regions
*/
* iterator over regions
* @return first residue not contained in regions
*/
- public int firstResidueOutsideIterator(Iterator<int[]> it);
+ int firstResidueOutsideIterator(Iterator<int[]> it);
+
+ /**
+ * Answers true if this sequence has an associated Hidden Markov Model
+ *
+ * @return
+ */
+ boolean hasHMMProfile();
}
}