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JAL-3878 update branch from 2.12 merge from 2.11.2
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
2f365e6
..
8f1d160
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-48,6
+48,9
@@
public interface SequenceI extends ASequenceI
*/
public void setName(String name);
*/
public void setName(String name);
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
/**
* Get the display name
*/
/**
* Get the display name
*/
@@
-215,10
+218,10
@@
public interface SequenceI extends ASequenceI
* from 1), or null if no residues are included in the range
*
* @param fromColum
* from 1), or null if no residues are included in the range
*
* @param fromColum
- * - first column base 1
+ * - first column base 1. (0 and negative positions are rounded up)
* @param toColumn
* - last column, base 1
* @param toColumn
* - last column, base 1
- * @return
+ * @return null if fromColum>toColumn
*/
public ContiguousI findPositions(int fromColum, int toColumn);
*/
public ContiguousI findPositions(int fromColum, int toColumn);
@@
-357,13
+360,12
@@
public interface SequenceI extends ASequenceI
/**
* set the array of Database references for the sequence.
*
/**
* set the array of Database references for the sequence.
*
- * BH 2019.02.04 changes param to DBModlist
+ * BH 2019.02.04 changes param to DBModlist
*
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
*
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
- * @throws InvalidArgumentException
- * if the is not one created by Sequence itself
+ * @throws InvalidArgumentException if the is not one created by Sequence itself
*/
@Deprecated
public void setDBRefs(DBModList<DBRefEntry> dbs);
*/
@Deprecated
public void setDBRefs(DBModList<DBRefEntry> dbs);
@@
-448,8
+450,8
@@
public interface SequenceI extends ASequenceI
/**
* Returns a (possibly empty) list of any annotations that match on given
/**
* Returns a (possibly empty) list of any annotations that match on given
- * calcId (source), label (type) and description (observation instance). Null
- * values do not match.
+ * calcId (source), label (type) and description (observation instance).
+ * Null values do not match.
*
* @param calcId
* @param label
*
* @param calcId
* @param label
@@
-457,7
+459,6
@@
public interface SequenceI extends ASequenceI
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label, String description);
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label, String description);
-
/**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
/**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
@@
-517,6
+518,11
@@
public interface SequenceI extends ASequenceI
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
+ /**
+ * Answers true if the sequence has annotation for Hidden Markov Model
+ * information content, else false
+ */
+ boolean hasHMMAnnotation();
/**
* Returns a (possibly empty) list of sequence features that overlap the given
/**
* Returns a (possibly empty) list of sequence features that overlap the given
@@
-532,8
+538,7
@@
public interface SequenceI extends ASequenceI
* optional feature types to restrict results to
* @return
*/
* optional feature types to restrict results to
* @return
*/
- List<SequenceFeature> findFeatures(int fromCol, int toCol,
- String... types);
+ List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
/**
* Method to call to indicate that the sequence (characters or alignment/gaps)
/**
* Method to call to indicate that the sequence (characters or alignment/gaps)
@@
-541,7
+546,7
@@
public interface SequenceI extends ASequenceI
* positions to be invalidated.
*/
void sequenceChanged();
* positions to be invalidated.
*/
void sequenceChanged();
-
+
/**
*
* @return BitSet corresponding to index [0,length) where Comparison.isGap()
/**
*
* @return BitSet corresponding to index [0,length) where Comparison.isGap()
@@
-573,8
+578,9
@@
public interface SequenceI extends ASequenceI
* @param chromosomeId
* @param map
*/
* @param chromosomeId
* @param map
*/
- void setGeneLoci(String speciesId, String assemblyId, String chromosomeId,
- MapList map);
+ void setGeneLoci(String speciesId, String assemblyId,
+ String chromosomeId, MapList map);
+
/**
* Returns the sequence string constructed from the substrings of a sequence
/**
* Returns the sequence string constructed from the substrings of a sequence
@@
-597,4
+603,12
@@
public interface SequenceI extends ASequenceI
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
+
+ /**
+ * Answers true if this sequence has an associated Hidden Markov Model
+ *
+ * @return
+ */
+ boolean hasHMMProfile();
}
}
+