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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
7c3eb41
..
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);
@@
-515,6
+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
@@
-596,5
+604,11
@@
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();
}
}