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Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
64a57ba
..
e0c738e
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-147,12
+147,12
@@
public interface SequenceI
public SequenceI getSubSequence(int start, int end);
/**
public SequenceI getSubSequence(int start, int end);
/**
- * DOCUMENT ME!
+ * get the i'th character in this sequence's local reference frame (ie from
+ * 0-number of characters lying from start-end)
*
* @param i
*
* @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * index
+ * @return character or ' '
*/
public char getCharAt(int i);
*/
public char getCharAt(int i);
@@
-315,10
+315,22
@@
public interface SequenceI
public SequenceI getDatasetSequence();
public SequenceI getDatasetSequence();
+ /**
+ * Returns a new array containing this sequence's annotations, or null.
+ */
public AlignmentAnnotation[] getAnnotation();
public AlignmentAnnotation[] getAnnotation();
+ /**
+ * Returns true if this sequence has the given annotation (by object
+ * identity).
+ */
public boolean hasAnnotation(AlignmentAnnotation ann);
public boolean hasAnnotation(AlignmentAnnotation ann);
+ /**
+ * Add the given annotation, if not already added, and set its sequence ref to
+ * be this sequence. Does nothing if this sequence's annotations already
+ * include this annotation (by identical object reference).
+ */
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
@@
-347,12
+359,11
@@
public interface SequenceI
public AlignmentAnnotation[] getAnnotation(String label);
/**
public AlignmentAnnotation[] getAnnotation(String label);
/**
- * Return a list of any annotations which match the given calcId (source) and
- * label (type). Null values do not match.
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source) and label (type). Null values do not match.
*
* @param calcId
* @param label
*
* @param calcId
* @param label
- * @return
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label);
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label);
@@
-403,4
+414,10
@@
public interface SequenceI
*/
public void setRNA(RNA rna);
*/
public void setRNA(RNA rna);
+ /**
+ *
+ * @return list of insertions (gap characters) in sequence
+ */
+ public List<int[]> getInsertions();
+
}
}