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getHiddenSequences
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
2a39847
..
7fe4627
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-219,33
+219,19
@@
public interface AlignmentI
*/
\r
public void deleteAllGroups();
\r
\r
*/
\r
public void deleteAllGroups();
\r
\r
- /**
\r
- * Adds a super group. A SuperGroup is a group of groups.
\r
- *
\r
- * @param sg Adds a new SuperGroup to alignment
\r
- */
\r
- public void addSuperGroup(SuperGroup sg);
\r
\r
/**
\r
\r
/**
\r
- * Removes SuperGroup from alignment.
\r
- *
\r
- * @param sg This SuperGroup will be deleted from alignment.
\r
+ * Adds a new AlignmentAnnotation to this alignment
\r
*/
\r
*/
\r
- public void removeSuperGroup(SuperGroup sg);
\r
+ public void addAnnotation(AlignmentAnnotation aa);
\r
\r
/**
\r
\r
/**
\r
- * Finds any SuperGroup that a given SequenceGroup may be part of.
\r
- *
\r
- * @param sg SequenceGroup to search for.
\r
- *
\r
- * @return SuperGroup that contains the given SequenceGroup.
\r
+ * Adds a new AlignmentAnnotation to this alignment,
\r
+ * associated to Sequence starting at sequence index
\r
*/
\r
*/
\r
- public SuperGroup getSuperGroup(SequenceGroup sg);
\r
+ public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);
\r
\r
\r
- /**
\r
- * Adds a new AlignmentAnnotation to this alignment
\r
- */
\r
- public void addAnnotation(AlignmentAnnotation aa);
\r
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index);
\r
\r
/**
\r
* Deletes a specific AlignmentAnnotation from the alignment.
\r
\r
/**
\r
* Deletes a specific AlignmentAnnotation from the alignment.
\r
@@
-300,6
+286,14
@@
public interface AlignmentI
public Alignment getDataset();
\r
\r
public void setDataset(Alignment dataset);
\r
public Alignment getDataset();
\r
\r
public void setDataset(Alignment dataset);
\r
+ /**
\r
+ * pads sequences with gaps (to ensure the set looks like an alignment)
\r
+ * @return boolean true if alignment was modified
\r
+ */
\r
+ public boolean padGaps();
\r
+
\r
+ public void adjustSequenceAnnotations();
\r
\r
\r
+ public HiddenSequences getHiddenSequences();
\r
\r
}
\r
\r
}
\r