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JAL-2629 HMMs dropped on the alignment now map to the rf annotation
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
2abb1f8
..
f4ee3a2
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-358,6
+358,8
@@
public interface AlignmentI extends AnnotatedCollectionI
HiddenSequences getHiddenSequences();
HiddenSequences getHiddenSequences();
+ HiddenColumns getHiddenColumns();
+
/**
* Compact representation of alignment
*
/**
* Compact representation of alignment
*
@@
-578,13
+580,18
@@
public interface AlignmentI extends AnnotatedCollectionI
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+ public void setHiddenColumns(HiddenColumns cols);
+
/**
/**
- * Calculate the visible start and end index of an alignment. The result is
- * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+ * Insert a sequence at a position in an alignment
*
*
- * @param hiddenCols
- * @return
+ * @param i
+ * The idnex of the position.
+ * @param snew
+ * The new sequence.
*/
*/
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+ void insertSequenceAt(int i, SequenceI snew);
+
+
}
}