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JAL-2388 Tidies and unit tests
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
1ecff9a
..
2e61f9d
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-147,7
+147,9
@@
public interface AlignmentI extends AnnotatedCollectionI
SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
- * Deletes a sequence from the alignment
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param s
* Sequence to be deleted.
*
* @param s
* Sequence to be deleted.
@@
-155,7
+157,9
@@
public interface AlignmentI extends AnnotatedCollectionI
void deleteSequence(SequenceI s);
/**
void deleteSequence(SequenceI s);
/**
- * Deletes a sequence from the alignment.
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param i
* Index of sequence to be deleted.
*
* @param i
* Index of sequence to be deleted.
@@
-163,6
+167,14
@@
public interface AlignmentI extends AnnotatedCollectionI
void deleteSequence(int i);
/**
void deleteSequence(int i);
/**
+ * Deletes a sequence in the alignment which has been hidden.
+ *
+ * @param i
+ * Index of sequence to be deleted
+ */
+ void deleteHiddenSequence(int i);
+
+ /**
* Finds sequence in alignment using sequence name as query.
*
* @param name
* Finds sequence in alignment using sequence name as query.
*
* @param name
@@
-346,6
+358,8
@@
public interface AlignmentI extends AnnotatedCollectionI
HiddenSequences getHiddenSequences();
HiddenSequences getHiddenSequences();
+ HiddenColumns getHiddenColumns();
+
/**
* Compact representation of alignment
*
/**
* Compact representation of alignment
*
@@
-574,4
+588,7
@@
public interface AlignmentI extends AnnotatedCollectionI
* @return
*/
public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
* @return
*/
public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
+ public void setHiddenColumns(HiddenColumns cols);
+
}
}