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Merge remote-tracking branch 'origin/develop' into bug/JAL-2491
[jalview.git]
/
src
/
jalview
/
datamodel
/
CigarArray.java
diff --git
a/src/jalview/datamodel/CigarArray.java
b/src/jalview/datamodel/CigarArray.java
index
f6e5862
..
aab82a1
100644
(file)
--- a/
src/jalview/datamodel/CigarArray.java
+++ b/
src/jalview/datamodel/CigarArray.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import htsjdk.samtools.Cigar;
+
import java.util.List;
public class CigarArray extends CigarBase
import java.util.List;
public class CigarArray extends CigarBase
@@
-85,12
+87,12
@@
public class CigarArray extends CigarBase
* @param columnSelection
* @param selectionGroup
*/
* @param columnSelection
* @param selectionGroup
*/
- public CigarArray(AlignmentI alignment, ColumnSelection columnSelection,
+ public CigarArray(AlignmentI alignment, HiddenColumns hidden,
SequenceGroup selectionGroup)
{
this(constructSeqCigarArray(alignment, selectionGroup));
constructFromAlignment(alignment,
SequenceGroup selectionGroup)
{
this(constructSeqCigarArray(alignment, selectionGroup));
constructFromAlignment(alignment,
- columnSelection != null ? columnSelection.getHiddenColumns()
+ hidden != null ? hidden.getHiddenRegions()
: null, selectionGroup);
}
: null, selectionGroup);
}