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JAL-2588 overview tab docs, whats new and release notes
[jalview.git]
/
src
/
jalview
/
datamodel
/
CigarArray.java
diff --git
a/src/jalview/datamodel/CigarArray.java
b/src/jalview/datamodel/CigarArray.java
index
a48a178
..
b6224c2
100644
(file)
--- a/
src/jalview/datamodel/CigarArray.java
+++ b/
src/jalview/datamodel/CigarArray.java
@@
-20,8
+20,6
@@
*/
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
@@
-70,7
+68,8
@@
public class CigarArray extends CigarBase
for (int c = 0; c < cigars.length; c++)
{
refCigars[c] = cigars[c];
for (int c = 0; c < cigars.length; c++)
{
refCigars[c] = cigars[c];
- if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))
+ if (!((cigars[c] instanceof SeqCigar)
+ || cigars[c] instanceof CigarCigar))
{
seqcigararray = false;
}
{
seqcigararray = false;
}
@@
-92,8
+91,8
@@
public class CigarArray extends CigarBase
{
this(constructSeqCigarArray(alignment, selectionGroup));
constructFromAlignment(alignment,
{
this(constructSeqCigarArray(alignment, selectionGroup));
constructFromAlignment(alignment,
- hidden != null ? hidden.getListOfCols()
- : null, selectionGroup);
+ hidden != null ? hidden.getHiddenColumnsCopy() : null,
+ selectionGroup);
}
private static int[] _calcStartEndBounds(AlignmentI alignment,
}
private static int[] _calcStartEndBounds(AlignmentI alignment,
@@
-220,7
+219,7
@@
public class CigarArray extends CigarBase
}
/**
}
/**
- * @see Cigar.getSequenceAndDeletions
+ * @see CigarBase.getSequenceAndDeletions
* @param GapChar
* char
* @return Object[][]
* @param GapChar
* char
* @return Object[][]