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JAL-2110 generic rather than specific check for gap character
[jalview.git]
/
src
/
jalview
/
datamodel
/
Mapping.java
diff --git
a/src/jalview/datamodel/Mapping.java
b/src/jalview/datamodel/Mapping.java
index
a0a050f
..
1c196be
100644
(file)
--- a/
src/jalview/datamodel/Mapping.java
+++ b/
src/jalview/datamodel/Mapping.java
@@
-20,6
+20,7
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.util.Comparison;
import jalview.util.MapList;
import java.util.Iterator;
import jalview.util.MapList;
import java.util.Iterator;
@@
-258,7
+259,8
@@
public class Mapping
int truePos = sequencePos - (start - 1);
while (alignedBases < truePos && alignedColumn < alignedSeq.length)
{
int truePos = sequencePos - (start - 1);
while (alignedBases < truePos && alignedColumn < alignedSeq.length)
{
- if (alignedSeq[alignedColumn++] != gap)
+ char c = alignedSeq[alignedColumn++];
+ if (c != gap && !Comparison.isGap(c))
{
alignedBases++;
}
{
alignedBases++;
}