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JAL-2416 tidy up after switch from ' ' to '-' in score matrices
[jalview.git]
/
src
/
jalview
/
analysis
/
scoremodels
/
ScoreMatrix.java
diff --git
a/src/jalview/analysis/scoremodels/ScoreMatrix.java
b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index
b904432
..
f7da9f3
100644
(file)
--- a/
src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/
src/jalview/analysis/scoremodels/ScoreMatrix.java
@@
-394,7
+394,7
@@
public class ScoreMatrix implements SimilarityScoreModelI,
SimilarityParamsI options)
{
char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
SimilarityParamsI options)
{
char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
- : Comparison.GAP_DASH;
+ : gapCharacter;
String[] seqs = seqstrings.getSequenceStrings(gapChar);
return findSimilarities(seqs, options);
}
String[] seqs = seqstrings.getSequenceStrings(gapChar);
return findSimilarities(seqs, options);
}