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JAL-2416 better encapsulated 'constants' for BLOSUM62, PAM250
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignSeq.java
diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
61ff012
..
ed4e3bc
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-118,8
+118,7
@@
public class AlignSeq
int gapExtend = 20;
int gapExtend = 20;
- float[][] lookup = ((ScoreMatrix) ScoreModels.getInstance().forName(
- ScoreModels.BLOSUM62)).getMatrix();
+ float[][] lookup = ScoreModels.getInstance().getBlosum62().getMatrix();
// ResidueProperties.getBLOSUM62();
// ResidueProperties.getBLOSUM62();
@@
-604,8
+603,7
@@
public class AlignSeq
.append(String.valueOf(s2str.length())).append(")")
.append(NEWLINE).append(NEWLINE);
.append(String.valueOf(s2str.length())).append(")")
.append(NEWLINE).append(NEWLINE);
- PairwiseSeqScoreModel pam250 = (PairwiseSeqScoreModel) ScoreModels
- .getInstance().forName(ScoreModels.PAM250);
+ PairwiseSeqScoreModel pam250 = ScoreModels.getInstance().getPam250();
for (int j = 0; j < nochunks; j++)
{
for (int j = 0; j < nochunks; j++)
{