git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into features/JAL-2393customMatrices
[jalview.git]
/
src
/
jalview
/
analysis
/
PCA.java
diff --git
a/src/jalview/analysis/PCA.java
b/src/jalview/analysis/PCA.java
index
9babaee
..
b6766c6
100755
(executable)
--- a/
src/jalview/analysis/PCA.java
+++ b/
src/jalview/analysis/PCA.java
@@
-20,9
+20,10
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import jalview.analysis.scoremodels.PairwiseDistanceModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.math.MatrixI;
import jalview.math.MatrixI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
import java.io.PrintStream;
import java.io.PrintStream;
@@
-80,14
+81,15
@@
public class PCA implements Runnable
String sm = s_m;
if (sm != null)
{
String sm = s_m;
if (sm != null)
{
- scoreMatrix = ResidueProperties.getScoreMatrix(sm);
+ scoreMatrix = (ScoreMatrix) ((PairwiseDistanceModel) ScoreModels
+ .getInstance()
+ .forName(sm)).getScoreModel();
}
if (scoreMatrix == null)
{
// either we were given a non-existent score matrix or a scoremodel that
// isn't based on a pairwise symbol score matrix
}
if (scoreMatrix == null)
{
// either we were given a non-existent score matrix or a scoremodel that
// isn't based on a pairwise symbol score matrix
- scoreMatrix = ResidueProperties
- .getScoreMatrix(sm = (nucleotides ? "DNA" : "BLOSUM62"));
+ scoreMatrix = ScoreModels.getInstance().getDefaultModel(!nucleotides);
}
details.append("PCA calculation using " + sm
+ " sequence similarity matrix\n========\n\n");
}
details.append("PCA calculation using " + sm
+ " sequence similarity matrix\n========\n\n");