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JAL-2416 JAL-2403 remove unused '*' row/column from score matrices
[jalview.git]
/
src
/
jalview
/
analysis
/
PCA.java
diff --git
a/src/jalview/analysis/PCA.java
b/src/jalview/analysis/PCA.java
index
b481e89
..
5d2e7e7
100755
(executable)
--- a/
src/jalview/analysis/PCA.java
+++ b/
src/jalview/analysis/PCA.java
@@
-20,6
+20,7
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import jalview.analysis.scoremodels.PIDModel;
import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
@@
-235,6
+236,14
@@
public class PCA implements Runnable
{
result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
similarityParams);
{
result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
similarityParams);
+ if (scoreModel instanceof PIDModel)
+ {
+ /*
+ * scale % identities to width of alignment for backwards
+ * compatibility with Jalview 2.10.1 SeqSpace PCA calculation
+ */
+ result.multiply(av.getWidth() / 100d);
+ }
}
else if (scoreModel instanceof DistanceScoreModelI)
{
}
else if (scoreModel instanceof DistanceScoreModelI)
{