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JAL-3407 add GPL license to Jalview source files
[jalview.git]
/
src
/
jalview
/
analysis
/
scoremodels
/
PIDModel.java
diff --git
a/src/jalview/analysis/scoremodels/PIDModel.java
b/src/jalview/analysis/scoremodels/PIDModel.java
index
c1e8b42
..
ddfe5e4
100644
(file)
--- a/
src/jalview/analysis/scoremodels/PIDModel.java
+++ b/
src/jalview/analysis/scoremodels/PIDModel.java
@@
-152,15
+152,17
@@
public class PIDModel extends SimilarityScoreModel
protected MatrixI findSimilarities(String[] seqs,
SimilarityParamsI options)
{
protected MatrixI findSimilarities(String[] seqs,
SimilarityParamsI options)
{
- // TODO reuse code in ScoreMatrix instead somehow
- double[][] values = new double[seqs.length][];
+ /*
+ * calculation is symmetric so just compute lower diagonal
+ */
+ double[][] values = new double[seqs.length][seqs.length];
for (int row = 0; row < seqs.length; row++)
{
for (int row = 0; row < seqs.length; row++)
{
- values[row] = new double[seqs.length];
- for (int col = 0; col < seqs.length; col++)
+ for (int col = row; col < seqs.length; col++)
{
double total = computePID(seqs[row], seqs[col], options);
values[row][col] = total;
{
double total = computePID(seqs[row], seqs[col], options);
values[row][col] = total;
+ values[col][row] = total;
}
}
return new Matrix(values);
}
}
return new Matrix(values);