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JAL-1483 cut and paste from SW score model to allow scores based on sequences to...
[jalview.git]
/
src
/
jalview
/
viewmodel
/
PCAModel.java
diff --git
a/src/jalview/viewmodel/PCAModel.java
b/src/jalview/viewmodel/PCAModel.java
index
bb1519d
..
00cc94b
100644
(file)
--- a/
src/jalview/viewmodel/PCAModel.java
+++ b/
src/jalview/viewmodel/PCAModel.java
@@
-35,6
+35,7
@@
public class PCAModel
seqstrings = seqstrings2;
seqs = seqs2;
nucleotide = nucleotide2;
seqstrings = seqstrings2;
seqs = seqs2;
nucleotide = nucleotide2;
+ score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
}
private volatile PCA pca;
}
private volatile PCA pca;
@@
-44,6
+45,11
@@
public class PCAModel
AlignmentView seqstrings;
SequenceI[] seqs;
AlignmentView seqstrings;
SequenceI[] seqs;
+
+ /**
+ * Score matrix used to calculate PC
+ */
+ String score_matrix;
/**
* use the identity matrix for calculating similarity between sequences.
/**
* use the identity matrix for calculating similarity between sequences.
@@
-62,7
+68,7
@@
public class PCAModel
public void run()
{
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
+ pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide, score_matrix);
pca.setJvCalcMode(jvCalcMode);
pca.run();
pca.setJvCalcMode(jvCalcMode);
pca.run();
@@
-224,4
+230,14
@@
public class PCAModel
jvCalcMode = state;
}
jvCalcMode = state;
}
+ public String getScore_matrix()
+ {
+ return score_matrix;
+ }
+
+ public void setScore_matrix(String score_matrix)
+ {
+ this.score_matrix = score_matrix;
+ }
+
}
}