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JAL-3026-JAL-3063 transpiler and runtime update
[jalview.git]
/
src
/
jalview
/
viewmodel
/
PCAModel.java
diff --git
a/src/jalview/viewmodel/PCAModel.java
b/src/jalview/viewmodel/PCAModel.java
index
0121e5c
..
5e7fca2
100644
(file)
--- a/
src/jalview/viewmodel/PCAModel.java
+++ b/
src/jalview/viewmodel/PCAModel.java
@@
-41,7
+41,7
@@
public class PCAModel
SequenceI[] seqs;
/*
SequenceI[] seqs;
/*
- * Score model used to calculate PCA
+ * Name of score model used to calculate PCA
*/
ScoreModelI scoreModel;
*/
ScoreModelI scoreModel;
@@
-49,8
+49,6
@@
public class PCAModel
private Vector<SequencePoint> points;
private Vector<SequencePoint> points;
- private boolean jvCalcMode = true;
-
private SimilarityParamsI similarityParams;
/**
private SimilarityParamsI similarityParams;
/**
@@
-60,16
+58,16
@@
public class PCAModel
* @param seqData
* @param sqs
* @param nuc
* @param seqData
* @param sqs
* @param nuc
- * @param sm
+ * @param modelName
* @param params
*/
* @param params
*/
- public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
- SimilarityParamsI params)
+ public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ ScoreModelI modelName, SimilarityParamsI params)
{
seqstrings = seqData;
seqs = sqs;
nucleotide = nuc;
{
seqstrings = seqData;
seqs = sqs;
nucleotide = nuc;
- scoreModel = sm;
+ scoreModel = modelName;
similarityParams = params;
}
similarityParams = params;
}
@@
-222,11
+220,6
@@
public class PCAModel
return pts;
}
return pts;
}
- public void setJvCalcMode(boolean state)
- {
- jvCalcMode = state;
- }
-
public String getScoreModelName()
{
return scoreModel == null ? "" : scoreModel.getName();
public String getScoreModelName()
{
return scoreModel == null ? "" : scoreModel.getName();