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JAL-3130 Lots of deprecation fixes. See utils/deprecation_auto_fixes.sh for commands...
[jalview.git]
/
src
/
jalview
/
viewmodel
/
PCAModel.java
diff --git
a/src/jalview/viewmodel/PCAModel.java
b/src/jalview/viewmodel/PCAModel.java
index
a4f57be
..
1693294
100644
(file)
--- a/
src/jalview/viewmodel/PCAModel.java
+++ b/
src/jalview/viewmodel/PCAModel.java
@@
-37,7
+37,7
@@
public class PCAModel
/*
* inputs
*/
/*
* inputs
*/
- private final AlignmentView seqstrings;
+ private AlignmentView inputData;
private final SequenceI[] seqs;
private final SequenceI[] seqs;
@@
-72,7
+72,7
@@
public class PCAModel
public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
ScoreModelI modelName, SimilarityParamsI params)
{
public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
ScoreModelI modelName, SimilarityParamsI params)
{
- seqstrings = seqData;
+ inputData = seqData;
seqs = sqs;
nucleotide = nuc;
scoreModel = modelName;
seqs = sqs;
nucleotide = nuc;
scoreModel = modelName;
@@
-85,7
+85,7
@@
public class PCAModel
*/
public void calculate()
{
*/
public void calculate()
{
- pca = new PCA(seqstrings, scoreModel, similarityParams);
+ pca = new PCA(inputData, scoreModel, similarityParams);
pca.run(); // executes in same thread, wait for completion
// Now find the component coordinates
pca.run(); // executes in same thread, wait for completion
// Now find the component coordinates
@@
-166,9
+166,14
@@
public class PCAModel
return pca.getDetails();
}
return pca.getDetails();
}
- public AlignmentView getSeqtrings()
+ public AlignmentView getInputData()
{
{
- return seqstrings;
+ return inputData;
+ }
+
+ public void setInputData(AlignmentView data)
+ {
+ inputData = data;
}
public String getPointsasCsv(boolean transformed, int xdim, int ydim,
}
public String getPointsasCsv(boolean transformed, int xdim, int ydim,