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JAL-1767 minor field tidying prior to functional changes
[jalview.git]
/
src
/
jalview
/
viewmodel
/
PCAModel.java
diff --git
a/src/jalview/viewmodel/PCAModel.java
b/src/jalview/viewmodel/PCAModel.java
index
5e7fca2
..
0dcdbca
100644
(file)
--- a/
src/jalview/viewmodel/PCAModel.java
+++ b/
src/jalview/viewmodel/PCAModel.java
@@
-32,24
+32,30
@@
import java.util.Vector;
public class PCAModel
{
public class PCAModel
{
- private volatile PCA pca;
-
- int top;
+ /*
+ * inputs
+ */
+ private final AlignmentView seqstrings;
- AlignmentView seqstrings;
+ private final SequenceI[] seqs;
- SequenceI[] seqs;
+ private final SimilarityParamsI similarityParams;
/*
/*
- * Name of score model used to calculate PCA
+ * options - score model, nucleotide / protein
*/
*/
- ScoreModelI scoreModel;
+ private ScoreModelI scoreModel;
private boolean nucleotide = false;
private boolean nucleotide = false;
- private Vector<SequencePoint> points;
+ /*
+ * outputs
+ */
+ private volatile PCA pca;
- private SimilarityParamsI similarityParams;
+ int top;
+
+ private Vector<SequencePoint> points;
/**
* Constructor given sequence data, score model and score calculation
/**
* Constructor given sequence data, score model and score calculation
@@
-88,7
+94,7
@@
public class PCAModel
// top = pca.getM().height() - 1;
top = height - 1;
// top = pca.getM().height() - 1;
top = height - 1;
- points = new Vector<SequencePoint>();
+ points = new Vector<>();
float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
for (int i = 0; i < height; i++)
float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
for (int i = 0; i < height; i++)