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 928d35e..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
 {
-  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 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
@@ -62,8 +68,7 @@ public class PCAModel
    * @param params
    */
   public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
-          ScoreModelI modelName,
-          SimilarityParamsI params)
+          ScoreModelI modelName, SimilarityParamsI params)
   {
     seqstrings = seqData;
     seqs = sqs;
@@ -89,7 +94,7 @@ public class PCAModel
     // 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++)