JAL-1767 refactoring and tidying of RotatableCanvas and related

[jalview.git] / src / jalview / viewmodel / PCAModel.java

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 55e7300..3403887 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -22,7 +22,10 @@ package jalview.viewmodel;
 
 import jalview.analysis.PCA;
 import jalview.api.RotatableCanvasI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Point;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequencePoint;
 
@@ -30,50 +33,59 @@ import java.util.Vector;
 
 public class PCAModel
 {
+  /*
+   * inputs
+   */
+  private final AlignmentView seqstrings;
 
-  public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
-          boolean nucleotide2)
-  {
-    seqstrings = seqstrings2;
-    seqs = seqs2;
-    nucleotide = nucleotide2;
-    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
-  }
+  private final SequenceI[] seqs;
 
-  private volatile PCA pca;
+  private final SimilarityParamsI similarityParams;
 
-  int top;
-
-  AlignmentView seqstrings;
+  /*
+   * options - score model, nucleotide / protein
+   */
+  private ScoreModelI scoreModel;
 
-  SequenceI[] seqs;
+  private boolean nucleotide = false;
 
-  /**
-   * Score matrix used to calculate PC
+  /*
+   * outputs
    */
-  String score_matrix;
+  private PCA pca;
 
-  /**
-   * use the identity matrix for calculating similarity between sequences.
-   */
-  private boolean nucleotide = false;
+  int top;
 
   private Vector<SequencePoint> points;
 
-  private boolean jvCalcMode = true;
-
-  public boolean isJvCalcMode()
+  /**
+   * Constructor given sequence data, score model and score calculation
+   * parameter options.
+   * 
+   * @param seqData
+   * @param sqs
+   * @param nuc
+   * @param modelName
+   * @param params
+   */
+  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+          ScoreModelI modelName, SimilarityParamsI params)
   {
-    return jvCalcMode;
+    seqstrings = seqData;
+    seqs = sqs;
+    nucleotide = nuc;
+    scoreModel = modelName;
+    similarityParams = params;
   }
 
-  public void run()
+  /**
+   * Performs the PCA calculation (in the same thread) and extracts result data
+   * needed for visualisation by PCAPanel
+   */
+  public void calculate()
   {
-    String[] sequenceStrings = seqstrings.getSequenceStrings(' ');
-    pca = new PCA(sequenceStrings, nucleotide,
-            score_matrix);
-    pca.setJvCalcMode(jvCalcMode);
-    pca.run();
+    pca = new PCA(seqstrings, scoreModel, similarityParams);
+    pca.run(); // executes in same thread, wait for completion
 
     // Now find the component coordinates
     int ii = 0;
@@ -87,8 +99,8 @@ public class PCAModel
     // top = pca.getM().height() - 1;
     top = height - 1;
 
-    points = new Vector<SequencePoint>();
-    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+    points = new Vector<>();
+    Point[] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
     for (int i = 0; i < height; i++)
     {
@@ -135,7 +147,7 @@ public class PCAModel
   public void updateRcView(int dim1, int dim2, int dim3)
   {
     // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
-    float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
+    Point[] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
 
     for (int i = 0; i < pca.getHeight(); i++)
     {
@@ -191,13 +203,10 @@ public class PCAModel
       }
       else
       {
-        // output current x,y,z coords for points
-        fl = getPointPosition(s);
-        for (int d = 0; d < fl.length; d++)
-        {
-          csv.append(",");
-          csv.append(fl[d]);
-        }
+        Point p = points.elementAt(s).coord;
+        csv.append(",").append(p.x);
+        csv.append(",").append(p.y);
+        csv.append(",").append(p.z);
       }
       csv.append("\n");
     }
@@ -212,26 +221,21 @@ public class PCAModel
   public double[] getPointPosition(int s)
   {
     double pts[] = new double[3];
-    float[] p = points.elementAt(s).coord;
-    pts[0] = p[0];
-    pts[1] = p[1];
-    pts[2] = p[2];
+    Point p = points.elementAt(s).coord;
+    pts[0] = p.x;
+    pts[1] = p.y;
+    pts[2] = p.z;
     return pts;
   }
 
-  public void setJvCalcMode(boolean state)
-  {
-    jvCalcMode = state;
-  }
-
-  public String getScore_matrix()
+  public String getScoreModelName()
   {
-    return score_matrix;
+    return scoreModel == null ? "" : scoreModel.getName();
   }
 
-  public void setScore_matrix(String score_matrix)
+  public void setScoreModel(ScoreModelI sm)
   {
-    this.score_matrix = score_matrix;
+    this.scoreModel = sm;
   }
 
 }