JAL-2738 copy to spikes/mungo

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index f863ade..5e7fca2 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,26 +20,18 @@
  */
 package jalview.viewmodel;
 
-import java.util.Vector;
-
 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.SequenceI;
 import jalview.datamodel.SequencePoint;
-import jalview.api.RotatableCanvasI;
+
+import java.util.Vector;
 
 public class PCAModel
 {
-
-  public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
-          boolean nucleotide2)
-  {
-    seqstrings = seqstrings2;
-    seqs = seqs2;
-    nucleotide = nucleotide2;
-    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
-  }
-
   private volatile PCA pca;
 
   int top;
@@ -48,31 +40,40 @@ public class PCAModel
 
   SequenceI[] seqs;
 
-  /**
-   * Score matrix used to calculate PC
+  /*
+   * Name of score model used to calculate PCA
    */
-  String score_matrix;
+  ScoreModelI scoreModel;
 
-  /**
-   * use the identity matrix for calculating similarity between sequences.
-   */
   private boolean nucleotide = false;
 
   private Vector<SequencePoint> points;
 
-  private boolean jvCalcMode = true;
+  private SimilarityParamsI similarityParams;
 
-  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()
   {
-
-    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
-            score_matrix);
-    pca.setJvCalcMode(jvCalcMode);
+    pca = new PCA(seqstrings, scoreModel, similarityParams);
     pca.run();
 
     // Now find the component coordinates
@@ -83,32 +84,23 @@ public class PCAModel
       ii++;
     }
 
-    double[][] comps = new double[ii][ii];
-
-    for (int i = 0; i < ii; i++)
-    {
-      if (pca.getEigenvalue(i) > 1e-4)
-      {
-        comps[i] = pca.component(i);
-      }
-    }
-
-    top = pca.getM().rows - 1;
+    int height = pca.getHeight();
+    // top = pca.getM().height() - 1;
+    top = height - 1;
 
     points = new Vector<SequencePoint>();
     float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
-    for (int i = 0; i < pca.getM().rows; i++)
+    for (int i = 0; i < height; i++)
     {
       SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
       points.addElement(sp);
     }
-
   }
 
   public void updateRc(RotatableCanvasI rc)
   {
-    rc.setPoints(points, pca.getM().rows);
+    rc.setPoints(points, pca.getHeight());
   }
 
   public boolean isNucleotide()
@@ -146,9 +138,9 @@ public class PCAModel
     // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
     float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
 
-    for (int i = 0; i < pca.getM().rows; i++)
+    for (int i = 0; i < pca.getHeight(); i++)
     {
-      ((SequencePoint) points.elementAt(i)).coord = scores[i];
+      points.elementAt(i).coord = scores[i];
     }
   }
 
@@ -228,19 +220,14 @@ public class PCAModel
     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;
   }
 
 }