X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=0121e5c8d7ec209c113c61aa0ce1ed6d1f7f0b9e;hb=933794f42ed55d57850424e3459a54cd2d92c933;hp=aa90b93f9009485a12fa9d3ac4cc294442458e15;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index aa90b93..0121e5c 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,24 +1,37 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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;
-  }
-
   private volatile PCA pca;
 
   int top;
@@ -27,25 +40,42 @@ public class PCAModel
 
   SequenceI[] seqs;
 
-  /**
-   * use the identity matrix for calculating similarity between sequences.
+  /*
+   * Score model used to calculate PCA
    */
+  ScoreModelI scoreModel;
+
   private boolean nucleotide = false;
 
   private Vector<SequencePoint> points;
 
   private boolean jvCalcMode = true;
 
-  public boolean isJvCalcMode()
+  private SimilarityParamsI similarityParams;
+
+  /**
+   * Constructor given sequence data, score model and score calculation
+   * parameter options.
+   * 
+   * @param seqData
+   * @param sqs
+   * @param nuc
+   * @param sm
+   * @param params
+   */
+  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
+          SimilarityParamsI params)
   {
-    return jvCalcMode;
+    seqstrings = seqData;
+    seqs = sqs;
+    nucleotide = nuc;
+    scoreModel = sm;
+    similarityParams = params;
   }
 
   public void run()
   {
-
-    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
-    pca.setJvCalcMode(jvCalcMode);
+    pca = new PCA(seqstrings, scoreModel, similarityParams);
     pca.run();
 
     // Now find the component coordinates
@@ -56,32 +86,23 @@ 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()
@@ -119,9 +140,9 @@ 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];
     }
   }
 
@@ -206,4 +227,14 @@ public class PCAModel
     jvCalcMode = state;
   }
 
+  public String getScoreModelName()
+  {
+    return scoreModel == null ? "" : scoreModel.getName();
+  }
+
+  public void setScoreModel(ScoreModelI sm)
+  {
+    this.scoreModel = sm;
+  }
+
 }