Merge branch 'develop' into features/JAL-2393customMatrices

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 55e7300..f216009 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -22,6 +22,8 @@ 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.SequenceI;
 import jalview.datamodel.SequencePoint;
@@ -30,16 +32,6 @@ 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;
@@ -48,20 +40,39 @@ public class PCAModel
 
   SequenceI[] seqs;
 
-  /**
-   * Score matrix used to calculate PC
+  /*
+   * 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;
+
+  /**
+   * 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)
+  {
+    seqstrings = seqData;
+    seqs = sqs;
+    nucleotide = nuc;
+    scoreModel = sm;
+    similarityParams = params;
+  }
+
   public boolean isJvCalcMode()
   {
     return jvCalcMode;
@@ -69,9 +80,7 @@ public class PCAModel
 
   public void run()
   {
-    String[] sequenceStrings = seqstrings.getSequenceStrings(' ');
-    pca = new PCA(sequenceStrings, nucleotide,
-            score_matrix);
+    pca = new PCA(seqstrings, scoreModel, similarityParams);
     pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
@@ -224,14 +233,14 @@ public class PCAModel
     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;
   }
 
 }