JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

[jalview.git] / src / jalview / analysis / PCA.java

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index b6766c6..738da7d 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -20,9 +20,10 @@
  */
 package jalview.analysis;
 
-import jalview.analysis.scoremodels.PairwiseDistanceModel;
-import jalview.analysis.scoremodels.ScoreMatrix;
-import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.DistanceScoreModelI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityScoreModelI;
+import jalview.datamodel.AlignmentView;
 import jalview.math.MatrixI;
 
 import java.io.PrintStream;
@@ -42,56 +43,16 @@ public class PCA implements Runnable
 
   StringBuilder details = new StringBuilder(1024);
 
-  private String[] seqs;
+  private AlignmentView seqs;
 
-  private ScoreMatrix scoreMatrix;
+  private ScoreModelI scoreModel;
 
-  /**
-   * Creates a new PCA object. By default, uses blosum62 matrix to generate
-   * sequence similarity matrices
-   * 
-   * @param s
-   *          Set of amino acid sequences to perform PCA on
-   */
-  public PCA(String[] s)
-  {
-    this(s, false);
-  }
-
-  /**
-   * Creates a new PCA object. By default, uses blosum62 matrix to generate
-   * sequence similarity matrices
-   * 
-   * @param s
-   *          Set of sequences to perform PCA on
-   * @param nucleotides
-   *          if true, uses standard DNA/RNA matrix for sequence similarity
-   *          calculation.
-   */
-  public PCA(String[] s, boolean nucleotides)
-  {
-    this(s, nucleotides, null);
-  }
-
-  public PCA(String[] s, boolean nucleotides, String s_m)
+  public PCA(AlignmentView s, ScoreModelI sm)
   {
     this.seqs = s;
 
-    scoreMatrix = null;
-    String sm = s_m;
-    if (sm != null)
-    {
-      scoreMatrix = (ScoreMatrix) ((PairwiseDistanceModel) ScoreModels
-              .getInstance()
-              .forName(sm)).getScoreModel();
-    }
-    if (scoreMatrix == null)
-    {
-      // either we were given a non-existent score matrix or a scoremodel that
-      // isn't based on a pairwise symbol score matrix
-      scoreMatrix = ScoreModels.getInstance().getDefaultModel(!nucleotides);
-    }
-    details.append("PCA calculation using " + sm
+    scoreModel = sm;
+    details.append("PCA calculation using " + sm.getName()
             + " sequence similarity matrix\n========\n\n");
   }
 
@@ -212,7 +173,7 @@ public class PCA implements Runnable
               + (jvCalcMode ? "Jalview variant" : "Original SeqSpace")
               + "\n");
 
-      eigenvector = scoreMatrix.computePairwiseScores(seqs);
+      eigenvector = computeSimilarity(seqs);
 
       details.append(" --- OrigT * Orig ---- \n");
       eigenvector.print(ps, "%8.2f");
@@ -254,6 +215,38 @@ public class PCA implements Runnable
     // + (System.currentTimeMillis() - now) + "ms"));
   }
 
+  /**
+   * Computes a pairwise similarity matrix for the given sequence regions using
+   * the configured score model. If the score model is a similarity model, then
+   * it computes the result directly. If it is a distance model, then use it to
+   * compute pairwise distances, and convert these to similarity scores by
+   * substracting from the maximum value.
+   * 
+   * @param av
+   * @return
+   */
+  MatrixI computeSimilarity(AlignmentView av)
+  {
+    MatrixI result = null;
+    if (scoreModel instanceof SimilarityScoreModelI)
+    {
+      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av);
+    }
+    else if (scoreModel instanceof DistanceScoreModelI)
+    {
+      result = ((DistanceScoreModelI) scoreModel).findDistances(av);
+      double maxDistance = result.getMaxValue();
+      result.subtractAllFrom(maxDistance);
+    }
+    else
+    {
+      System.err
+              .println("Unexpected type of score model, cannot calculate similarity");
+    }
+
+    return result;
+  }
+
   public void setJvCalcMode(boolean calcMode)
   {
     this.jvCalcMode = calcMode;
@@ -268,6 +261,6 @@ public class PCA implements Runnable
   public int getHeight()
   {
     // TODO can any of seqs[] be null?
-    return seqs.length;
+    return seqs.getSequences().length;
   }
 }