JAL-2379 computePairwiseScores() moved to ScoreMatrix

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 1a4060c..d978451 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -20,7 +20,6 @@
  */
 package jalview.analysis;
 
-import jalview.math.Matrix;
 import jalview.math.MatrixI;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.ScoreMatrix;
@@ -263,9 +262,7 @@ public class PCA implements Runnable
               + (jvCalcMode ? "Jalview variant" : "Original SeqSpace")
               + "\n");
 
-      // MatrixI mt = m.transpose();
-      // eigenvector = mt.preMultiply(jvCalcMode ? m2 : m);
-      eigenvector = computePairwiseScores();
+      eigenvector = scoreMatrix.computePairwiseScores(seqs);
 
       details.append(" --- OrigT * Orig ---- \n");
       eigenvector.print(ps, "%8.2f");
@@ -307,48 +304,6 @@ public class PCA implements Runnable
     // + (System.currentTimeMillis() - now) + "ms"));
   }
 
-  /**
-   * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
-   * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
-   * computed using the current score matrix. For example
-   * <ul>
-   * <li>Sequences:</li>
-   * <li>FKL</li>
-   * <li>RSD</li>
-   * <li>QIA</li>
-   * <li>GWC</li>
-   * <li>Score matrix is BLOSUM62</li>
-   * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
-   * <li>product [2, 1] = R.R + S.S + D.D = 5 + 4 + 6 = 15</li>
-   * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
-   * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
-   * <li>product[0, 1] = F.R + K.S + L.D = -3 + 0 + -3 = -7
-   * <li>and so on</li>
-   * </ul>
-   */
-  MatrixI computePairwiseScores()
-  {
-    double[][] values = new double[seqs.length][];
-    for (int row = 0; row < seqs.length; row++)
-    {
-      values[row] = new double[seqs.length];
-      for (int col = 0; col < seqs.length; col++)
-      {
-        int total = 0;
-        int width = Math.min(seqs[row].length(), seqs[col].length());
-        for (int i = 0; i < width; i++)
-        {
-          char c1 = seqs[row].charAt(i);
-          char c2 = seqs[col].charAt(i);
-          int score = scoreMatrix.getPairwiseScore(c1, c2);
-          total += score;
-        }
-        values[row][col] = total;
-      }
-    }
-    return new Matrix(values);
-  }
-
   public void setJvCalcMode(boolean calcMode)
   {
     this.jvCalcMode = calcMode;

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index c47654a..b5e3ef1 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -21,6 +21,8 @@
 package jalview.schemes;
 
 import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
 
 public class ScoreMatrix extends PairwiseSeqScoreModel
 {
@@ -77,10 +79,11 @@ public class ScoreMatrix extends PairwiseSeqScoreModel
   }
 
   /**
+   * Answers the score for substituting first char in A1 with first char in A2
    * 
    * @param A1
    * @param A2
-   * @return score for substituting first char in A1 with first char in A2
+   * @return
    */
   public int getPairwiseScore(String A1, String A2)
   {
@@ -100,32 +103,36 @@ public class ScoreMatrix extends PairwiseSeqScoreModel
               : ResidueProperties.nucleotideIndex[d];
 
       /*
+       * FIXME: 2.10.1 PCA treats gap as [22] or 'X', but Tree
+       * calculation treats as [23]; which is correct?
+       */
+      /*
        * hack to convert unassigned / unknown (including gap)
        * to index of unknown (X for amino acids, N for nucleotide)
        * TODO: statically assign gap characters to this index?
        */
-      if (type == 0)
-      {
-        if (a == ResidueProperties.maxProteinIndex)
-        {
-          a = ResidueProperties.aaIndex['X'];
-        }
-        if (b == ResidueProperties.maxProteinIndex)
-        {
-          b = ResidueProperties.aaIndex['X'];
-        }
-      }
-      if (type != 0)
-      {
-        if (a == ResidueProperties.maxNucleotideIndex)
-      {
-          a = ResidueProperties.nucleotideIndex['N'];
-      }
-        if (b == ResidueProperties.maxNucleotideIndex)
-      {
-          b = ResidueProperties.nucleotideIndex['N'];
-        }
-      }
+//      if (type == 0)
+//      {
+//        if (a == ResidueProperties.maxProteinIndex)
+//        {
+//          a = ResidueProperties.aaIndex['X'];
+//        }
+//        if (b == ResidueProperties.maxProteinIndex)
+//        {
+//          b = ResidueProperties.aaIndex['X'];
+//        }
+//      }
+//      if (type != 0)
+//      {
+//        if (a == ResidueProperties.maxNucleotideIndex)
+//        {
+//          a = ResidueProperties.nucleotideIndex['N'];
+//        }
+//        if (b == ResidueProperties.maxNucleotideIndex)
+//        {
+//          b = ResidueProperties.nucleotideIndex['N'];
+//        }
+//      }
       pog = matrix[a][b];
     } catch (Exception e)
     {
@@ -197,4 +204,47 @@ public class ScoreMatrix extends PairwiseSeqScoreModel
     }
     return sb.toString();
   }
+
+  /**
+   * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
+   * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
+   * computed using the current score matrix. For example
+   * <ul>
+   * <li>Sequences:</li>
+   * <li>FKL</li>
+   * <li>R-D</li>
+   * <li>QIA</li>
+   * <li>GWC</li>
+   * <li>Score matrix is BLOSUM62</li>
+   * <li>Gaps treated same as X (unknown)</li>
+   * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
+   * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
+   * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
+   * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
+   * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
+   * <li>and so on</li>
+   * </ul>
+   */
+  public MatrixI computePairwiseScores(String[] seqs)
+  {
+    double[][] values = new double[seqs.length][];
+    for (int row = 0; row < seqs.length; row++)
+    {
+      values[row] = new double[seqs.length];
+      for (int col = 0; col < seqs.length; col++)
+      {
+        int total = 0;
+        int width = Math.min(seqs[row].length(), seqs[col].length());
+        for (int i = 0; i < width; i++)
+        {
+          char c1 = seqs[row].charAt(i);
+          char c2 = seqs[col].charAt(i);
+          int score = getPairwiseScore(c1, c2);
+          total += score;
+        }
+        values[row][col] = total;
+      }
+    }
+    return new Matrix(values);
+  }
 }

diff --git a/test/jalview/analysis/PCATest.java b/test/jalview/analysis/PCATest.java
deleted file mode 100644 (file)
index 815b71f..0000000
--- a/test/jalview/analysis/PCATest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package jalview.analysis;
-
-import static org.testng.Assert.assertEquals;
-
-import jalview.math.MatrixI;
-
-import org.testng.annotations.Test;
-
-public class PCATest
-{
-  @Test(groups = "Functional")
-  public void testComputePairwiseScores()
-  {
-    String[] seqs = new String[] { "FKL", "R-D", "QIA", "GWC" };
-    PCA pca = new PCA(seqs, false, "BLOSUM62");
-
-    MatrixI pairwise = pca.computePairwiseScores();
-
-    /*
-     * should be NxN where N = number of sequences
-     */
-    assertEquals(pairwise.height(), 4);
-    assertEquals(pairwise.width(), 4);
-
-    /*
-     * should be symmetrical (because BLOSUM62 is)
-     */
-    for (int i = 0; i < pairwise.height(); i++)
-    {
-      for (int j = 0; j < pairwise.width(); j++)
-      {
-        assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i),
-                "Not symmetric");
-      }
-    }
-    /*
-     * verify expected BLOSUM dot product scores
-     * Note: gap is treated like 'X' [22] in the matrix
-     */
-    // F.F + K.K + L.L = 6 + 5 + 4 = 15
-    assertEquals(pairwise.getValue(0, 0), 15d);
-    // R.R + X.X + D.D = 5 + -1 + 6 = 10
-    assertEquals(pairwise.getValue(1, 1), 10d);
-    // Q.Q + I.I + A.A = 5 + 4 + 4 = 13
-    assertEquals(pairwise.getValue(2, 2), 13d);
-    // G.G + W.W + C.C = 6 + 11 + 9 = 26
-    assertEquals(pairwise.getValue(3, 3), 26d);
-    // F.R + K.X + L.D = -3 + -1 + -3 = -8
-    assertEquals(pairwise.getValue(0, 1), -8d);
-    // F.Q + K.I + L.A = -3 + -3 + -1 = -7
-    assertEquals(pairwise.getValue(0, 2), -7d);
-    // F.G + K.W + L.C = -3 + -3 + -1 = -7
-    assertEquals(pairwise.getValue(0, 3), -7d);
-    // R.Q + X.I + D.A = 1 + -1 + -2 = -2
-    assertEquals(pairwise.getValue(1, 2), -2d);
-    // R.G + X.W + D.C = -2 + -2 + -3 = -7
-    assertEquals(pairwise.getValue(1, 3), -7d);
-    // Q.G + I.W + A.C = -2 + -3 + 0 = -5
-    assertEquals(pairwise.getValue(2, 3), -5d);
-  }
-}

diff --git a/test/jalview/schemes/ScoreMatrixTest.java b/test/jalview/schemes/ScoreMatrixTest.java
index 0ae7375..99af601 100644 (file)
--- a/test/jalview/schemes/ScoreMatrixTest.java
+++ b/test/jalview/schemes/ScoreMatrixTest.java
@@ -2,6 +2,8 @@ package jalview.schemes;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.math.MatrixI;
+
 import org.testng.annotations.Test;
 
 public class ScoreMatrixTest
@@ -23,13 +25,6 @@ public class ScoreMatrixTest
       assertEquals(m[row].length, rows);
       for (int col = 0; col < rows; col++)
       {
-        // if (m[row][col] != m[col][row])
-        // {
-        // System.out.println(String.format("%s [%d, %d] [%s, %s]",
-        // sm.getName(), m[row][col], m[col][row],
-        // ResidueProperties.aa[row],
-        // ResidueProperties.aa[col]));
-        // }
         assertEquals(m[row][col], m[col][row], String.format("%s [%s, %s]",
                 sm.getName(), ResidueProperties.aa[row],
                 ResidueProperties.aa[col]));
@@ -43,4 +38,132 @@ public class ScoreMatrixTest
     assertEquals(rows, (sm.isDNA() ? ResidueProperties.maxNucleotideIndex
             : ResidueProperties.maxProteinIndex) + 1);
   }
+
+  /**
+   * A test that just asserts the expected values in the Blosum62 score matrix
+   */
+  @Test(groups = "Functional")
+  public void testBlosum62_values()
+  {
+    ScoreMatrix sm = ResidueProperties.getScoreMatrix("BLOSUM62");
+
+    /*
+     * verify expected scores against ARNDCQEGHILKMFPSTWYVBZX
+     * scraped from https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
+     */
+    verifyValues(sm, 'A', new int[] { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1,
+        -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0 });
+    verifyValues(sm, 'R', new int[] { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3,
+        -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1 });
+    verifyValues(sm, 'N', new int[] { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3,
+        0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1 });
+    verifyValues(sm, 'D', new int[] { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3,
+        -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1 });
+    verifyValues(sm, 'C', new int[] { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1,
+        -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2 });
+    verifyValues(sm, 'Q', new int[] { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2,
+        1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1 });
+    verifyValues(sm, 'E', new int[] { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3,
+        1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 });
+    verifyValues(sm, 'G', new int[] { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4,
+        -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1 });
+    verifyValues(sm, 'H', new int[] { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3,
+        -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1 });
+    verifyValues(sm, 'I', new int[] { -1, -3, -3, -3, -1, -3, -3, -4, -3,
+        4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1 });
+    verifyValues(sm, 'L', new int[] { -1, -2, -3, -4, -1, -2, -3, -4, -3,
+        2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1 });
+    verifyValues(sm, 'K', new int[] { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3,
+        -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1 });
+    verifyValues(sm, 'M', new int[] { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1,
+        2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1 });
+    verifyValues(sm, 'F', new int[] { -2, -3, -3, -3, -2, -3, -3, -3, -1,
+        0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1 });
+    verifyValues(sm, 'P', new int[] { -1, -2, -2, -1, -3, -1, -1, -2, -2,
+        -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2 });
+    verifyValues(sm, 'S', new int[] { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2,
+        0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0 });
+    verifyValues(sm, 'T', new int[] { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1,
+        -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0 });
+    verifyValues(sm, 'W', new int[] { -3, -3, -4, -4, -2, -2, -3, -2, -2,
+        -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2 });
+    verifyValues(sm, 'Y', new int[] { -2, -2, -2, -3, -2, -1, -2, -3, 2,
+        -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1 });
+    verifyValues(sm, 'V', new int[] { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3,
+        1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1 });
+    verifyValues(sm, 'B', new int[] { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3,
+        -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1 });
+    verifyValues(sm, 'Z', new int[] { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3,
+        1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 });
+    verifyValues(sm, 'X', new int[] { 0, -1, -1, -1, -2, -1, -1, -1, -1,
+        -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1 });
+  }
+  /**
+   * Helper method to check pairwise scores for one residue
+   * 
+   * @param sm
+   * @param res
+   * @param expected
+   *          score values against 'res', in ResidueProperties.aaIndex order
+   */
+  private void verifyValues(ScoreMatrix sm, char res, int[] expected)
+  {
+    for (int j = 0; j < expected.length; j++)
+    {
+      char c2 = ResidueProperties.aa[j].charAt(0);
+      assertEquals(sm.getPairwiseScore(res, c2), expected[j],
+              String.format("%s->%s", res, c2));
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testComputePairwiseScores()
+  {
+    String[] seqs = new String[] { "FKL", "R-D", "QIA", "GWC" };
+    ScoreMatrix sm = ResidueProperties.getScoreMatrix("BLOSUM62");
+  
+    MatrixI pairwise = sm.computePairwiseScores(seqs);
+  
+    /*
+     * should be NxN where N = number of sequences
+     */
+    assertEquals(pairwise.height(), 4);
+    assertEquals(pairwise.width(), 4);
+  
+    /*
+     * should be symmetrical (because BLOSUM62 is)
+     */
+    for (int i = 0; i < pairwise.height(); i++)
+    {
+      for (int j = 0; j < pairwise.width(); j++)
+      {
+        assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i),
+                "Not symmetric");
+      }
+    }
+    /*
+     * verify expected BLOSUM dot product scores
+     * Note: gap is treated like 'X' [22] in the matrix
+     */
+    // F.F + K.K + L.L = 6 + 5 + 4 = 15
+    assertEquals(pairwise.getValue(0, 0), 15d);
+    // R.R + X.X + D.D = 5 + -1 + 6 = 10
+    assertEquals(pairwise.getValue(1, 1), 10d);
+    // Q.Q + I.I + A.A = 5 + 4 + 4 = 13
+    assertEquals(pairwise.getValue(2, 2), 13d);
+    // G.G + W.W + C.C = 6 + 11 + 9 = 26
+    assertEquals(pairwise.getValue(3, 3), 26d);
+    // F.R + K.X + L.D = -3 + -1 + -3 = -8
+    assertEquals(pairwise.getValue(0, 1), -8d);
+    // F.Q + K.I + L.A = -3 + -3 + -1 = -7
+    assertEquals(pairwise.getValue(0, 2), -7d);
+    // F.G + K.W + L.C = -3 + -3 + -1 = -7
+    assertEquals(pairwise.getValue(0, 3), -7d);
+    // R.Q + X.I + D.A = 1 + -1 + -2 = -2
+    assertEquals(pairwise.getValue(1, 2), -2d);
+    // R.G + X.W + D.C = -2 + -2 + -3 = -7
+    assertEquals(pairwise.getValue(1, 3), -7d);
+    // Q.G + I.W + A.C = -2 + -3 + 0 = -5
+    assertEquals(pairwise.getValue(2, 3), -5d);
+  }
 }