JAL-2416 replaced dependency on ResidueProperties with loaded score

matrix

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 86dd3bc..ceca6d6 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -27,7 +27,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.Format;
 import jalview.util.MapList;
@@ -111,25 +110,22 @@ public class AlignSeq
 
   int gapExtend = 20;
 
-  float[][] lookup = ScoreModels.getInstance().getBlosum62().getMatrix();
+  float[][] lookup;
 
-  int defInt = 23;
+  int gapIndex = 23;
 
   StringBuffer output = new StringBuffer();
 
-  String type;
+  String type; // AlignSeq.PEP or AlignSeq.DNA
 
-  private int[] charToInt;
+  private ScoreMatrix scoreModel;
 
   /**
    * Creates a new AlignSeq object.
    * 
-   * @param s1
-   *          DOCUMENT ME!
-   * @param s2
-   *          DOCUMENT ME!
-   * @param type
-   *          DOCUMENT ME!
+   * @param s1 first sequence for alignment
+   * @param s2 second sequence for alignment
+   * @param type molecule type, either AlignSeq.PEP or AlignSeq.DNA
    */
   public AlignSeq(SequenceI s1, SequenceI s2, String type)
   {
@@ -324,82 +320,37 @@ public class AlignSeq
       return;
     }
 
-    // System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());
     seq1 = new int[s1str.length()];
 
-    // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());
     seq2 = new int[s2str.length()];
 
-    // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
     score = new float[s1str.length()][s2str.length()];
 
-    // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
     E = new float[s1str.length()][s2str.length()];
 
-    // System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
     F = new float[s1str.length()][s2str.length()];
     traceback = new int[s1str.length()][s2str.length()];
 
-    // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
-    seq1 = stringToInt(s1str, type);
-
-    // System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
-    seq2 = stringToInt(s2str, type);
-
-    // System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-    // long tstart = System.currentTimeMillis();
-    // calcScoreMatrix();
-    // long tend = System.currentTimeMillis();
-    // System.out.println("Time take to calculate score matrix = " +
-    // (tend-tstart) + " ms");
-    // printScoreMatrix(score);
-    // System.out.println();
-    // printScoreMatrix(traceback);
-    // System.out.println();
-    // printScoreMatrix(E);
-    // System.out.println();
-    // /printScoreMatrix(F);
-    // System.out.println();
-    // tstart = System.currentTimeMillis();
-    // traceAlignment();
-    // tend = System.currentTimeMillis();
-    // System.out.println("Time take to traceback alignment = " + (tend-tstart)
-    // + " ms");
-  }
-
-  private void setDefaultParams(String type)
-  {
-    setType(type);
+    seq1 = indexEncode(s1str);
 
-    if (type.equals(AlignSeq.PEP))
-    {
-      lookup = ScoreModels.getInstance().getDefaultModel(true).getMatrix();
-    }
-    else if (type.equals(AlignSeq.DNA))
-    {
-      lookup = ScoreModels.getInstance().getDefaultModel(false).getMatrix();
-    }
+    seq2 = indexEncode(s2str);
   }
 
-  private void setType(String type2)
+  private void setDefaultParams(String moleculeType)
   {
-    this.type = type2;
-    if (type.equals(AlignSeq.PEP))
-    {
-      charToInt = ResidueProperties.aaIndex;
-      defInt = ResidueProperties.maxProteinIndex;
-    }
-    else if (type.equals(AlignSeq.DNA))
-    {
-      charToInt = ResidueProperties.nucleotideIndex;
-      defInt = ResidueProperties.maxNucleotideIndex;
-    }
-    else
+    if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType))
     {
       output.append("Wrong type = dna or pep only");
       throw new Error(MessageManager.formatMessage(
-              "error.unknown_type_dna_or_pep", new String[] { type2 }));
+              "error.unknown_type_dna_or_pep",
+              new String[] { moleculeType }));
     }
+
+    type = moleculeType;
+    scoreModel = ScoreModels.getInstance().getDefaultModel(
+            PEP.equals(type));
+    lookup = scoreModel.getMatrix();
+    gapIndex = scoreModel.getMatrixIndex(' ');
   }
 
   /**
@@ -408,7 +359,7 @@ public class AlignSeq
   public void traceAlignment()
   {
     // Find the maximum score along the rhs or bottom row
-    float max = -9999;
+    float max = -Float.MAX_VALUE;
 
     for (int i = 0; i < seq1.length; i++)
     {
@@ -442,21 +393,17 @@ public class AlignSeq
     aseq1 = new int[seq1.length + seq2.length];
     aseq2 = new int[seq1.length + seq2.length];
 
+    StringBuilder sb1 = new StringBuilder(aseq1.length);
+    StringBuilder sb2 = new StringBuilder(aseq2.length);
+
     count = (seq1.length + seq2.length) - 1;
 
-    while ((i > 0) && (j > 0))
+    while (i > 0 && j > 0)
     {
-      if ((aseq1[count] != defInt) && (i >= 0))
-      {
-        aseq1[count] = seq1[i];
-        astr1 = s1str.charAt(i) + astr1;
-      }
-
-      if ((aseq2[count] != defInt) && (j > 0))
-      {
-        aseq2[count] = seq2[j];
-        astr2 = s2str.charAt(j) + astr2;
-      }
+      aseq1[count] = seq1[i];
+      sb1.append(s1str.charAt(i));
+      aseq2[count] = seq2[j];
+      sb2.append(s2str.charAt(j));
 
       trace = findTrace(i, j);
 
@@ -468,14 +415,14 @@ public class AlignSeq
       else if (trace == 1)
       {
         j--;
-        aseq1[count] = defInt;
-        astr1 = "-" + astr1.substring(1);
+        aseq1[count] = gapIndex;
+        sb1.replace(sb1.length() - 1, sb1.length(), "-");
       }
       else if (trace == -1)
       {
         i--;
-        aseq2[count] = defInt;
-        astr2 = "-" + astr2.substring(1);
+        aseq2[count] = gapIndex;
+        sb2.replace(sb2.length() - 1, sb2.length(), "-");
       }
 
       count--;
@@ -484,17 +431,24 @@ public class AlignSeq
     seq1start = i + 1;
     seq2start = j + 1;
 
-    if (aseq1[count] != defInt)
+    if (aseq1[count] != gapIndex)
     {
       aseq1[count] = seq1[i];
-      astr1 = s1str.charAt(i) + astr1;
+      sb1.append(s1str.charAt(i));
     }
 
-    if (aseq2[count] != defInt)
+    if (aseq2[count] != gapIndex)
     {
       aseq2[count] = seq2[j];
-      astr2 = s2str.charAt(j) + astr2;
+      sb2.append(s2str.charAt(j));
     }
+
+    /*
+     * we built the character strings backwards, so now
+     * reverse them to convert to sequence strings
+     */
+    astr1 = sb1.reverse().toString();
+    astr2 = sb2.reverse().toString();
   }
 
   /**
@@ -804,45 +758,24 @@ public class AlignSeq
   }
 
   /**
-   * DOCUMENT ME!
+   * Converts the character string to an array of integers which are the
+   * corresponding indices to the characters in the score matrix
    * 
    * @param s
-   *          DOCUMENT ME!
-   * @param type
-   *          DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
-  int[] stringToInt(String s, String type)
+  int[] indexEncode(String s)
   {
-    int[] seq1 = new int[s.length()];
+    int[] encoded = new int[s.length()];
 
     for (int i = 0; i < s.length(); i++)
     {
-      // String ss = s.substring(i, i + 1).toUpperCase();
       char c = s.charAt(i);
-      if ('a' <= c && c <= 'z')
-      {
-        // TO UPPERCASE !!!
-        c -= ('a' - 'A');
-      }
-
-      try
-      {
-        seq1[i] = charToInt[c]; // set accordingly from setType
-        if (seq1[i] < 0 || seq1[i] > defInt) // set from setType: 23 for
-                                             // peptides, or 4 for NA.
-        {
-          seq1[i] = defInt;
-        }
-
-      } catch (Exception e)
-      {
-        seq1[i] = defInt;
-      }
+      encoded[i] = scoreModel.getMatrixIndex(c);
     }
 
-    return seq1;
+    return encoded;
   }
 
   /**

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index 4cb5329..c12f544 100644 (file)
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -20,9 +20,11 @@
  */
 package jalview.analysis;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.datamodel.Sequence;
 import jalview.gui.JvOptionPane;
 
 import org.testng.annotations.BeforeClass;
@@ -45,10 +47,32 @@ public class AlignSeqTest
     assertNull(AlignSeq.extractGaps(null, "ACG"));
     assertNull(AlignSeq.extractGaps("-. ", null));
 
-    assertEquals(" AC-G.T", AlignSeq.extractGaps("", " AC-G.T"));
-    assertEquals("AC-G.T", AlignSeq.extractGaps(" ", " AC-G.T"));
-    assertEquals("ACG.T", AlignSeq.extractGaps(" -", " AC-G.T"));
-    assertEquals("ACGT", AlignSeq.extractGaps(" -.", " AC-G.T ."));
-    assertEquals(" ACG.T", AlignSeq.extractGaps("-", " AC-G.T"));
+    assertEquals(AlignSeq.extractGaps("", " AC-G.T"), " AC-G.T");
+    assertEquals(AlignSeq.extractGaps(" ", " AC-G.T"), "AC-G.T");
+    assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
+    assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
+    assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIndexEncode_nucleotide()
+  {
+    AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
+            "s2", "ACGT"), AlignSeq.DNA);
+    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
+        7, 7, 8, 8, 9, 9, 10, -1, 11, -1 };
+    String s = "aAcCgGtTuUiIxXrRyYnN .-?";
+    assertArrayEquals(expected, as.indexEncode(s));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIndexEncode_peptide()
+  {
+    AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
+            "s2", "RQW"), AlignSeq.PEP);
+    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, 23, 24,
+        -1, -1, -1 };
+    String s = "aArRnNzZxX *.-?";
+    assertArrayEquals(expected, as.indexEncode(s));
   }
 }