JAL-2416 removed DNA and PAM250 matrices from ResidueProperties

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index f2f7ea9..61ff012 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,13 +20,15 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
 import jalview.util.Comparison;
 import jalview.util.Format;
 import jalview.util.MapList;
@@ -59,11 +61,11 @@ public class AlignSeq
   static String[] pep = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I",
       "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
 
-  int[][] score;
+  float[][] score;
 
-  int[][] E;
+  float[][] E;
 
-  int[][] F;
+  float[][] F;
 
   int[][] traceback;
 
@@ -106,7 +108,7 @@ public class AlignSeq
   int count;
 
   /** DOCUMENT ME!! */
-  public int maxscore;
+  public float maxscore;
 
   float pid;
 
@@ -116,7 +118,10 @@ public class AlignSeq
 
   int gapExtend = 20;
 
-  int[][] lookup = ResidueProperties.getBLOSUM62();
+  float[][] lookup = ((ScoreMatrix) ScoreModels.getInstance().forName(
+          ScoreModels.BLOSUM62)).getMatrix();
+
+  // ResidueProperties.getBLOSUM62();
 
   String[] intToStr = pep;
 
@@ -165,7 +170,7 @@ public class AlignSeq
    * 
    * @return DOCUMENT ME!
    */
-  public int getMaxScore()
+  public float getMaxScore()
   {
     return maxscore;
   }
@@ -381,13 +386,13 @@ public class AlignSeq
     seq2 = new int[s2str.length()];
 
     // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-    score = new int[s1str.length()][s2str.length()];
+    score = new float[s1str.length()][s2str.length()];
 
     // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
-    E = new int[s1str.length()][s2str.length()];
+    E = new float[s1str.length()][s2str.length()];
 
     // System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
-    F = new int[s1str.length()][s2str.length()];
+    F = new float[s1str.length()][s2str.length()];
     traceback = new int[s1str.length()][s2str.length()];
 
     // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
@@ -423,11 +428,11 @@ public class AlignSeq
 
     if (type.equals(AlignSeq.PEP))
     {
-      lookup = ResidueProperties.getDefaultPeptideMatrix();
+      lookup = ScoreModels.getInstance().getDefaultModel(true).getMatrix();
     }
     else if (type.equals(AlignSeq.DNA))
     {
-      lookup = ResidueProperties.getDefaultDnaMatrix();
+      lookup = ScoreModels.getInstance().getDefaultModel(false).getMatrix();
     }
   }
 
@@ -460,7 +465,7 @@ public class AlignSeq
   public void traceAlignment()
   {
     // Find the maximum score along the rhs or bottom row
-    int max = -9999;
+    float max = -9999;
 
     for (int i = 0; i < seq1.length; i++)
     {
@@ -577,7 +582,8 @@ public class AlignSeq
       }
     }
     int len = 72 - maxid - 1;
-    int nochunks = ((aseq1.length - count) / len) + 1;
+    int nochunks = ((aseq1.length - count) / len)
+            + ((aseq1.length - count) % len > 0 ? 1 : 0);
     pid = 0;
 
     output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
@@ -598,6 +604,9 @@ public class AlignSeq
             .append(String.valueOf(s2str.length())).append(")")
             .append(NEWLINE).append(NEWLINE);
 
+    PairwiseSeqScoreModel pam250 = (PairwiseSeqScoreModel) ScoreModels
+            .getInstance().forName(ScoreModels.PAM250);
+
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
@@ -614,22 +623,27 @@ public class AlignSeq
       output.append(NEWLINE);
       output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
 
-      // Print out the matching chars
+      /*
+       * Print out the match symbols:
+       * | for exact match (ignoring case)
+       * . if PAM250 score is positive
+       * else a space
+       */
       for (int i = 0; i < len; i++)
       {
         if ((i + (j * len)) < astr1.length())
         {
-          if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
-                  && !jalview.util.Comparison.isGap(astr1.charAt(i
-                          + (j * len))))
+          char c1 = astr1.charAt(i + (j * len));
+          char c2 = astr2.charAt(i + (j * len));
+          boolean sameChar = Comparison.isSameResidue(c1, c2, false);
+          if (sameChar && !Comparison.isGap(c1))
           {
             pid++;
             output.append("|");
           }
           else if (type.equals("pep"))
           {
-            if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
-                    astr2.charAt(i + (j * len))) > 0)
+            if (pam250.getPairwiseScore(c1, c2) > 0)
             {
               output.append(".");
             }
@@ -662,9 +676,7 @@ public class AlignSeq
     }
 
     pid = pid / (aseq1.length - count) * 100;
-    output = output.append(new Format("Percentage ID = %2.2f\n\n")
-            .form(pid));
-
+    output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
     try
     {
       os.print(output.toString());
@@ -726,7 +738,7 @@ public class AlignSeq
   public int findTrace(int i, int j)
   {
     int t = 0;
-    int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
+    float max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
 
     if (F[i][j] > max)
     {
@@ -841,27 +853,27 @@ public class AlignSeq
   /**
    * DOCUMENT ME!
    * 
-   * @param i1
+   * @param f1
    *          DOCUMENT ME!
-   * @param i2
+   * @param f2
    *          DOCUMENT ME!
-   * @param i3
+   * @param f3
    *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  public int max(int i1, int i2, int i3)
+  public float max(float f1, float f2, float f3)
   {
-    int max = i1;
+    float max = f1;
 
-    if (i2 > i1)
+    if (f2 > f1)
     {
-      max = i2;
+      max = f2;
     }
 
-    if (i3 > max)
+    if (f3 > max)
     {
-      max = i3;
+      max = f3;
     }
 
     return max;
@@ -870,20 +882,20 @@ public class AlignSeq
   /**
    * DOCUMENT ME!
    * 
-   * @param i1
+   * @param f1
    *          DOCUMENT ME!
-   * @param i2
+   * @param f2
    *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  public int max(int i1, int i2)
+  public float max(float f1, float f2)
   {
-    int max = i1;
+    float max = f1;
 
-    if (i2 > i1)
+    if (f2 > f1)
     {
-      max = i2;
+      max = f2;
     }
 
     return max;
@@ -948,6 +960,7 @@ public class AlignSeq
   public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
           int psize)
   {
+    // TODO method dosen't seem to be referenced anywhere delete??
     int max = -1000;
     int min = 1000;
 
@@ -1110,7 +1123,7 @@ public class AlignSeq
       {
         SequenceI bestm = null;
         AlignSeq bestaseq = null;
-        int bestscore = 0;
+        float bestscore = 0;
         for (SequenceI msq : al.getSequences())
         {
           AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein);