X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=e2c14e91e590cff8a69b98a08ff588702a228b31;hb=ae783be4cfa1df7fd59a4d0895df8bd1534d334c;hp=6a74dfccd4e87457dd2166bebfc1d1c0d3f024b3;hpb=613a7a5d1fe2758f0bb620e49eeb87fa45b5458f;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 6a74dfc..e2c14e9 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -30,10 +30,25 @@ import jalview.util.Comparison;
 
 import java.util.Arrays;
 
+/**
+ * A class that models a substitution score matrix for any given alphabet of
+ * symbols
+ */
 public class ScoreMatrix implements SimilarityScoreModelI,
         PairwiseScoreModelI
 {
-  private static final char GAP_CHARACTER = Comparison.GAP_DASH;
+  /*
+   * an arbitrary score to assign for identity of an unknown symbol
+   * (this is the value on the diagonal in the * column of the NCBI matrix)
+   * (though a case could be made for using the minimum diagonal value)
+   */
+  private static final int UNKNOWN_IDENTITY_SCORE = 1;
+
+  /*
+   * this fields records which gap character (if any) is used in the alphabet;
+   * space, dash or dot are recognised as gap symbols
+   */
+  private char gapCharacter = '0';
 
   /*
    * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
@@ -51,10 +66,16 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
   /*
    * the name of the model as shown in menus
+   * each score model in use should have a unique name
    */
   private String name;
 
   /*
+   * a description for the model as shown in tooltips
+   */
+  private String description;
+
+  /*
    * the characters that the model provides scores for
    */
   private char[] symbols;
@@ -76,6 +97,10 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    */
   private boolean peptide;
 
+  private float minValue;
+
+  private float maxValue;
+
   /**
    * Constructor given a name, symbol alphabet, and matrix of scores for pairs
    * of symbols. The matrix should be square and of the same size as the
@@ -110,6 +135,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
     symbolIndex = buildSymbolIndex(alphabet);
 
+    findMinMax();
+
     /*
      * crude heuristic for now...
      */
@@ -117,6 +144,31 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   /**
+   * Record the minimum and maximum score values
+   */
+  protected void findMinMax()
+  {
+    float min = Float.MAX_VALUE;
+    float max = -Float.MAX_VALUE;
+    if (matrix != null)
+    {
+      for (float[] row : matrix)
+      {
+        if (row != null)
+        {
+          for (float f : row)
+          {
+            min = Math.min(min, f);
+            max = Math.max(max, f);
+          }
+        }
+      }
+    }
+    minValue = min;
+    maxValue = max;
+  }
+
+  /**
    * Returns an array A where A[i] is the position in the alphabet array of the
    * character whose value is i. For example if the alphabet is { 'A', 'D', 'X'
    * } then A['D'] = A[68] = 1.
@@ -126,17 +178,25 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * Mappings are added automatically for lower case symbols (for non case
    * sensitive scoring), unless they are explicitly present in the alphabet (are
    * scored separately in the score matrix).
+   * <p>
+   * the gap character (space, dash or dot) included in the alphabet (if any) is
+   * recorded in a field
    * 
    * @param alphabet
    * @return
    */
-  static short[] buildSymbolIndex(char[] alphabet)
+  short[] buildSymbolIndex(char[] alphabet)
   {
     short[] index = new short[MAX_ASCII + 1];
     Arrays.fill(index, UNMAPPED);
     short pos = 0;
     for (char c : alphabet)
     {
+      if (Comparison.isGap(c))
+      {
+        gapCharacter = c;
+      }
+
       if (c <= MAX_ASCII)
       {
         index[c] = pos;
@@ -165,6 +225,12 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   @Override
+  public String getDescription()
+  {
+    return description;
+  }
+
+  @Override
   public boolean isDNA()
   {
     return !peptide;
@@ -217,8 +283,22 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   /**
-   * Returns the pairwise score for substituting c with d, or zero if c or d is
-   * an unscored or unexpected character
+   * Answers the matrix index for the gap character, or -1 if unmapped in the
+   * matrix. Use this method only if using <code>getMatrix</code> in order to
+   * compute scores directly (without symbol lookup) for efficiency.
+   * 
+   * @return
+   * @see #getMatrix()
+   */
+  public int getGapIndex()
+  {
+    return getMatrixIndex(gapCharacter);
+  }
+
+  /**
+   * Returns the pairwise score for substituting c with d. If either c or d is
+   * an unexpected character, returns 1 for identity (c == d), else the minimum
+   * score value in the matrix.
    */
   @Override
   public float getPairwiseScore(char c, char d)
@@ -240,7 +320,14 @@ public class ScoreMatrix implements SimilarityScoreModelI,
     {
       return matrix[cIndex][dIndex];
     }
-    return 0;
+
+    /*
+     * one or both symbols not found in the matrix
+     * currently scoring as 1 (for identity) or the minimum
+     * matrix score value (otherwise)
+     * (a case could be made for using minimum row/column value instead)
+     */
+    return c == d ? UNKNOWN_IDENTITY_SCORE : getMinimumScore();
   }
 
   /**
@@ -277,7 +364,6 @@ public class ScoreMatrix implements SimilarityScoreModelI,
     else
     {
       sb.append("ScoreMatrix ").append(getName()).append("\n");
-      sb.append(symbols).append("\n");
     }
     for (char sym : symbols)
     {
@@ -353,7 +439,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
           SimilarityParamsI options)
   {
     char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
-            : Comparison.GAP_DASH;
+            : gapCharacter;
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
     return findSimilarities(seqs, options);
   }
@@ -412,8 +498,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
         }
       }
 
-      char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
-      char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
+      char c1 = i >= len1 ? gapCharacter : seq1.charAt(i);
+      char c2 = i >= len2 ? gapCharacter : seq2.charAt(i);
       boolean gap1 = Comparison.isGap(c1);
       boolean gap2 = Comparison.isGap(c2);
 
@@ -483,8 +569,23 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * 
    * @return
    */
-  public String getSymbols()
+  String getSymbols()
   {
     return new String(symbols);
   }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
+
+  public float getMinimumScore()
+  {
+    return minValue;
+  }
+
+  public float getMaximumScore()
+  {
+    return maxValue;
+  }
 }