X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=9bec6e4cd7d795f6d0b621cf34c74f2171619f58;hb=773ac00a0ac2eb882e993e567a650ee4d7df3dda;hp=41d73838b98e6b83c690c7d0d009816d40d1d5b9;hpb=baad2f0ba2b171dd3d52c17afa46ef800334ea5e;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 41d7383..9bec6e4 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -22,7 +22,6 @@ package jalview.analysis.scoremodels;
import jalview.api.analysis.PairwiseScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
import jalview.datamodel.AlignmentView;
import jalview.math.Matrix;
import jalview.math.MatrixI;
@@ -30,9 +29,22 @@ import jalview.util.Comparison;
import java.util.Arrays;
-public class ScoreMatrix implements SimilarityScoreModelI,
+/**
+ * A class that models a substitution score matrix for any given alphabet of
+ * symbols. Instances of this class are immutable and thread-safe.
+ */
+public class ScoreMatrix extends SimilarityScoreModel implements
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;
+
/*
* Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
* for pairwise scoring; 2.10.2 uses gap score (last column) in
@@ -49,10 +61,16 @@ 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;
@@ -74,26 +92,50 @@ 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
* alphabet, for example 20x20 for a 20 symbol alphabet.
*
- * @param name
+ * @param theName
+ * Unique, human readable name for the matrix
+ * @param alphabet
+ * the symbols to which scores apply
+ * @param values
+ * Pairwise scores indexed according to the symbol alphabet
+ */
+ public ScoreMatrix(String theName, char[] alphabet, float[][] values)
+ {
+ this(theName, null, alphabet, values);
+ }
+
+ /**
+ * Constructor given a name, description, symbol alphabet, and matrix of
+ * scores for pairs of symbols. The matrix should be square and of the same
+ * size as the alphabet, for example 20x20 for a 20 symbol alphabet.
+ *
+ * @param theName
* Unique, human readable name for the matrix
+ * @param theDescription
+ * descriptive display name suitable for use in menus
* @param alphabet
* the symbols to which scores apply
- * @param matrix
+ * @param values
* Pairwise scores indexed according to the symbol alphabet
*/
- public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
+ public ScoreMatrix(String theName, String theDescription,
+ char[] alphabet, float[][] values)
{
- if (alphabet.length != matrix.length)
+ if (alphabet.length != values.length)
{
throw new IllegalArgumentException(
"score matrix size must match alphabet size");
}
- for (float[] row : matrix)
+ for (float[] row : values)
{
if (row.length != alphabet.length)
{
@@ -102,12 +144,15 @@ public class ScoreMatrix implements SimilarityScoreModelI,
}
}
- this.matrix = matrix;
- this.name = name;
+ this.matrix = values;
+ this.name = theName;
+ this.description = theDescription;
this.symbols = alphabet;
symbolIndex = buildSymbolIndex(alphabet);
+ findMinMax();
+
/*
* crude heuristic for now...
*/
@@ -115,6 +160,31 @@ 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.
@@ -124,11 +194,14 @@ 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).
+ *
+ * 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);
@@ -163,6 +236,12 @@ public class ScoreMatrix implements SimilarityScoreModelI,
}
@Override
+ public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
public boolean isDNA()
{
return !peptide;
@@ -215,8 +294,9 @@ 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
+ * 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)
@@ -238,7 +318,14 @@ 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();
}
/**
@@ -275,7 +362,6 @@ public class ScoreMatrix implements SimilarityScoreModelI,
else
{
sb.append("ScoreMatrix ").append(getName()).append("\n");
- sb.append(symbols).append("\n");
}
for (char sym : symbols)
{
@@ -345,12 +431,14 @@ public class ScoreMatrix implements SimilarityScoreModelI,
*
product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
* and so on
*
+ * This method is thread-safe.
*/
@Override
public MatrixI findSimilarities(AlignmentView seqstrings,
SimilarityParamsI options)
{
- char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X') : ' ';
+ char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
+ : GAP_CHARACTER;
String[] seqs = seqstrings.getSequenceStrings(gapChar);
return findSimilarities(seqs, options);
}
@@ -408,9 +496,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
break;
}
}
- // Change GAP_SPACE to GAP_DASH if we adopt - for gap in matrices
- char c1 = i >= len1 ? Comparison.GAP_SPACE : seq1.charAt(i);
- char c2 = i >= len2 ? Comparison.GAP_SPACE : seq2.charAt(i);
+
+ char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
+ char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
boolean gap1 = Comparison.isGap(c1);
boolean gap2 = Comparison.isGap(c2);
@@ -429,7 +517,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
/*
* gap-residue: score if options say so
*/
- if (!params.includesGaps())
+ if (!params.includeGaps())
{
continue;
}
@@ -480,8 +568,18 @@ public class ScoreMatrix implements SimilarityScoreModelI,
*
* @return
*/
- public String getSymbols()
+ String getSymbols()
{
return new String(symbols);
}
+
+ public float getMinimumScore()
+ {
+ return minValue;
+ }
+
+ public float getMaximumScore()
+ {
+ return maxValue;
+ }
}