X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=9bec6e4cd7d795f6d0b621cf34c74f2171619f58;hb=e0aacff0a162fdf1beb71cd5965b6ff4f8c9de0d;hp=84e91aebc3c555aba5efc0dad30cb6533b4c9b27;hpb=2a9d6da50bb346c1f8cd38f104c958b7e8e6eff0;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 84e91ae..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;
@@ -32,16 +31,19 @@ import java.util.Arrays;
/**
* A class that models a substitution score matrix for any given alphabet of
- * symbols
+ * symbols. Instances of this class are immutable and thread-safe.
*/
-public class ScoreMatrix implements SimilarityScoreModelI,
+public class ScoreMatrix extends SimilarityScoreModel implements
PairwiseScoreModelI
{
+ private static final char GAP_CHARACTER = Comparison.GAP_DASH;
+
/*
- * this fields records which gap character (if any) is used in the alphabet;
- * space, dash or dot are recognised as gap symbols
+ * 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 char gapCharacter = '0';
+ private static final int UNKNOWN_IDENTITY_SCORE = 1;
/*
* Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
@@ -93,7 +95,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
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
@@ -108,6 +110,26 @@ public class ScoreMatrix implements SimilarityScoreModelI,
*/
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 values
+ * Pairwise scores indexed according to the symbol alphabet
+ */
+ public ScoreMatrix(String theName, String theDescription,
+ char[] alphabet, float[][] values)
+ {
if (alphabet.length != values.length)
{
throw new IllegalArgumentException(
@@ -124,6 +146,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
this.matrix = values;
this.name = theName;
+ this.description = theDescription;
this.symbols = alphabet;
symbolIndex = buildSymbolIndex(alphabet);
@@ -185,11 +208,6 @@ public class ScoreMatrix implements SimilarityScoreModelI,
short pos = 0;
for (char c : alphabet)
{
- if (Comparison.isGap(c))
- {
- gapCharacter = c;
- }
-
if (c <= MAX_ASCII)
{
index[c] = pos;
@@ -276,21 +294,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
}
/**
- * Answers the matrix index for the gap character, or -1 if unmapped in the
- * matrix. Use this method only if using getMatrix
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, 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)
@@ -315,10 +321,11 @@ public class ScoreMatrix implements SimilarityScoreModelI,
/*
* one or both symbols not found in the matrix
- * note: a possible strategy here would be to return the minimum
- * matrix value if c != d
+ * 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 0;
+ return c == d ? UNKNOWN_IDENTITY_SCORE : getMinimumScore();
}
/**
@@ -424,13 +431,14 @@ public class ScoreMatrix implements SimilarityScoreModelI,
*