X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=6cdfacbe56695b322b074d05cf90fef8565b37ea;hb=fc895e8dacdbb7f49df0ec5c9f475b841082e9b3;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..6cdfacb 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -20,9 +20,10 @@
*/
package jalview.analysis.scoremodels;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
import jalview.datamodel.AlignmentView;
import jalview.math.Matrix;
import jalview.math.MatrixI;
@@ -32,16 +33,20 @@ 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, so the same
+ * object is returned from calls to getInstance().
*/
-public class ScoreMatrix implements SimilarityScoreModelI,
- PairwiseScoreModelI
+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)
@@ -108,6 +113,26 @@ 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 +149,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
this.matrix = values;
this.name = theName;
+ this.description = theDescription;
this.symbols = alphabet;
symbolIndex = buildSymbolIndex(alphabet);
@@ -185,11 +211,6 @@ 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 +297,9 @@ 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 +324,11 @@ 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 +434,14 @@ public class ScoreMatrix implements SimilarityScoreModelI,
*