X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=c53ecdb22d9e8a80cb4b5f57e1325c0900d424fe;hb=447c5c1b22bd12a78730640321264fb38c39ec7b;hp=e2c14e91e590cff8a69b98a08ff588702a228b31;hpb=ae783be4cfa1df7fd59a4d0895df8bd1534d334c;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index e2c14e9..c53ecdb 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;
@@ -32,11 +33,14 @@ 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;
+
/*
* 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)
@@ -45,18 +49,13 @@ public class ScoreMatrix implements SimilarityScoreModelI,
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)
* for pairwise scoring; 2.10.2 uses gap score (last column) in
* score matrix (JAL-2397)
* Set this flag to true (via Groovy) for 2.10.1 behaviour
*/
- private static boolean scoreGapAsAny = false;
+ // BH 2019.05.08 was static but not ever set
+ private boolean scoreGapAsAny = false;
public static final short UNMAPPED = (short) -1;
@@ -101,6 +100,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
private float maxValue;
+ private boolean symmetric;
+
/**
* 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
@@ -115,6 +116,26 @@ 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(
@@ -131,12 +152,15 @@ public class ScoreMatrix implements SimilarityScoreModelI,
this.matrix = values;
this.name = theName;
+ this.description = theDescription;
this.symbols = alphabet;
symbolIndex = buildSymbolIndex(alphabet);
findMinMax();
+ symmetric = checkSymmetry();
+
/*
* crude heuristic for now...
*/
@@ -144,6 +168,27 @@ public class ScoreMatrix implements SimilarityScoreModelI,
}
/**
+ * Answers true if the matrix is symmetric, else false. Usually, substitution
+ * matrices are symmetric, which allows calculations to be short cut.
+ *
+ * @return
+ */
+ private boolean checkSymmetry()
+ {
+ for (int i = 0; i < matrix.length; i++)
+ {
+ for (int j = i; j < matrix.length; j++)
+ {
+ if (matrix[i][j] != matrix[j][i])
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
* Record the minimum and maximum score values
*/
protected void findMinMax()
@@ -192,11 +237,6 @@ 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;
@@ -283,19 +323,6 @@ 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. If either c or d is
* an unexpected character, returns 1 for identity (c == d), else the minimum
* score value in the matrix.
@@ -433,13 +460,14 @@ public class ScoreMatrix implements SimilarityScoreModelI,
*