X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=41d73838b98e6b83c690c7d0d009816d40d1d5b9;hb=baad2f0ba2b171dd3d52c17afa46ef800334ea5e;hp=f0115bfca2874ae34f8a9d2c18623802c98838e1;hpb=c6e8e8ccd10f21698226ae37196cd9680e6804a0;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index f0115bf..41d7383 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -20,23 +20,28 @@
*/
package jalview.analysis.scoremodels;
-import jalview.api.analysis.ScoreModelI;
+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;
+import jalview.util.Comparison;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
import java.util.Arrays;
-import java.util.StringTokenizer;
-public class ScoreMatrix extends PairwiseSeqScoreModel implements
- ScoreModelI
+public class ScoreMatrix implements SimilarityScoreModelI,
+ PairwiseScoreModelI
{
- public static final short UNMAPPED = (short) -1;
-
- private static final String DELIMITERS = " ,\t";
+ /*
+ * 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;
- private static final String COMMENT_CHAR = "#";
+ public static final short UNMAPPED = (short) -1;
private static final String BAD_ASCII_ERROR = "Unexpected character %s in getPairwiseScore";
@@ -70,7 +75,9 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
private boolean peptide;
/**
- * Constructor
+ * 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
* Unique, human readable name for the matrix
@@ -81,6 +88,20 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
*/
public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
{
+ if (alphabet.length != matrix.length)
+ {
+ throw new IllegalArgumentException(
+ "score matrix size must match alphabet size");
+ }
+ for (float[] row : matrix)
+ {
+ if (row.length != alphabet.length)
+ {
+ throw new IllegalArgumentException(
+ "score matrix size must be square");
+ }
+ }
+
this.matrix = matrix;
this.name = name;
this.symbols = alphabet;
@@ -153,10 +174,44 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
return peptide;
}
- @Override
+ /**
+ * Returns a copy of the score matrix as used in getPairwiseScore. If using
+ * this matrix directly, callers must also call
+ * getMatrixIndex
in order to get the matrix index for each
+ * character (symbol).
+ *
+ * @return
+ * @see #getMatrixIndex(char)
+ */
public float[][] getMatrix()
{
- return matrix;
+ float[][] v = new float[matrix.length][matrix.length];
+ for (int i = 0; i < matrix.length; i++)
+ {
+ v[i] = Arrays.copyOf(matrix[i], matrix[i].length);
+ }
+ return v;
+ }
+
+ /**
+ * Answers the matrix index for a given 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.
+ *
+ * @param c
+ * @return
+ * @see #getMatrix()
+ */
+ public int getMatrixIndex(char c)
+ {
+ if (c < symbolIndex.length)
+ {
+ return symbolIndex[c];
+ }
+ else
+ {
+ return UNMAPPED;
+ }
}
/**
@@ -166,12 +221,12 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
@Override
public float getPairwiseScore(char c, char d)
{
- if (c > MAX_ASCII)
+ if (c >= symbolIndex.length)
{
System.err.println(String.format(BAD_ASCII_ERROR, c));
return 0;
}
- if (d > MAX_ASCII)
+ if (d >= symbolIndex.length)
{
System.err.println(String.format(BAD_ASCII_ERROR, d));
return 0;
@@ -196,7 +251,12 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
}
/**
- * Print the score matrix, optionally formatted as html, with the alphabet symbols as column headings and at the start of each row
+ * Print the score matrix, optionally formatted as html, with the alphabet
+ * symbols as column headings and at the start of each row.
+ *
+ * The non-html format should give an output which can be parsed as a score + * matrix file + * * @param html * @return */ @@ -212,6 +272,11 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements sb.append("
" : ""); } + else + { + sb.append("ScoreMatrix ").append(getName()).append("\n"); + sb.append(symbols).append("\n"); + } for (char sym : symbols) { if (html) @@ -251,138 +316,172 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements } /** - * Parse a score matrix from the given input stream and returns a ScoreMatrix - * object. If parsing fails, error messages are written to syserr and null is - * returned. It is the caller's responsibility to close the input stream. + * Answers the number of symbols coded for (also equal to the number of rows + * and columns of the score matrix) * - * @param is * @return */ - public static ScoreMatrix parse(InputStream is) + public int getSize() { - ScoreMatrix sm = null; - BufferedReader br = new BufferedReader(new InputStreamReader(is)); - int lineNo = 0; - String name = null; - String alphabet = null; - float[][] scores = null; - int size = 0; - int row = 0; - - try - { - String data; + return symbols.length; + } - while ((data = br.readLine()) != null) + /** + * Computes an NxN matrix where N is the number of sequences, and entry [i, j] + * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores + * computed using the current score matrix. For example + * |
---|