X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=b904432d6652d41c15f802f13aed860ac0dd1c49;hb=adca107ff292173bc844ad4a5c6c7eba958ad24a;hp=9da28ebda2e448260757f1152d7345634ca180fe;hpb=86f56c7a53d72066544ff74c893188d304598bec;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 9da28eb..b904432 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -20,13 +20,37 @@
*/
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;
+import jalview.util.Comparison;
import java.util.Arrays;
-public class ScoreMatrix implements PairwiseScoreModelI
+/**
+ * A class that models a substitution score matrix for any given alphabet of
+ * symbols
+ */
+public class ScoreMatrix implements SimilarityScoreModelI,
+ PairwiseScoreModelI
{
+ /*
+ * 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;
+
public static final short UNMAPPED = (short) -1;
private static final String BAD_ASCII_ERROR = "Unexpected character %s in getPairwiseScore";
@@ -35,10 +59,16 @@ public class ScoreMatrix implements PairwiseScoreModelI
/*
* 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;
@@ -60,28 +90,26 @@ public class ScoreMatrix implements PairwiseScoreModelI
*/
private boolean peptide;
- 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
* 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 matrix
+ * @param values
* Pairwise scores indexed according to the symbol alphabet
*/
- public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
+ public ScoreMatrix(String theName, 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)
{
@@ -90,8 +118,8 @@ public class ScoreMatrix implements PairwiseScoreModelI
}
}
- this.matrix = matrix;
- this.name = name;
+ this.matrix = values;
+ this.name = theName;
this.symbols = alphabet;
symbolIndex = buildSymbolIndex(alphabet);
@@ -112,17 +140,25 @@ public class ScoreMatrix implements PairwiseScoreModelI
* 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);
short pos = 0;
for (char c : alphabet)
{
+ if (Comparison.isGap(c))
+ {
+ gapCharacter = c;
+ }
+
if (c <= MAX_ASCII)
{
index[c] = pos;
@@ -151,6 +187,12 @@ public class ScoreMatrix implements PairwiseScoreModelI
}
@Override
+ public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
public boolean isDNA()
{
return !peptide;
@@ -203,6 +245,19 @@ public class ScoreMatrix implements PairwiseScoreModelI
}
/**
+ * 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
*/
@@ -334,7 +389,25 @@ public class ScoreMatrix implements PairwiseScoreModelI
*
and so on
*
*/
- public MatrixI computePairwiseScores(String[] seqs)
+ @Override
+ public MatrixI findSimilarities(AlignmentView seqstrings,
+ SimilarityParamsI options)
+ {
+ char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
+ : Comparison.GAP_DASH;
+ String[] seqs = seqstrings.getSequenceStrings(gapChar);
+ return findSimilarities(seqs, options);
+ }
+
+ /**
+ * Computes pairwise similarities of a set of sequences using the given
+ * parameters
+ *
+ * @param seqs
+ * @param params
+ * @return
+ */
+ protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
{
double[][] values = new double[seqs.length][];
for (int row = 0; row < seqs.length; row++)
@@ -342,15 +415,7 @@ public class ScoreMatrix implements PairwiseScoreModelI
values[row] = new double[seqs.length];
for (int col = 0; col < seqs.length; col++)
{
- int total = 0;
- int width = Math.min(seqs[row].length(), seqs[col].length());
- for (int i = 0; i < width; i++)
- {
- char c1 = seqs[row].charAt(i);
- char c2 = seqs[col].charAt(i);
- float score = getPairwiseScore(c1, c2);
- total += score;
- }
+ double total = computeSimilarity(seqs[row], seqs[col], params);
values[row][col] = total;
}
}
@@ -358,6 +423,68 @@ public class ScoreMatrix implements PairwiseScoreModelI
}
/**
+ * Calculates the pairwise similarity of two strings using the given
+ * calculation parameters
+ *
+ * @param seq1
+ * @param seq2
+ * @param params
+ * @return
+ */
+ protected double computeSimilarity(String seq1, String seq2,
+ SimilarityParamsI params)
+ {
+ int len1 = seq1.length();
+ int len2 = seq2.length();
+ double total = 0;
+
+ int width = Math.max(len1, len2);
+ for (int i = 0; i < width; i++)
+ {
+ if (i >= len1 || i >= len2)
+ {
+ /*
+ * off the end of one sequence; stop if we are only matching
+ * on the shorter sequence length, else treat as trailing gap
+ */
+ if (params.denominateByShortestLength())
+ {
+ break;
+ }
+ }
+
+ char c1 = i >= len1 ? gapCharacter : seq1.charAt(i);
+ char c2 = i >= len2 ? gapCharacter : seq2.charAt(i);
+ boolean gap1 = Comparison.isGap(c1);
+ boolean gap2 = Comparison.isGap(c2);
+
+ if (gap1 && gap2)
+ {
+ /*
+ * gap-gap: include if options say so, else ignore
+ */
+ if (!params.includeGappedColumns())
+ {
+ continue;
+ }
+ }
+ else if (gap1 || gap2)
+ {
+ /*
+ * gap-residue: score if options say so
+ */
+ if (!params.includeGaps())
+ {
+ continue;
+ }
+ }
+ float score = getPairwiseScore(c1, c2);
+ total += score;
+ }
+ return total;
+ }
+
+ /**
* Answers a hashcode computed from the symbol alphabet and the matrix score
* values
*/
@@ -392,11 +519,6 @@ public class ScoreMatrix implements PairwiseScoreModelI
return false;
}
- public boolean isSymmetric()
- {
- return symmetric;
- }
-
/**
* Returns the alphabet the matrix scores for, as a string of characters
*
@@ -406,4 +528,9 @@ public class ScoreMatrix implements PairwiseScoreModelI
{
return new String(symbols);
}
+
+ public void setDescription(String desc)
+ {
+ description = desc;
+ }
}