--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis.scoremodels;
+
+import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.AlignmentView;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
+import jalview.util.Comparison;
+
+import java.util.Arrays;
+
+/**
+ * A class that models a substitution score matrix for any given alphabet of
+ * symbols. Instances of this class are immutable and thread-safe.
+ */
+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)
+ * (though a case could be made for using the minimum diagonal value)
+ */
+ private static final int UNKNOWN_IDENTITY_SCORE = 1;
+
+ /*
+ * 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";
+
+ private static final int MAX_ASCII = 127;
+
+ /*
+ * 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;
+
+ /*
+ * the score matrix; both dimensions must equal the number of symbols
+ * matrix[i][j] is the substitution score for replacing symbols[i] with symbols[j]
+ */
+ private float[][] matrix;
+
+ /*
+ * quick lookup to convert from an ascii character value to the index
+ * of the corresponding symbol in the score matrix
+ */
+ private short[] symbolIndex;
+
+ /*
+ * true for Protein Score matrix, false for dna score matrix
+ */
+ private boolean peptide;
+
+ 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
+ * alphabet, for example 20x20 for a 20 symbol alphabet.
+ *
+ * @param theName
+ * Unique, human readable name for the matrix
+ * @param alphabet
+ * the symbols to which scores apply
+ * @param values
+ * Pairwise scores indexed according to the symbol alphabet
+ */
+ 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(
+ "score matrix size must match alphabet size");
+ }
+ for (float[] row : values)
+ {
+ if (row.length != alphabet.length)
+ {
+ throw new IllegalArgumentException(
+ "score matrix size must be square");
+ }
+ }
+
+ this.matrix = values;
+ this.name = theName;
+ this.description = theDescription;
+ this.symbols = alphabet;
+
+ symbolIndex = buildSymbolIndex(alphabet);
+
+ findMinMax();
+
+ /*
+ * crude heuristic for now...
+ */
+ peptide = alphabet.length >= 20;
+ }
+
+ /**
+ * Record the minimum and maximum score values
+ */
+ protected void findMinMax()
+ {
+ float min = Float.MAX_VALUE;
+ float max = -Float.MAX_VALUE;
+ if (matrix != null)
+ {
+ for (float[] row : matrix)
+ {
+ if (row != null)
+ {
+ for (float f : row)
+ {
+ min = Math.min(min, f);
+ max = Math.max(max, f);
+ }
+ }
+ }
+ }
+ minValue = min;
+ maxValue = max;
+ }
+
+ /**
+ * Returns an array A where A[i] is the position in the alphabet array of the
+ * character whose value is i. For example if the alphabet is { 'A', 'D', 'X'
+ * } then A['D'] = A[68] = 1.
+ * <p>
+ * Unmapped characters (not in the alphabet) get an index of -1.
+ * <p>
+ * 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).
+ * <p>
+ * the gap character (space, dash or dot) included in the alphabet (if any) is
+ * recorded in a field
+ *
+ * @param alphabet
+ * @return
+ */
+ short[] buildSymbolIndex(char[] alphabet)
+ {
+ short[] index = new short[MAX_ASCII + 1];
+ Arrays.fill(index, UNMAPPED);
+ short pos = 0;
+ for (char c : alphabet)
+ {
+ if (c <= MAX_ASCII)
+ {
+ index[c] = pos;
+ }
+
+ /*
+ * also map lower-case character (unless separately mapped)
+ */
+ if (c >= 'A' && c <= 'Z')
+ {
+ short lowerCase = (short) (c + ('a' - 'A'));
+ if (index[lowerCase] == UNMAPPED)
+ {
+ index[lowerCase] = pos;
+ }
+ }
+ pos++;
+ }
+ return index;
+ }
+
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
+ public boolean isDNA()
+ {
+ return !peptide;
+ }
+
+ @Override
+ public boolean isProtein()
+ {
+ return peptide;
+ }
+
+ /**
+ * Returns a copy of the score matrix as used in getPairwiseScore. If using
+ * this matrix directly, callers <em>must</em> also call
+ * <code>getMatrixIndex</code> in order to get the matrix index for each
+ * character (symbol).
+ *
+ * @return
+ * @see #getMatrixIndex(char)
+ */
+ public float[][] getMatrix()
+ {
+ 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 <code>getMatrix</code> 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;
+ }
+ }
+
+ /**
+ * 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)
+ {
+ if (c >= symbolIndex.length)
+ {
+ System.err.println(String.format(BAD_ASCII_ERROR, c));
+ return 0;
+ }
+ if (d >= symbolIndex.length)
+ {
+ System.err.println(String.format(BAD_ASCII_ERROR, d));
+ return 0;
+ }
+
+ int cIndex = symbolIndex[c];
+ int dIndex = symbolIndex[d];
+ if (cIndex != UNMAPPED && dIndex != UNMAPPED)
+ {
+ return matrix[cIndex][dIndex];
+ }
+
+ /*
+ * one or both symbols not found in the matrix
+ * 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 c == d ? UNKNOWN_IDENTITY_SCORE : getMinimumScore();
+ }
+
+ /**
+ * pretty print the matrix
+ */
+ @Override
+ public String toString()
+ {
+ return outputMatrix(false);
+ }
+
+ /**
+ * Print the score matrix, optionally formatted as html, with the alphabet
+ * symbols as column headings and at the start of each row.
+ * <p>
+ * The non-html format should give an output which can be parsed as a score
+ * matrix file
+ *
+ * @param html
+ * @return
+ */
+ public String outputMatrix(boolean html)
+ {
+ StringBuilder sb = new StringBuilder(512);
+
+ /*
+ * heading row with alphabet
+ */
+ if (html)
+ {
+ sb.append("<table border=\"1\">");
+ sb.append(html ? "<tr><th></th>" : "");
+ }
+ else
+ {
+ sb.append("ScoreMatrix ").append(getName()).append("\n");
+ }
+ for (char sym : symbols)
+ {
+ if (html)
+ {
+ sb.append("<th> ").append(sym).append(" </th>");
+ }
+ else
+ {
+ sb.append("\t").append(sym);
+ }
+ }
+ sb.append(html ? "</tr>\n" : "\n");
+
+ /*
+ * table of scores
+ */
+ for (char c1 : symbols)
+ {
+ if (html)
+ {
+ sb.append("<tr><td>");
+ }
+ sb.append(c1).append(html ? "</td>" : "");
+ for (char c2 : symbols)
+ {
+ sb.append(html ? "<td>" : "\t")
+ .append(matrix[symbolIndex[c1]][symbolIndex[c2]])
+ .append(html ? "</td>" : "");
+ }
+ sb.append(html ? "</tr>\n" : "\n");
+ }
+ if (html)
+ {
+ sb.append("</table>");
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Answers the number of symbols coded for (also equal to the number of rows
+ * and columns of the score matrix)
+ *
+ * @return
+ */
+ public int getSize()
+ {
+ return symbols.length;
+ }
+
+ /**
+ * 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
+ * <ul>
+ * <li>Sequences:</li>
+ * <li>FKL</li>
+ * <li>R-D</li>
+ * <li>QIA</li>
+ * <li>GWC</li>
+ * <li>Score matrix is BLOSUM62</li>
+ * <li>Gaps treated same as X (unknown)</li>
+ * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
+ * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
+ * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
+ * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
+ * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
+ * <li>and so on</li>
+ * </ul>
+ * This method is thread-safe.
+ */
+ @Override
+ public MatrixI findSimilarities(AlignmentView seqstrings,
+ SimilarityParamsI options)
+ {
+ char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
+ : GAP_CHARACTER;
+ 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++)
+ {
+ values[row] = new double[seqs.length];
+ for (int col = 0; col < seqs.length; col++)
+ {
+ double total = computeSimilarity(seqs[row], seqs[col], params);
+ values[row][col] = total;
+ }
+ }
+ return new Matrix(values);
+ }
+
+ /**
+ * 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 ? GAP_CHARACTER : seq1.charAt(i);
+ char c2 = i >= len2 ? GAP_CHARACTER : 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
+ */
+ @Override
+ public int hashCode()
+ {
+ int hs = Arrays.hashCode(symbols);
+ for (float[] row : matrix)
+ {
+ hs = hs * 31 + Arrays.hashCode(row);
+ }
+ return hs;
+ }
+
+ /**
+ * Answers true if the argument is a ScoreMatrix with the same symbol alphabet
+ * and score values, else false
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof ScoreMatrix))
+ {
+ return false;
+ }
+ ScoreMatrix sm = (ScoreMatrix) obj;
+ if (Arrays.equals(symbols, sm.symbols)
+ && Arrays.deepEquals(matrix, sm.matrix))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the alphabet the matrix scores for, as a string of characters
+ *
+ * @return
+ */
+ String getSymbols()
+ {
+ return new String(symbols);
+ }
+
+ public float getMinimumScore()
+ {
+ return minValue;
+ }
+
+ public float getMaximumScore()
+ {
+ return maxValue;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff