X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=f0115bfca2874ae34f8a9d2c18623802c98838e1;hb=c6e8e8ccd10f21698226ae37196cd9680e6804a0;hp=41aef8232fad754aeb6b6febfefc14483fa3881a;hpb=1750b2f1dcdb6e7de41d0ef7beda88dc3400afba;p=jalview.git diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java index 41aef82..f0115bf 100644 --- a/src/jalview/analysis/scoremodels/ScoreMatrix.java +++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java @@ -21,93 +21,169 @@ package jalview.analysis.scoremodels; import jalview.api.analysis.ScoreModelI; -import jalview.schemes.ResidueProperties; + +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 { - String name; + public static final short UNMAPPED = (short) -1; - @Override - public String getName() - { - return name; - } + private static final String DELIMITERS = " ,\t"; - /** - * reference to integer score matrix + private static final String COMMENT_CHAR = "#"; + + 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 */ - int[][] matrix; + private String name; - /** - * 0 for Protein Score matrix. 1 for dna score matrix + /* + * 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 */ - int type; + private short[] symbolIndex; + + /* + * true for Protein Score matrix, false for dna score matrix + */ + private boolean peptide; /** + * Constructor * * @param name * Unique, human readable name for the matrix + * @param alphabet + * the symbols to which scores apply * @param matrix - * Pairwise scores indexed according to appropriate symbol alphabet - * @param type - * 0 for Protein, 1 for NA + * Pairwise scores indexed according to the symbol alphabet */ - public ScoreMatrix(String name, int[][] matrix, int type) + public ScoreMatrix(String name, char[] alphabet, float[][] matrix) { this.matrix = matrix; - this.type = type; this.name = name; + this.symbols = alphabet; + + symbolIndex = buildSymbolIndex(alphabet); + + /* + * crude heuristic for now... + */ + peptide = alphabet.length >= 20; + } + + /** + * 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. + *
+ * Unmapped characters (not in the alphabet) get an index of -1. + *
+ * 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). + * + * @param alphabet + * @return + */ + static 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 boolean isDNA() { - return type == 1; + return !peptide; } @Override public boolean isProtein() { - return type == 0; + return peptide; } @Override - public int[][] getMatrix() + public float[][] getMatrix() { return matrix; } /** - * - * @param A1 - * @param A2 - * @return score for substituting first char in A1 with first char in A2 + * Returns the pairwise score for substituting c with d, or zero if c or d is + * an unscored or unexpected character */ - public int getPairwiseScore(String A1, String A2) - { - return getPairwiseScore(A1.charAt(0), A2.charAt(0)); - } - @Override - public int getPairwiseScore(char c, char d) + public float getPairwiseScore(char c, char d) { - int pog = 0; - - try + if (c > MAX_ASCII) { - int a = (type == 0) ? ResidueProperties.aaIndex[c] - : ResidueProperties.nucleotideIndex[c]; - int b = (type == 0) ? ResidueProperties.aaIndex[d] - : ResidueProperties.nucleotideIndex[d]; - - pog = matrix[a][b]; - } catch (Exception e) + System.err.println(String.format(BAD_ASCII_ERROR, c)); + return 0; + } + if (d > MAX_ASCII) { - // System.out.println("Unknown residue in " + A1 + " " + A2); + System.err.println(String.format(BAD_ASCII_ERROR, d)); + return 0; } - return pog; + int cIndex = symbolIndex[c]; + int dIndex = symbolIndex[d]; + if (cIndex != UNMAPPED && dIndex != UNMAPPED) + { + return matrix[cIndex][dIndex]; + } + return 0; } /** @@ -119,57 +195,194 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements 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 + * @param html + * @return + */ public String outputMatrix(boolean html) { - StringBuffer sb = new StringBuffer(); - int[] symbols = (type == 0) ? ResidueProperties.aaIndex - : ResidueProperties.nucleotideIndex; - int symMax = (type == 0) ? ResidueProperties.maxProteinIndex - : ResidueProperties.maxNucleotideIndex; - boolean header = true; + StringBuilder sb = new StringBuilder(512); + + /* + * heading row with alphabet + */ if (html) { sb.append("
" : ""); + } + for (char sym : symbols) + { + if (html) + { + sb.append(" | ").append(sym).append(" | "); + } + else + { + sb.append("\t").append(sym); + } + } + sb.append(html ? "
---|---|
"); + } + sb.append(c1).append(html ? " | " : ""); + for (char c2 : symbols) + { + sb.append(html ? "" : "\t") + .append(matrix[symbolIndex[c1]][symbolIndex[c2]]) + .append(html ? " | " : ""); + } + sb.append(html ? "