--- /dev/null
+package jalview.io;
+
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.StringTokenizer;
+
+/**
+ * A class that can parse a file containing a substitution matrix and register
+ * it for use in Jalview
+ * <p>
+ * Accepts 'NCBI' format (e.g.
+ * https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt), with the
+ * addition of a header line to provide a matrix name, e.g.
+ *
+ * <pre>
+ * ScoreMatrix BLOSUM62
+ * </pre>
+ *
+ * Also accepts 'AAindex' format (as described at
+ * http://www.genome.jp/aaindex/aaindex_help.html) with the minimum data
+ * required being
+ *
+ * <pre>
+ * H accession number (used as score matrix identifier in Jalview)
+ * D description (used for tooltip in Jalview)
+ * M rows = symbolList
+ * and the substitution scores
+ * </pre>
+ */
+public class ScoreMatrixFile extends AlignFile implements
+ AlignmentFileReaderI
+{
+ // first non-comment line identifier - also checked in IdentifyFile
+ public static final String SCOREMATRIX = "SCOREMATRIX";
+
+ private static final String DELIMITERS = " ,\t";
+
+ private static final String COMMENT_CHAR = "#";
+
+ private String matrixName;
+
+ /*
+ * aaindex format has scores for diagonal and below only
+ */
+ boolean isLowerDiagonalOnly;
+
+ /*
+ * ncbi format has symbols as first column on score rows
+ */
+ boolean hasGuideColumn;
+
+ /**
+ * Constructor
+ *
+ * @param source
+ * @throws IOException
+ */
+ public ScoreMatrixFile(FileParse source) throws IOException
+ {
+ super(false, source);
+ }
+
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
+ {
+ return null;
+ }
+
+ /**
+ * Parses the score matrix file, and if successful registers the matrix so it
+ * will be shown in Jalview menus. This method is not thread-safe (a separate
+ * instance of this class should be used by each thread).
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ ScoreMatrix sm = parseMatrix();
+
+ ScoreModels.getInstance().registerScoreModel(sm);
+ }
+
+ /**
+ * Parses the score matrix file and constructs a ScoreMatrix object. If an
+ * error is found in parsing, it is thrown as FileFormatException. Any
+ * warnings are written to syserr.
+ *
+ * @return
+ * @throws IOException
+ */
+ public ScoreMatrix parseMatrix() throws IOException
+ {
+ ScoreMatrix sm = null;
+ int lineNo = 0;
+ String name = null;
+ char[] alphabet = null;
+ float[][] scores = null;
+ int size = 0;
+ int row = 0;
+ String err = null;
+ String data;
+ isLowerDiagonalOnly = false;
+
+ while ((data = nextLine()) != null)
+ {
+ lineNo++;
+ data = data.trim();
+ if (data.startsWith(COMMENT_CHAR) || data.length() == 0)
+ {
+ continue;
+ }
+ if (data.toUpperCase().startsWith(SCOREMATRIX))
+ {
+ /*
+ * Parse name from ScoreMatrix <name>
+ * we allow any delimiter after ScoreMatrix then take the rest of the line
+ */
+ if (name != null)
+ {
+ throw new FileFormatException(
+ "Error: 'ScoreMatrix' repeated in file at line "
+ + lineNo);
+ }
+ StringTokenizer nameLine = new StringTokenizer(data, DELIMITERS);
+ if (nameLine.countTokens() < 2)
+ {
+ err = "Format error: expected 'ScoreMatrix <name>', found '"
+ + data + "' at line " + lineNo;
+ throw new FileFormatException(err);
+ }
+ nameLine.nextToken(); // 'ScoreMatrix'
+ name = nameLine.nextToken(); // next field
+ name = data.substring(1).substring(data.substring(1).indexOf(name));
+ continue;
+ }
+ else if (data.startsWith("H ") && name == null)
+ {
+ /*
+ * AAindex identifier
+ */
+ return parseAAIndexFormat(lineNo, data);
+ }
+ else if (name == null)
+ {
+ err = "Format error: 'ScoreMatrix <name>' should be the first non-comment line";
+ throw new FileFormatException(err);
+ }
+
+ /*
+ * next non-comment line after ScoreMatrix should be the
+ * column header line with the alphabet of scored symbols
+ */
+ if (alphabet == null)
+ {
+ StringTokenizer columnHeadings = new StringTokenizer(data,
+ DELIMITERS);
+ size = columnHeadings.countTokens();
+ alphabet = new char[size];
+ int col = 0;
+ while (columnHeadings.hasMoreTokens())
+ {
+ alphabet[col++] = columnHeadings.nextToken().charAt(0);
+ }
+ scores = new float[size][];
+ continue;
+ }
+
+ /*
+ * too much information
+ */
+ if (row >= size)
+ {
+ err = "Unexpected extra input line in score model file: '" + data
+ + "'";
+ throw new FileFormatException(err);
+ }
+
+ parseValues(data, lineNo, scores, row, alphabet);
+ row++;
+ }
+
+ /*
+ * out of data - check we found enough
+ */
+ if (row < size)
+ {
+ err = String
+ .format("Expected %d rows of score data in score matrix but only found %d",
+ size, row);
+ throw new FileFormatException(err);
+ }
+
+ /*
+ * If we get here, then name, alphabet and scores have been parsed successfully
+ */
+ sm = new ScoreMatrix(name, alphabet, scores);
+ matrixName = name;
+
+ return sm;
+ }
+
+ /**
+ * Parse input as AAIndex format, starting from the header line with the
+ * accession id
+ *
+ * @param lineNo
+ * @param data
+ * @return
+ * @throws IOException
+ */
+ protected ScoreMatrix parseAAIndexFormat(int lineNo, String data)
+ throws IOException
+ {
+ String name = data.substring(2).trim();
+ String description = null;
+
+ float[][] scores = null;
+ char[] alphabet = null;
+ int row = 0;
+ int size = 0;
+
+ while ((data = nextLine()) != null)
+ {
+ lineNo++;
+ data = data.trim();
+ if (skipAAindexLine(data))
+ {
+ continue;
+ }
+ if (data.startsWith("D "))
+ {
+ description = data.substring(2).trim();
+ }
+ else if (data.startsWith("M "))
+ {
+ alphabet = parseAAindexRowsColumns(lineNo, data);
+ size = alphabet.length;
+ scores = new float[size][size];
+ }
+ else if (scores == null)
+ {
+ throw new FileFormatException(
+ "No alphabet specified in matrix file");
+ }
+ else if (row >= size)
+ {
+ throw new FileFormatException("Too many data rows in matrix file");
+ }
+ else
+ {
+ parseValues(data, lineNo, scores, row, alphabet);
+ row++;
+ }
+ }
+
+ ScoreMatrix sm = new ScoreMatrix(name, description, alphabet, scores);
+ matrixName = name;
+
+ return sm;
+ }
+
+ /**
+ * Parse one row of score values, delimited by whitespace or commas. The line
+ * may optionally include the symbol from which the scores are defined. Values
+ * may be present for all columns, or only up to the diagonal (in which case
+ * upper diagonal values are set symmetrically).
+ *
+ * @param data
+ * the line to be parsed
+ * @param lineNo
+ * @param scores
+ * the score matrix to add data to
+ * @param row
+ * the row number / alphabet index position
+ * @param alphabet
+ * @return
+ * @throws exception
+ * if invalid, or too few, or too many values
+ */
+ protected void parseValues(String data, int lineNo, float[][] scores,
+ int row, char[] alphabet) throws FileFormatException
+ {
+ String err;
+ int size = alphabet.length;
+ StringTokenizer scoreLine = new StringTokenizer(data, DELIMITERS);
+
+ int tokenCount = scoreLine.countTokens();
+
+ /*
+ * inspect first row to see if it includes the symbol in the first column,
+ * and to see if it is lower diagonal values only (i.e. just one score)
+ */
+ if (row == 0)
+ {
+ if (data.startsWith(String.valueOf(alphabet[0])))
+ {
+ hasGuideColumn = true;
+ }
+ if (tokenCount == (hasGuideColumn ? 2 : 1))
+ {
+ isLowerDiagonalOnly = true;
+ }
+ }
+
+ if (hasGuideColumn)
+ {
+ /*
+ * check 'guide' symbol is the row'th letter of the alphabet
+ */
+ String symbol = scoreLine.nextToken();
+ if (symbol.length() > 1 || symbol.charAt(0) != alphabet[row])
+ {
+ err = String
+ .format("Error parsing score matrix at line %d, expected '%s' but found '%s'",
+ lineNo, alphabet[row], symbol);
+ throw new FileFormatException(err);
+ }
+ tokenCount = scoreLine.countTokens(); // excluding guide symbol
+ }
+
+ /*
+ * check the right number of values (lower diagonal or full format)
+ */
+ if (isLowerDiagonalOnly && tokenCount != row + 1)
+ {
+ err = String.format(
+ "Expected %d scores at line %d: '%s' but found %d", row + 1,
+ lineNo, data, tokenCount);
+ throw new FileFormatException(err);
+ }
+
+ if (!isLowerDiagonalOnly && tokenCount != size)
+ {
+ err = String.format(
+ "Expected %d scores at line %d: '%s' but found %d", size,
+ lineNo, data, scoreLine.countTokens());
+ throw new FileFormatException(err);
+ }
+
+ /*
+ * parse and set the values, setting the symmetrical value
+ * as well if lower diagonal format data
+ */
+ scores[row] = new float[size];
+ int col = 0;
+ String value = null;
+ while (scoreLine.hasMoreTokens())
+ {
+ try
+ {
+ value = scoreLine.nextToken();
+ scores[row][col] = Float.valueOf(value);
+ if (isLowerDiagonalOnly)
+ {
+ scores[col][row] = scores[row][col];
+ }
+ col++;
+ } catch (NumberFormatException e)
+ {
+ err = String.format(
+ "Invalid score value '%s' at line %d column %d", value,
+ lineNo, col);
+ throw new FileFormatException(err);
+ }
+ }
+ }
+
+ /**
+ * Parse the line in an aaindex file that looks like
+ *
+ * <pre>
+ * M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ * </pre>
+ *
+ * rejecting it if rows and cols do not match. Returns the string of
+ * characters in the row/cols alphabet.
+ *
+ * @param lineNo
+ * @param data
+ * @return
+ * @throws FileFormatException
+ */
+ protected char[] parseAAindexRowsColumns(int lineNo, String data)
+ throws FileFormatException
+ {
+ String err = "Unexpected aaIndex score matrix data at line " + lineNo
+ + ": " + data;
+
+ try
+ {
+ String[] toks = data.split(",");
+ String rowsAlphabet = toks[0].split("=")[1].trim();
+ String colsAlphabet = toks[1].split("=")[1].trim();
+ if (!rowsAlphabet.equals(colsAlphabet))
+ {
+ throw new FileFormatException("rows != cols");
+ }
+ return rowsAlphabet.toCharArray();
+ } catch (Throwable t)
+ {
+ throw new FileFormatException(err + " " + t.getMessage());
+ }
+ }
+
+ /**
+ * Answers true if line is one we are not interested in from AAindex format
+ * file
+ *
+ * @param data
+ * @return
+ */
+ protected boolean skipAAindexLine(String data)
+ {
+ if (data.startsWith(COMMENT_CHAR) || data.length() == 0)
+ {
+ return true;
+ }
+ if (data.startsWith("*") || data.startsWith("R ")
+ || data.startsWith("A ") || data.startsWith("T ")
+ || data.startsWith("J ") || data.startsWith("//"))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ public String getMatrixName()
+ {
+ return matrixName;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff