/*
 * The MIT License
 *
 * Copyright (c) 2012 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package net.sf.samtools;

import java.io.File;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;

import net.sf.samtools.util.StringUtil;

/**
 * this class enables creation of a SAMRecord object from a String in SAM text format.
 */
public class SAMLineParser {

    // From SAM specification
    private static final int QNAME_COL = 0;
    private static final int FLAG_COL = 1;
    private static final int RNAME_COL = 2;
    private static final int POS_COL = 3;
    private static final int MAPQ_COL = 4;
    private static final int CIGAR_COL = 5;
    private static final int MRNM_COL = 6;
    private static final int MPOS_COL = 7;
    private static final int ISIZE_COL = 8;
    private static final int SEQ_COL = 9;
    private static final int QUAL_COL = 10;

    private static final int NUM_REQUIRED_FIELDS = 11;

    // Read string must contain only these characters
    private static final Pattern VALID_BASES = Pattern
            .compile("^[acmgrsvtwyhkdbnACMGRSVTWYHKDBN.=]+$");

    /**
     * Allocate this once rather than for every line as a performance
     * optimization. The size is arbitrary -- merely large enough to handle the
     * maximum number of fields we might expect from a reasonable SAM file.
     */
    private final String[] mFields = new String[10000];

    /**
     * Add information about the origin (reader and position) to SAM records.
     */
    private final SAMFileReader mParentReader;
    private final SAMRecordFactory samRecordFactory;
    private final SAMFileReader.ValidationStringency validationStringency;
    private final SAMFileHeader mFileHeader;
    private final File mFile;

    private final TextTagCodec tagCodec = new TextTagCodec();

    private int currentLineNumber;
    private String currentLine;

    //
    // Constructors
    //

    /**
     * Public constructor. Use the default SAMRecordFactory and stringency.
     * @param samFileHeader SAM file header
     */
    public SAMLineParser(final SAMFileHeader samFileHeader) {

        this(new DefaultSAMRecordFactory(),
                SAMFileReader.ValidationStringency.DEFAULT_STRINGENCY, samFileHeader,
                null, null);
    }

    /**
     * Public constructor. Use the default SAMRecordFactory and stringency.
     * @param samFileHeader SAM file header
     * @param samFileReader SAM file reader For passing to SAMRecord.setFileSource, may be null.
     * @param samFile SAM file being read (for error message only, may be null)
     */
    public SAMLineParser(final SAMFileHeader samFileHeader,
                         final SAMFileReader samFileReader, final File samFile) {

        this(new DefaultSAMRecordFactory(),
                SAMFileReader.ValidationStringency.DEFAULT_STRINGENCY, samFileHeader,
                samFileReader, samFile);
    }

    /**
     * Public constructor.
     * @param samRecordFactory SamRecord Factory
     * @param validationStringency validation stringency
     * @param samFileHeader SAM file header
     * @param samFileReader SAM file reader For passing to SAMRecord.setFileSource, may be null.
     * @param samFile SAM file being read (for error message only, may be null)
     */
    public SAMLineParser(final SAMRecordFactory samRecordFactory,
                         final SAMFileReader.ValidationStringency validationStringency,
                         final SAMFileHeader samFileHeader, final SAMFileReader samFileReader,
                         final File samFile) {

        if (samRecordFactory == null)
            throw new NullPointerException("The SamRecordFactory must be set");

        if (validationStringency == null)
            throw new NullPointerException("The validationStringency must be set");

        if (samFileHeader == null)
            throw new NullPointerException("The mFileHeader must be set");

        this.samRecordFactory = samRecordFactory;
        this.validationStringency = validationStringency;
        this.mFileHeader = samFileHeader;

        // Can be null
        this.mParentReader = samFileReader;

        // Can be null
        this.mFile = samFile;
    }

    /**
     * Get the File header.
     * @return the SAM file header
     */
    private SAMFileHeader getFileHeader() {

        return this.mFileHeader;
    }

    /**
     * Get validation stringency.
     * @return validation stringency
     */
    private SAMFileReader.ValidationStringency getValidationStringency() {

        return this.validationStringency;
    }

    private int parseInt(final String s, final String fieldName) {
        final int ret;
        try {
            ret = Integer.parseInt(s);
        } catch (NumberFormatException e) {
            throw reportFatalErrorParsingLine("Non-numeric value in "
                    + fieldName + " column");
        }
        return ret;
    }

    private void validateReferenceName(final String rname, final String fieldName) {
        if (rname.equals("=")) {
            if (fieldName.equals("MRNM")) {
                return;
            }
            reportErrorParsingLine("= is not a valid value for "
                    + fieldName + " field.");
        }
        if (this.mFileHeader.getSequenceDictionary().size() != 0) {
            if (this.mFileHeader.getSequence(rname) == null) {
                reportErrorParsingLine(fieldName
                        + " '" + rname + "' not found in any SQ record");
            }
        }
    }

    /**
     * Parse a SAM line.
     * @param line line to parse
     * @return a new SAMRecord object
     */
    public SAMRecord parseLine(final String line) {

        return parseLine(line, -1);
    }

    /**
     * Parse a SAM line.
     * @param line line to parse
     * @param lineNumber line number in the file. If the line number is not known
     *          can be <=0.
     * @return a new SAMRecord object
     */
    public SAMRecord parseLine(final String line, final int lineNumber) {

        final String mCurrentLine = line;
        this.currentLineNumber = lineNumber;
        this.currentLine = line;

        final int numFields = StringUtil.split(mCurrentLine, mFields, '\t');
        if (numFields < NUM_REQUIRED_FIELDS) {
            throw reportFatalErrorParsingLine("Not enough fields");
        }
        if (numFields == mFields.length) {
            reportErrorParsingLine("Too many fields in SAM text record.");
        }
        for (int i = 0; i < numFields; ++i) {
            if (mFields[i].length() == 0) {
                reportErrorParsingLine("Empty field at position " + i + " (zero-based)");
            }
        }
        final SAMRecord samRecord =
                samRecordFactory.createSAMRecord(this.mFileHeader);
        samRecord.setValidationStringency(this.validationStringency);
        if (mParentReader != null)
            samRecord.setFileSource(new SAMFileSource(mParentReader, null));
        samRecord.setHeader(this.mFileHeader);
        samRecord.setReadName(mFields[QNAME_COL]);

        final int flags = parseInt(mFields[FLAG_COL], "FLAG");
        samRecord.setFlags(flags);

        String rname = mFields[RNAME_COL];
        if (!rname.equals("*")) {
            rname = SAMSequenceRecord.truncateSequenceName(rname);
            validateReferenceName(rname, "RNAME");
            samRecord.setReferenceName(rname);
        } else if (!samRecord.getReadUnmappedFlag()) {
            reportErrorParsingLine("RNAME is not specified but flags indicate mapped");
        }

        final int pos = parseInt(mFields[POS_COL], "POS");
        final int mapq = parseInt(mFields[MAPQ_COL], "MAPQ");
        final String cigar = mFields[CIGAR_COL];
        if (!SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(samRecord
                .getReferenceName())) {
            if (pos == 0) {
                reportErrorParsingLine("POS must be non-zero if RNAME is specified");
            }
            if (!samRecord.getReadUnmappedFlag() && cigar.equals("*")) {
                reportErrorParsingLine("CIGAR must not be '*' if RNAME is specified");
            }
        } else {
            if (pos != 0) {
                reportErrorParsingLine("POS must be zero if RNAME is not specified");
            }
            if (mapq != 0) {
                reportErrorParsingLine("MAPQ must be zero if RNAME is not specified");
            }
            if (!cigar.equals("*")) {
                reportErrorParsingLine("CIGAR must be '*' if RNAME is not specified");
            }
        }
        samRecord.setAlignmentStart(pos);
        samRecord.setMappingQuality(mapq);
        samRecord.setCigarString(cigar);

        String mateRName = mFields[MRNM_COL];
        if (mateRName.equals("*")) {
            if (samRecord.getReadPairedFlag() && !samRecord.getMateUnmappedFlag()) {
                reportErrorParsingLine("MRNM not specified but flags indicate mate mapped");
            }
        } else {
            if (!samRecord.getReadPairedFlag()) {
                reportErrorParsingLine("MRNM specified but flags indicate unpaired");
            }
            if (!"=".equals(mateRName)) {
                mateRName = SAMSequenceRecord.truncateSequenceName(mateRName);
            }
            validateReferenceName(mateRName, "MRNM");
            if (mateRName.equals("=")) {
                if (samRecord.getReferenceName() == null) {
                    reportErrorParsingLine("MRNM is '=', but RNAME is not set");
                }
                samRecord.setMateReferenceName(samRecord.getReferenceName());
            } else {
                samRecord.setMateReferenceName(mateRName);
            }
        }

        final int matePos = parseInt(mFields[MPOS_COL], "MPOS");
        final int isize = parseInt(mFields[ISIZE_COL], "ISIZE");
        if (!samRecord.getMateReferenceName().equals(
                SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
            if (matePos == 0) {
                reportErrorParsingLine("MPOS must be non-zero if MRNM is specified");
            }
        } else {
            if (matePos != 0) {
                reportErrorParsingLine("MPOS must be zero if MRNM is not specified");
            }
            if (isize != 0) {
                reportErrorParsingLine("ISIZE must be zero if MRNM is not specified");
            }
        }
        samRecord.setMateAlignmentStart(matePos);
        samRecord.setInferredInsertSize(isize);
        if (!mFields[SEQ_COL].equals("*")) {
            validateReadBases(mFields[SEQ_COL]);
            samRecord.setReadString(mFields[SEQ_COL]);
        } else {
            samRecord.setReadBases(SAMRecord.NULL_SEQUENCE);
        }
        if (!mFields[QUAL_COL].equals("*")) {
            if (samRecord.getReadBases() == SAMRecord.NULL_SEQUENCE) {
                reportErrorParsingLine("QUAL should not be specified if SEQ is not specified");
            }
            if (samRecord.getReadString().length() != mFields[QUAL_COL].length()) {
                reportErrorParsingLine("length(QUAL) != length(SEQ)");
            }
            samRecord.setBaseQualityString(mFields[QUAL_COL]);
        } else {
            samRecord.setBaseQualities(SAMRecord.NULL_QUALS);
        }

        for (int i = NUM_REQUIRED_FIELDS; i < numFields; ++i) {
            parseTag(samRecord, mFields[i]);
        }

        final List<SAMValidationError> validationErrors = samRecord.isValid();
        if (validationErrors != null) {
            for (final SAMValidationError errorMessage : validationErrors) {
                reportErrorParsingLine(errorMessage.getMessage());
            }
        }
        return samRecord;
    }

    private void validateReadBases(final String bases) {
        /*
        * Using regex is slow, so check for invalid characters via
        * isValidReadBase(), which hopefully the JIT will optimize. if
        * (!VALID_BASES.matcher(bases).matches()) {
        * reportErrorParsingLine("Invalid character in read bases"); }
        */
        for (int i = 0; i < bases.length(); ++i) {
            if (!isValidReadBase(bases.charAt(i))) {
                reportErrorParsingLine("Invalid character in read bases");
                return;
            }
        }
    }

    private boolean isValidReadBase(final char base) {
        switch (base) {
            case 'a':
            case 'c':
            case 'm':
            case 'g':
            case 'r':
            case 's':
            case 'v':
            case 't':
            case 'w':
            case 'y':
            case 'h':
            case 'k':
            case 'd':
            case 'b':
            case 'n':
            case 'A':
            case 'C':
            case 'M':
            case 'G':
            case 'R':
            case 'S':
            case 'V':
            case 'T':
            case 'W':
            case 'Y':
            case 'H':
            case 'K':
            case 'D':
            case 'B':
            case 'N':
            case '.':
            case '=':
                return true;
            default:
                return false;
        }
    }

    private void parseTag(final SAMRecord samRecord, final String tag) {
        Map.Entry<String, Object> entry = null;
        try {
            entry = tagCodec.decode(tag);
        } catch (SAMFormatException e) {
            reportErrorParsingLine(e);
        }
        if (entry != null) {
            if (entry.getValue() instanceof TagValueAndUnsignedArrayFlag) {
                final TagValueAndUnsignedArrayFlag valueAndFlag =
                        (TagValueAndUnsignedArrayFlag) entry.getValue();
                if (valueAndFlag.isUnsignedArray) {
                    samRecord.setUnsignedArrayAttribute(entry.getKey(),
                            valueAndFlag.value);
                } else {
                    samRecord.setAttribute(entry.getKey(), valueAndFlag.value);
                }
            } else {
                samRecord.setAttribute(entry.getKey(), entry.getValue());
            }
        }
    }

    //
    // Error methods
    //

    private RuntimeException reportFatalErrorParsingLine(final String reason) {
        return new SAMFormatException(makeErrorString(reason));
    }

    private void reportErrorParsingLine(final String reason) {
        final String errorMessage = makeErrorString(reason);

        if (validationStringency == SAMFileReader.ValidationStringency.STRICT) {
            throw new SAMFormatException(errorMessage);
        } else if (validationStringency == SAMFileReader.ValidationStringency.LENIENT) {
            System.err
                    .println("Ignoring SAM validation error due to lenient parsing:");
            System.err.println(errorMessage);
        }
    }

    private void reportErrorParsingLine(final Exception e) {
        final String errorMessage = makeErrorString(e.getMessage());
        if (validationStringency == SAMFileReader.ValidationStringency.STRICT) {
            throw new SAMFormatException(errorMessage);
        } else if (validationStringency == SAMFileReader.ValidationStringency.LENIENT) {
            System.err
                    .println("Ignoring SAM validation error due to lenient parsing:");
            System.err.println(errorMessage);
        }
    }

    private String makeErrorString(final String reason) {
        String fileMessage = "";
        if (mFile != null) {
            fileMessage = "File " + mFile + "; ";
        }
        return "Error parsing text SAM file. "
                + reason + "; " + fileMessage + "Line "
                + (this.currentLineNumber <= 0 ? "unknown" : this.currentLineNumber)
                + "\nLine: " + this.currentLine;
    }

}
