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A Java API for high-throughput sequencing data (HTS) formats
There is a newer version: 4.1.3
/*
 * The MIT License
 *
 * Copyright (c) 2009 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 htsjdk.samtools.reference;

import htsjdk.samtools.SAMException;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMTextHeaderCodec;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Lazy;

import java.io.File;
import java.io.InputStream;
import java.io.Serializable;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.function.Supplier;

/**
 * Provide core sequence dictionary functionality required by all fasta file readers.
 * @author Matt Hanna
 */
abstract class AbstractFastaSequenceFile implements ReferenceSequenceFile {
    private final Path path;
    private final String source;
    private final Lazy dictionary;

    /**
     * Finds and loads the sequence file dictionary.
     * @param file Fasta file to read.  Also acts as a prefix for supporting files.
     */
    AbstractFastaSequenceFile(final File file) {
        this(IOUtil.toPath(file));
    }

    /**
     * Finds and loads the sequence file dictionary.
     * @param path Fasta file to read.  Also acts as a prefix for supporting files.
     */
    AbstractFastaSequenceFile(final Path path) {
        this.path = path;
        this.source = path == null ? "unknown" : path.toAbsolutePath().toString();
        // ensure lambda is serializable (by Kryo, when used with Spark)
        this.dictionary = new Lazy<>((Supplier & Serializable) (() -> findAndLoadSequenceDictionary(path)));
    }

    /**
     * Constructs an {@link AbstractFastaSequenceFile} with an optional sequence dictionary.
     * @param path Fasta file to read.  Also acts as a prefix for supporting files.
     * @param source Named source used for error messages.
     * @param sequenceDictionary The sequence dictionary, or null if there isn't one.
     */
    AbstractFastaSequenceFile(final Path path, final String source, final SAMSequenceDictionary sequenceDictionary) {
        this.path = path;
        this.source = source;
        // ensure lambda is serializable (by Kryo, when used with Spark)
        this.dictionary = new Lazy<>((Supplier & Serializable) (() -> sequenceDictionary));
    }

    /** Attempts to find and load the sequence dictionary if present. */
    protected SAMSequenceDictionary findAndLoadSequenceDictionary(final Path fasta) {
        final Path dictPath = findSequenceDictionary(path);
        if (dictPath == null) return null;

        IOUtil.assertFileIsReadable(dictPath);
        try (InputStream dictionaryIn = IOUtil.openFileForReading(dictPath)) {
            return ReferenceSequenceFileFactory.loadDictionary(dictionaryIn);
        }
        catch (Exception e) {
            throw new SAMException("Could not open sequence dictionary file: " + dictPath, e);
        }
    }

    /** @deprecated use findSequenceDictionary(Path) instead. */
    @Deprecated protected static File findSequenceDictionary(final File file) {
        final Path dict = findSequenceDictionary(file.toPath());
        return dict == null ? null : dict.toFile();
    }

    /** Attempts to locate the sequence dictionary file adjacent to the reference fasta file. */
    protected static Path findSequenceDictionary(final Path fastaPath) {
        if (fastaPath == null) {
            return null;
        }
        // Try and locate the dictionary with the default method
        final Path dictionary = ReferenceSequenceFileFactory.getDefaultDictionaryForReferenceSequence(fastaPath);
        if (Files.exists(dictionary)) {
            return dictionary;
        }
        // try without removing the file extension
        final Path dictionaryExt = fastaPath.resolveSibling(fastaPath.getFileName().toString() + FileExtensions.DICT);
        if (Files.exists(dictionaryExt)) {
            return dictionaryExt;
        }
        else {
            return null;
        }
    }

    /** Returns the path to the reference file. */
    protected Path getPath() {
        return path;
    }

    /** Returns the named source of the reference file. */
    protected String getSource() {
        return source;
    }

    /**
     * Returns the list of sequence records associated with the reference sequence if found
     * otherwise null.
     */
    @Override
    public SAMSequenceDictionary getSequenceDictionary() {
        return this.dictionary.get();
    }

    /** Returns the full path to the reference file. */
    protected String getAbsolutePath() {
        if (path == null) {
            return null;
        }
        return path.toAbsolutePath().toString();
    }

    /** Returns the full path to the reference file, or the source if no path was specified. */
    public String toString() {
        return source;
    }

    /** default implementation -- override if index is supported */
    @Override
    public boolean isIndexed() {return false;}

    /** default implementation -- override if index is supported */
    @Override
    public ReferenceSequence getSequence( String contig ) {
        throw new UnsupportedOperationException("Index does not appear to exist for " + getSource() + ".  samtools faidx can be used to create an index");
    }

    /** default implementation -- override if index is supported */
    @Override
    public ReferenceSequence getSubsequenceAt( String contig, long start, long stop ) {
        throw new UnsupportedOperationException("Index does not appear to exist for " + getSource() + ".  samtools faidx can be used to create an index");
    }

}