/*
* 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.IOUtil;
import java.io.File;
import java.io.FileInputStream;
/**
* Provide core sequence dictionary functionality required by all fasta file readers.
* @author Matt Hanna
*/
abstract class AbstractFastaSequenceFile implements ReferenceSequenceFile {
protected final File file;
protected SAMSequenceDictionary sequenceDictionary;
/**
* 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.file = file;
final File dictionary = findSequenceDictionary(file);
if (dictionary != null) {
IOUtil.assertFileIsReadable(dictionary);
try {
final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
final BufferedLineReader reader = new BufferedLineReader(new FileInputStream(dictionary));
final SAMFileHeader header = codec.decode(reader,
dictionary.toString());
if (header.getSequenceDictionary() != null && header.getSequenceDictionary().size() > 0) {
this.sequenceDictionary = header.getSequenceDictionary();
}
reader.close();
}
catch (Exception e) {
throw new SAMException("Could not open sequence dictionary file: " + dictionary, e);
}
}
}
protected static File findSequenceDictionary(final File file) {
// Try and locate the dictionary
String dictionaryName = file.getAbsolutePath();
String dictionaryNameExt = file.getAbsolutePath();
boolean fileTypeSupported = false;
for (final String extension : ReferenceSequenceFileFactory.FASTA_EXTENSIONS) {
if (dictionaryName.endsWith(extension)) {
dictionaryNameExt = new String(dictionaryName);
dictionaryNameExt += IOUtil.DICT_FILE_EXTENSION;
dictionaryName = dictionaryName.substring(0, dictionaryName.lastIndexOf(extension));
dictionaryName += IOUtil.DICT_FILE_EXTENSION;
fileTypeSupported = true;
break;
}
}
if (!fileTypeSupported)
throw new IllegalArgumentException("File is not a supported reference file type: " + file.getAbsolutePath());
final File dictionary = new File(dictionaryName);
if (dictionary.exists())
return dictionary;
// try without removing the file extension
final File dictionaryExt = new File(dictionaryNameExt);
if (dictionaryExt.exists())
return dictionaryExt;
else return null;
}
/**
* Returns the list of sequence records associated with the reference sequence if found
* otherwise null.
*/
public SAMSequenceDictionary getSequenceDictionary() {
return this.sequenceDictionary;
}
/** Returns the full path to the reference file. */
public String toString() {
return this.file.getAbsolutePath();
}
/** default implementation -- override if index is supported */
public boolean isIndexed() {return false;}
/** default implementation -- override if index is supported */
public ReferenceSequence getSequence( String contig ) {
throw new UnsupportedOperationException();
}
/** default implementation -- override if index is supported */
public ReferenceSequence getSubsequenceAt( String contig, long start, long stop ) {
throw new UnsupportedOperationException("Index does not appear to exist for" + file.getAbsolutePath() + ". samtools faidx can be used to create an index");
}
}