htsjdk.samtools.reference.ReferenceSequenceFile Maven / Gradle / Ivy
/*
* 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.SAMSequenceDictionary;
import java.io.Closeable;
import java.io.IOException;
/**
* An interface for working with files of reference sequences regardless of the file format
* being used.
*
* @author Tim Fennell
*/
public interface ReferenceSequenceFile extends Closeable {
/**
* Must return a sequence dictionary with at least the following fields completed
* for each sequence: name, length.
*
* @return a list of sequence records representing the sequences in this reference file
*/
public SAMSequenceDictionary getSequenceDictionary();
/**
* Retrieves the next whole sequences from the file.
* @return a ReferenceSequence or null if at the end of the file
*/
public ReferenceSequence nextSequence();
/**
* Resets the ReferenceSequenceFile so that the next call to nextSequence() will return
* the first sequence in the file.
*/
public void reset();
/**
* @return true if getSequence and getSubsequenceAt methods are allowed.
*/
public boolean isIndexed();
/**
* Retrieves the complete sequence described by this contig.
* @param contig contig whose data should be returned.
* @return The full sequence associated with this contig.
* @throws UnsupportedOperationException if !sIndexed.
*/
public ReferenceSequence getSequence( String contig );
/**
* Gets the subsequence of the contig in the range [start,stop]
* @param contig Contig whose subsequence to retrieve.
* @param start inclusive, 1-based start of region.
* @param stop inclusive, 1-based stop of region.
* @return The partial reference sequence associated with this range.
* @throws UnsupportedOperationException if !sIndexed.
*/
public ReferenceSequence getSubsequenceAt( String contig, long start, long stop );
/**
* @return Reference name, file name, or something other human-readable representation.
*/
public String toString();
@Override
public void close() throws IOException;
}