com.milaboratory.core.io.sequence.fasta

Class RandomAccessFastaReader<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader<S>

All Implemented Interfaces:

AutoCloseable

public final class RandomAccessFastaReader<S extends Sequence<S>>
extends Object
implements AutoCloseable

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BUFFER_SIZE

Constructor Summary

Constructors

Constructor and Description
RandomAccessFastaReader(Path file, Alphabet<S> alphabet)
RandomAccessFastaReader(Path file, Alphabet<S> alphabet, boolean saveIndexFile)
RandomAccessFastaReader(Path file, RandomAccessFastaIndex index, Alphabet<S> alphabet)
RandomAccessFastaReader(SeekableByteChannel channel, RandomAccessFastaIndex index, Alphabet<S> alphabet, int bufferSize)
RandomAccessFastaReader(String file, Alphabet<S> alphabet)
RandomAccessFastaReader(String file, Alphabet<S> alphabet, boolean saveIndexFile)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
Alphabet<S>	getAlphabet()
RandomAccessFastaIndex	getIndex()
S	getSequence(int id, Range range)
S	getSequence(String id, Range range)
SequenceProvider<S>	getSequenceProvider(int id)
SequenceProvider<S>	getSequenceProvider(String id)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

See Also:

Constant Field Values

Constructor Detail

RandomAccessFastaReader

public RandomAccessFastaReader(String file,
                       Alphabet<S> alphabet)

RandomAccessFastaReader

public RandomAccessFastaReader(Path file,
                       Alphabet<S> alphabet)

RandomAccessFastaReader

public RandomAccessFastaReader(String file,
                       Alphabet<S> alphabet,
                       boolean saveIndexFile)

RandomAccessFastaReader

public RandomAccessFastaReader(Path file,
                       Alphabet<S> alphabet,
                       boolean saveIndexFile)

RandomAccessFastaReader

public RandomAccessFastaReader(Path file,
                       RandomAccessFastaIndex index,
                       Alphabet<S> alphabet)

RandomAccessFastaReader

public RandomAccessFastaReader(SeekableByteChannel channel,
                       RandomAccessFastaIndex index,
                       Alphabet<S> alphabet,
                       int bufferSize)

Method Detail

getAlphabet

public Alphabet<S> getAlphabet()

getIndex

public RandomAccessFastaIndex getIndex()

getSequenceProvider

public SequenceProvider<S> getSequenceProvider(int id)

getSequenceProvider

public SequenceProvider<S> getSequenceProvider(String id)

getSequence

public S getSequence(int id,
            Range range)

getSequence

public S getSequence(String id,
            Range range)

close

public void close()
           throws Exception

Specified by:

close in interface AutoCloseable

Throws:

Exception