net.sf.jfasta.impl

Class FASTAFileReaderImpl

java.lang.Object

net.sf.kerner.utils.io.buffered.AbstractBufferedReader

net.sf.jfasta.impl.FASTAFileReaderImpl

All Implemented Interfaces:

Closeable, AutoCloseable, FASTAFileReader, net.sf.kerner.utils.io.buffered.IOIterable<FASTAElement>

public class FASTAFileReaderImpl
extends net.sf.kerner.utils.io.buffered.AbstractBufferedReader
implements FASTAFileReader

Implementation for FASTAFileReader.

Example:

last reviewed: 2013-04-29

 TODO example
 

Version:

2010-11-06

Author:

Alexander Kerner

Field Summary

Fields

Modifier and Type	Field and Description
protected char[]	alphabet Alphabet that is used for sequence validity checking.
static char[]	DNA_ALPHABET A default alphabet for DNA.
static char[]	DNA_ALPHABET_IGNORE_CASE A default alphabet for DNA.
static char[]	DNA_ALPHABET_IGNORE_CASE_STRICT A default alphabet for DNA.
static char[]	DNA_ALPHABET_STRICT A default alphabet for DNA.

Fields inherited from class net.sf.kerner.utils.io.buffered.AbstractBufferedReader

reader

Constructor Summary

Constructors

Constructor and Description
FASTAFileReaderImpl(BufferedReader reader) Builds a new FASTAFileReaderImpl.
FASTAFileReaderImpl(BufferedReader reader, char[] alphabet)
FASTAFileReaderImpl(File file) Builds a new FASTAFileReaderImpl.
FASTAFileReaderImpl(File file, char[] alphabet)
FASTAFileReaderImpl(InputStream stream) Builds a new FASTAFileReaderImpl.
FASTAFileReaderImpl(InputStream stream, char[] alphabet)
FASTAFileReaderImpl(Reader reader) Builds a new FASTAFileReaderImpl.
FASTAFileReaderImpl(Reader reader, char[] alphabet)

Method Summary

Methods

Modifier and Type	Method and Description
FASTAElementIterator	getIterator()
FASTAFile	read() Reads all FASTAElements at once in one FASTAFile.

Methods inherited from class net.sf.kerner.utils.io.buffered.AbstractBufferedReader

close

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.jfasta.FASTAFileReader

close

Field Detail

DNA_ALPHABET_IGNORE_CASE

public static final char[] DNA_ALPHABET_IGNORE_CASE

A default alphabet for DNA.

{ 'A', 'a', 'T', 't','G', 'g', 'C', 'c', 'N', 'n' }

DNA_ALPHABET_IGNORE_CASE_STRICT

public static final char[] DNA_ALPHABET_IGNORE_CASE_STRICT

A default alphabet for DNA.

{ 'A', 'a', 'T', 't','G', 'g', 'C', 'c'}

DNA_ALPHABET

public static final char[] DNA_ALPHABET

A default alphabet for DNA.

{ 'A', 'T', 'G', 'C', 'N' }

DNA_ALPHABET_STRICT

public static final char[] DNA_ALPHABET_STRICT

A default alphabet for DNA.

{ 'A', 'T', 'G', 'C' }

alphabet

protected final char[] alphabet

Alphabet that is used for sequence validity checking. If null, sequence is not validated.

Constructor Detail

FASTAFileReaderImpl

public FASTAFileReaderImpl(BufferedReader reader)

Builds a new FASTAFileReaderImpl. this FASTAFileReaderImpl will not perform any sequence validation.

Parameters:

reader - reader from which stream is read

FASTAFileReaderImpl

public FASTAFileReaderImpl(BufferedReader reader,
                   char[] alphabet)

FASTAFileReaderImpl

public FASTAFileReaderImpl(File file)
                    throws IOException

Builds a new FASTAFileReaderImpl. this FASTAFileReaderImpl will not perform any sequence validation.

Parameters:

file - file from which stream is read

Throws:

IOException

FASTAFileReaderImpl

public FASTAFileReaderImpl(File file,
                   char[] alphabet)
                    throws IOException

Throws:

IOException

FASTAFileReaderImpl

public FASTAFileReaderImpl(InputStream stream)

Builds a new FASTAFileReaderImpl. this FASTAFileReaderImpl will not perform any sequence validation.

Parameters:

stream - stream from which is read

FASTAFileReaderImpl

public FASTAFileReaderImpl(InputStream stream,
                   char[] alphabet)

FASTAFileReaderImpl

public FASTAFileReaderImpl(Reader reader)

Builds a new FASTAFileReaderImpl. this FASTAFileReaderImpl will not perform any sequence validation.

Parameters:

reader - reader from which stream is read

FASTAFileReaderImpl

public FASTAFileReaderImpl(Reader reader,
                   char[] alphabet)

Method Detail

getIterator

public FASTAElementIterator getIterator()
                                 throws IOException

Specified by:

getIterator in interface FASTAFileReader

Specified by:

getIterator in interface net.sf.kerner.utils.io.buffered.IOIterable<FASTAElement>

Throws:

IOException

read

public FASTAFile read()
               throws IOException

Description copied from interface: FASTAFileReader

Reads all FASTAElements at once in one FASTAFile.

Use this with care, since FASTA files can be huge!

Specified by:

read in interface FASTAFileReader

Returns:

FASTAFile that has been read

Throws:

IOException