net.sf.jfasta

Interface FASTAFileReader

All Superinterfaces:

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

All Known Implementing Classes:

FASTAFileReaderImpl

public interface FASTAFileReader
extends net.sf.kerner.utils.io.buffered.IOIterable<FASTAElement>

A FASTAFileReader is used to read a FASTA file.

last reviewed: 2013-04-29

Version:

2010-11-06

Author:

Alexander Kerner

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes this reader.
FASTAElementIterator	getIterator()
FASTAFile	read() Reads all FASTAElements at once in one FASTAFile.

Method Detail

close

void close()

Closes this reader.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

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

See Also:

Reader.close()

getIterator

FASTAElementIterator getIterator()
                                 throws IOException

Specified by:

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

Throws:

IOException

read

FASTAFile read()
               throws IOException

Reads all FASTAElements at once in one FASTAFile.

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

Returns:

FASTAFile that has been read

Throws:

IOException