org.utgenome.format.fasta
Class FASTAPullParser

java.lang.Object
  org.utgenome.format.fasta.FASTAPullParser

public class FASTAPullParser
extends Object

A pull parser for FASTA format files

Author:

leo

Constructor Summary

	FASTAPullParser(File fastaFile) Create a pull parse for the given FASTA file.
	FASTAPullParser(File fastaFile, int bufferSize)
	FASTAPullParser(Reader reader) Create a pull parser from a given text reader
protected	FASTAPullParser(String fastaFile, InputStream in, int bufferSize)

Method Summary

void	close()
static FASTAPullParser	newGZIPFileReader(InputStream gzInput)
static FASTAPullParser	newTARFileReader(InputStream tarFileInput)
static FASTAPullParser	newTARGZFileReader(InputStream targzInput)
String	nextDescriptionLine()
FASTASequence	nextSequence() read the next fasta sequence;
String	nextSequenceLine()

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTAPullParser

public FASTAPullParser(Reader reader)

Create a pull parser from a given text reader

Parameters:

reader -

FASTAPullParser

public FASTAPullParser(File fastaFile)
                throws IOException

Create a pull parse for the given FASTA file. The file can be text (.fa, .fasta, etc.), tar.gz or gz format.

Parameters:

fastaFile -

Throws:

IOException

FASTAPullParser

public FASTAPullParser(File fastaFile,
                       int bufferSize)
                throws IOException

Throws:

IOException

FASTAPullParser

protected FASTAPullParser(String fastaFile,
                          InputStream in,
                          int bufferSize)
                   throws IOException

Throws:

IOException

Method Detail

newTARFileReader

public static FASTAPullParser newTARFileReader(InputStream tarFileInput)
                                        throws IOException

Throws:

IOException

newTARGZFileReader

public static FASTAPullParser newTARGZFileReader(InputStream targzInput)
                                          throws IOException

Throws:

IOException

newGZIPFileReader

public static FASTAPullParser newGZIPFileReader(InputStream gzInput)
                                         throws IOException

Throws:

IOException

nextSequence

public FASTASequence nextSequence()
                           throws UTGBException,
                                  IOException

read the next fasta sequence;

Returns:

the next fasta sequence, or null when there is no more sequence to read.

Throws:

InvalidFormatException - when the input fasta data format is invalid

IOException

UTGBException

nextSequenceLine

public String nextSequenceLine()
                        throws IOException

Throws:

IOException

nextDescriptionLine

public String nextDescriptionLine()
                           throws IOException

Throws:

IOException

close

public void close()
           throws IOException

Throws:

IOException