org.biojava.bio.seq.io

Class FastaAlignmentFormat

java.lang.Object

org.biojava.bio.seq.io.FastaAlignmentFormat

All Implemented Interfaces:

AlignmentFormat

public class FastaAlignmentFormat
extends Object
implements AlignmentFormat

This class implements the AlignmentFormat interface to read FASTA alignments. It is modeled after the MSFAlignmentFormat class.

Author:

Nimesh Singh

Field Summary

Fields

Modifier and Type	Field and Description
static int	DNA
static int	PROTEIN

Constructor Summary

Constructors

Constructor and Description
FastaAlignmentFormat()

Method Summary

Modifier and Type	Method and Description
Alignment	read(BufferedReader br) Reads an alignment in FASTA format.
void	write(OutputStream os, Alignment align, int fileType) Writes out the alignment to an FASTA file.
void	writeDna(OutputStream os, Alignment align)
void	writeProtein(OutputStream os, Alignment align)

Methods inherited from class java.lang.Object

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

Field Detail

DNA

public static final int DNA

See Also:

Constant Field Values

PROTEIN

public static final int PROTEIN

See Also:

Constant Field Values

Constructor Detail

FastaAlignmentFormat

public FastaAlignmentFormat()

Method Detail

read

public Alignment read(BufferedReader br)

Reads an alignment in FASTA format.

Specified by:

read in interface AlignmentFormat

Parameters:

br - the reader from which to read in the alignment

write

public void write(OutputStream os,
                  Alignment align,
                  int fileType)
           throws BioException,
                  IllegalSymbolException

Writes out the alignment to an FASTA file.

Throws:

BioException

IllegalSymbolException

writeDna

public void writeDna(OutputStream os,
                     Alignment align)
              throws BioException,
                     IllegalSymbolException

Throws:

BioException

IllegalSymbolException

writeProtein

public void writeProtein(OutputStream os,
                         Alignment align)
                  throws BioException,
                         IllegalSymbolException

Throws:

BioException

IllegalSymbolException