Package org.biojava.bio.seq.io

Class MSFAlignmentFormat

java.lang.Object

org.biojava.bio.seq.io.MSFAlignmentFormat

All Implemented Interfaces:

AlignmentFormat

public class MSFAlignmentFormat
extends java.lang.Object
implements AlignmentFormat

Author:

raemig, Thomas Down, Keith James, Nimesh Singh, Mark Schreiber, Matthew Pocock, Bradford Powell

Constructor Summary

Constructors

Constructor	Description
MSFAlignmentFormat()

Method Summary

Modifier and Type	Method	Description
static void	main(java.lang.String[] args)	used to quick test the code
Alignment	read(java.io.BufferedReader reader)	Reads an MSF Alignment File
void	write(java.io.OutputStream os, Alignment align, int fileType)
void	writeDna(java.io.OutputStream os, Alignment align)
void	writeProtein(java.io.OutputStream os, Alignment align)

Methods inherited from class java.lang.Object

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

Constructor Detail

MSFAlignmentFormat

public MSFAlignmentFormat()

Method Detail

main

public static void main(java.lang.String[] args)

used to quick test the code

Parameters:

args -

read

public Alignment read(java.io.BufferedReader reader)

Reads an MSF Alignment File

Specified by:

read in interface AlignmentFormat

Parameters:

reader - The file reader

Returns:

Alignment A SimpleAlignment consisting of the sequences in the file.

write

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

Throws:

BioException

IllegalSymbolException

writeDna

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

Throws:

BioException

IllegalSymbolException

writeProtein

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

Throws:

BioException

IllegalSymbolException