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

Constructor Summary

MSFAlignmentFormat()

Method Summary

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

BioException

IllegalSymbolException

writeDna

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

BioException

IllegalSymbolException

writeProtein

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

BioException

IllegalSymbolException