org.biojava.bio.seq.io
Class MSFAlignmentFormat

java.lang.Object
  extended byorg.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
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