MSFAlignmentFormat (biojava-legacy 1.9.7 API)

java.lang.Object

org.biojava.bio.seq.io.MSFAlignmentFormat

All Implemented Interfaces:: AlignmentFormat

public class MSFAlignmentFormat extends 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(String[] args)

used to quick test the code

Alignment

read(BufferedReader reader)

Reads an MSF Alignment File

void

write(OutputStream os, Alignment align, int fileType)

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

Constructor Details
- MSFAlignmentFormat
  
  public MSFAlignmentFormat()
Method Details
- main
  
  public static void main(String[] args)
  
  used to quick test the code
  
  Parameters:
  
  args -
- read
  
  public Alignment read(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(OutputStream os, Alignment align, int fileType) throws BioException, IllegalSymbolException
  
  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