org.biojava.bio.seq.io
Class FastaAlignmentFormat

java.lang.Object
  extended by 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
static int DNA
           
static int PROTEIN
           
 
Constructor Summary
FastaAlignmentFormat()
           
 
Method Summary
 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