FastaAlignmentFormat (biojava-legacy 1.9.7 API)

java.lang.Object

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

Fields

Modifier and Type

Field

Description

static final int

DNA

static final int

PROTEIN
Constructor Summary

Constructors

Constructor

Description

FastaAlignmentFormat()
Method Summary

Modifier and Type

Method

Description

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 Details
- DNA
  
  public static final int DNA
  See Also:
  
  Constant Field Values
- PROTEIN
  
  public static final int PROTEIN
  See Also:
  
  Constant Field Values
Constructor Details
- FastaAlignmentFormat
  
  public FastaAlignmentFormat()
Method Details
- 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