org.biojava.bio.seq.io
Class FastaAlignmentFormat
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DNA
public static final int DNA
- See Also:
- Constant Field Values
PROTEIN
public static final int PROTEIN
- See Also:
- Constant Field Values
FastaAlignmentFormat
public FastaAlignmentFormat()
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