org.biojava.bio.seq.io
Class MSFAlignmentFormat
java.lang.Object
org.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, Bradford Powell
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MSFAlignmentFormat
public MSFAlignmentFormat()
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