Package 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
-
-
Constructor Summary
Constructors Constructor Description MSFAlignmentFormat()
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static void
main(java.lang.String[] args)
used to quick test the codeAlignment
read(java.io.BufferedReader reader)
Reads an MSF Alignment Filevoid
write(java.io.OutputStream os, Alignment align, int fileType)
void
writeDna(java.io.OutputStream os, Alignment align)
void
writeProtein(java.io.OutputStream os, Alignment align)
-
-
-
Constructor Detail
-
MSFAlignmentFormat
public MSFAlignmentFormat()
-
-
Method Detail
-
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 interfaceAlignmentFormat
- 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
-
-