Package org.biojava.bio.seq.io
Class MSFAlignmentFormat
java.lang.Object
org.biojava.bio.seq.io.MSFAlignmentFormat
- All Implemented Interfaces:
AlignmentFormat
- Author:
- raemig, Thomas Down, Keith James, Nimesh Singh, Mark Schreiber, Matthew Pocock, Bradford Powell
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic void
used to quick test the coderead
(BufferedReader reader) Reads an MSF Alignment Filevoid
write
(OutputStream os, Alignment align, int fileType) void
writeDna
(OutputStream os, Alignment align) void
writeProtein
(OutputStream os, Alignment align)
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Constructor Details
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MSFAlignmentFormat
public MSFAlignmentFormat()
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Method Details
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main
used to quick test the code- Parameters:
args
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read
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.
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write
public void write(OutputStream os, Alignment align, int fileType) throws BioException, IllegalSymbolException - Throws:
BioException
IllegalSymbolException
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writeDna
- Throws:
BioException
IllegalSymbolException
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writeProtein
public void writeProtein(OutputStream os, Alignment align) throws BioException, IllegalSymbolException - Throws:
BioException
IllegalSymbolException
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