org.biojavax.bio.phylo.io.phylip

Class PHYLIPFileFormat

java.lang.Object

org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat

public class PHYLIPFileFormat
extends Object

Reads PHYLIP interleaved alignment files and fires events at a PHYLIPFileListener object.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Method Summary

Methods

Modifier and Type	Method and Description
static void	parse(PHYLIPFileListener listener, BufferedReader reader)
static void	parseFile(PHYLIPFileListener listener, File inputFile)
static void	parseInputStream(PHYLIPFileListener listener, InputStream inputStream)
static void	parseReader(PHYLIPFileListener listener, Reader inputReader)
static void	writeFile(File file, Alignment alignment) Writes the given Alignment in PHYLIP format to a file.
static void	writeStream(OutputStream os, Alignment alignment) Writes the given Alignment in PHYLIP format to a stream.
static void	writeWriter(Writer writer, Alignment alignment) Writes the given Alignment in PHYLIP format to a writer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

parseFile

public static void parseFile(PHYLIPFileListener listener,
             File inputFile)
                      throws IOException,
                             ParseException

Throws:

IOException

ParseException

parseInputStream

public static void parseInputStream(PHYLIPFileListener listener,
                    InputStream inputStream)
                             throws IOException,
                                    ParseException

Throws:

IOException

ParseException

parseReader

public static void parseReader(PHYLIPFileListener listener,
               Reader inputReader)
                        throws IOException,
                               ParseException

Throws:

IOException

ParseException

parse

public static void parse(PHYLIPFileListener listener,
         BufferedReader reader)
                  throws IOException,
                         ParseException

Throws:

IOException

ParseException

writeFile

public static void writeFile(File file,
             Alignment alignment)
                      throws IOException

Writes the given Alignment in PHYLIP format to a file.

Parameters:

file - the file to write to.

alignment - the Alignment object to write.

Throws:

IOException - if there is a problem during writing.

writeStream

public static void writeStream(OutputStream os,
               Alignment alignment)
                        throws IOException

Writes the given Alignment in PHYLIP format to a stream.

Parameters:

os - the stream to write to.

alignment - the Alignment object to write.

Throws:

IOException - if there is a problem during writing.

writeWriter

public static void writeWriter(Writer writer,
               Alignment alignment)
                        throws IOException

Writes the given Alignment in PHYLIP format to a writer.

Parameters:

writer - the writer to write to.

alignment - the Alignment object to write.

Throws:

IOException - if there is a problem during writing.