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

java.lang.Object
  extended by 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
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.