Package org.biojavax.bio.phylo.io.nexus

Class NexusFileFormat

java.lang.Object

org.biojavax.bio.phylo.io.nexus.NexusFileFormat

public class NexusFileFormat
extends Object

Reads/writes Nexus files and fires events at a NexusFileListener object. Blocks are parsed using NexusBlockParser objects provided at runtime. Each of those objects should probably have a NexusBlockListener object associated with them that receives events generated from the processed data in the block.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Field Summary

Fields

Modifier and Type	Field	Description
static String	NEW_LINE	New-line symbol.

Method Summary

Modifier and Type	Method	Description
static void	parseFile(NexusFileListener listener, File inputFile)	Parse a file and send events to the given listener.
static void	parseInputStream(NexusFileListener listener, InputStream inputStream)	Parse a stream and send events to the given listener.
static void	parseReader(NexusFileListener listener, Reader inputReader)	Parse a reader and send events to the given listener.
static void	writeFile(File file, NexusFile nexusFile)	Writes the given Nexus output to a file.
static void	writeStream(OutputStream os, NexusFile nexusFile)	Writes the given Nexus output to a stream.
static void	writeWriter(Writer writer, NexusFile nexusFile)	Writes the given Nexus output to a writer.

Methods inherited from class java.lang.Object

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

Field Detail

NEW_LINE

public static final String NEW_LINE

New-line symbol.

Method Detail

parseFile

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

Parse a file and send events to the given listener.

Parameters:

listener - the listener that will receive events.

inputFile - the file to parse.

Throws:

IOException - if anything goes wrong with reading the file.

ParseException - if the file format is incorrect.

parseInputStream

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

Parse a stream and send events to the given listener.

Parameters:

listener - the listener that will receive events.

inputStream - the stream to parse.

Throws:

IOException - if anything goes wrong with reading the stream.

ParseException - if the stream format is incorrect.

parseReader

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

Parse a reader and send events to the given listener.

Parameters:

listener - the listener that will receive events.

inputReader - the file to parse.

Throws:

IOException - if anything goes wrong with reading the reader.

ParseException - if the reader format is incorrect.

writeFile

public static void writeFile(File file,
                             NexusFile nexusFile)
                      throws IOException

Writes the given Nexus output to a file.

Parameters:

file - the file to write to.

nexusFile - the Nexus output to write.

Throws:

IOException - if there is a problem during writing.

writeStream

public static void writeStream(OutputStream os,
                               NexusFile nexusFile)
                        throws IOException

Writes the given Nexus output to a stream.

Parameters:

os - the stream to write to.

nexusFile - the Nexus output to write.

Throws:

IOException - if there is a problem during writing.

writeWriter

public static void writeWriter(Writer writer,
                               NexusFile nexusFile)
                        throws IOException

Writes the given Nexus output to a writer.

Parameters:

writer - the writer to write to.

nexusFile - the Nexus output to write.

Throws:

IOException - if there is a problem during writing.