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

java.lang.Object
  extended by 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
static String NEW_LINE
          New-line symbol.
 
Method Summary
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.


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