## 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
`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.