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

Class NexusFileFormat

  • public class NexusFileFormat
extends java.lang.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 java.lang.String NEW_LINE
      New-line symbol.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void parseFile​(NexusFileListener listener, java.io.File inputFile)
      Parse a file and send events to the given listener.
      static void parseInputStream​(NexusFileListener listener, java.io.InputStream inputStream)
      Parse a stream and send events to the given listener.
      static void parseReader​(NexusFileListener listener, java.io.Reader inputReader)
      Parse a reader and send events to the given listener.
      static void writeFile​(java.io.File file, NexusFile nexusFile)
      Writes the given Nexus output to a file.
      static void writeStream​(java.io.OutputStream os, NexusFile nexusFile)
      Writes the given Nexus output to a stream.
      static void writeWriter​(java.io.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 java.lang.String NEW_LINE
        New-line symbol.

    • Method Detail

      • parseFile

        public static void parseFile​(NexusFileListener listener,
                             java.io.File inputFile)
                      throws java.io.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:
        java.io.IOException - if anything goes wrong with reading the file.
        ParseException - if the file format is incorrect.

      • parseInputStream

        public static void parseInputStream​(NexusFileListener listener,
                                    java.io.InputStream inputStream)
                             throws java.io.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:
        java.io.IOException - if anything goes wrong with reading the stream.
        ParseException - if the stream format is incorrect.

      • parseReader

        public static void parseReader​(NexusFileListener listener,
                               java.io.Reader inputReader)
                        throws java.io.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:
        java.io.IOException - if anything goes wrong with reading the reader.
        ParseException - if the reader format is incorrect.

      • writeFile

        public static void writeFile​(java.io.File file,
                             NexusFile nexusFile)
                      throws java.io.IOException
        Writes the given Nexus output to a file.
        Parameters:
        file - the file to write to.
        nexusFile - the Nexus output to write.
        Throws:
        java.io.IOException - if there is a problem during writing.

      • writeStream

        public static void writeStream​(java.io.OutputStream os,
                               NexusFile nexusFile)
                        throws java.io.IOException
        Writes the given Nexus output to a stream.
        Parameters:
        os - the stream to write to.
        nexusFile - the Nexus output to write.
        Throws:
        java.io.IOException - if there is a problem during writing.

      • writeWriter

        public static void writeWriter​(java.io.Writer writer,
                               NexusFile nexusFile)
                        throws java.io.IOException
        Writes the given Nexus output to a writer.
        Parameters:
        writer - the writer to write to.
        nexusFile - the Nexus output to write.
        Throws:
        java.io.IOException - if there is a problem during writing.