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 Details

  • Method Details

    • 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.