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MSFAlignmentFormat (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.bio.seq.io.MSFAlignmentFormat
  • All Implemented Interfaces:
    AlignmentFormat
    public class MSFAlignmentFormat
extends Object
implements AlignmentFormat
    Author:
    raemig, Thomas Down, Keith James, Nimesh Singh, Mark Schreiber, Matthew Pocock, Bradford Powell

    • Constructor Summary

      Constructors 
      Constructor Description
      MSFAlignmentFormat()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static void main​(String[] args)

      used to quick test the code
      Alignment read​(BufferedReader reader)

      Reads an MSF Alignment File
      void write​(OutputStream os, Alignment align, int fileType)  
      void writeDna​(OutputStream os, Alignment align)  
      void writeProtein​(OutputStream os, Alignment align)  

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • MSFAlignmentFormat

        public MSFAlignmentFormat()

    • Method Detail

      • main

        public static void main​(String[] args)

        used to quick test the code

        Parameters:
        args -

      • read

        public Alignment read​(BufferedReader reader)

        Reads an MSF Alignment File

        Specified by:
        read in interface AlignmentFormat
        Parameters:
        reader - The file reader
        Returns:
        Alignment A SimpleAlignment consisting of the sequences in the file.

      • write

        public void write​(OutputStream os,
                  Alignment align,
                  int fileType)
           throws BioException,
                  IllegalSymbolException
        Throws:
        BioException
        IllegalSymbolException

      • writeDna

        public void writeDna​(OutputStream os,
                     Alignment align)
              throws BioException,
                     IllegalSymbolException
        Throws:
        BioException
        IllegalSymbolException

      • writeProtein

        public void writeProtein​(OutputStream os,
                         Alignment align)
                  throws BioException,
                         IllegalSymbolException
        Throws:
        BioException
        IllegalSymbolException