Class FastaAlignmentFormat

  • All Implemented Interfaces:
    AlignmentFormat

    public class FastaAlignmentFormat
    extends java.lang.Object
    implements AlignmentFormat
    This class implements the AlignmentFormat interface to read FASTA alignments. It is modeled after the MSFAlignmentFormat class.
    Author:
    Nimesh Singh
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static int DNA  
      static int PROTEIN  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Alignment read​(java.io.BufferedReader br)
      Reads an alignment in FASTA format.
      void write​(java.io.OutputStream os, Alignment align, int fileType)
      Writes out the alignment to an FASTA file.
      void writeDna​(java.io.OutputStream os, Alignment align)  
      void writeProtein​(java.io.OutputStream os, Alignment align)  
      • Methods inherited from class java.lang.Object

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