Class FastaParser


  • public class FastaParser
    extends java.lang.Object
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.util.regex.Pattern FASTA_DESC_LINE  
    • Constructor Summary

      Constructors 
      Constructor Description
      FastaParser()  
    • Field Detail

      • FASTA_DESC_LINE

        public static final java.util.regex.Pattern FASTA_DESC_LINE
    • Constructor Detail

      • FastaParser

        public FastaParser()
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
      • isLikelyFasta

        public static boolean isLikelyFasta​(java.io.File f)
                                     throws java.io.IOException
        Throws:
        java.io.IOException
      • isLikelyFasta

        public static boolean isLikelyFasta​(java.io.InputStream is)
                                     throws java.io.IOException
        Throws:
        java.io.IOException
      • parseMsa

        public static Msa parseMsa​(java.io.File f)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • parseMsa

        public static Msa parseMsa​(java.io.InputStream is)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • parseMsa

        public static Msa parseMsa​(java.lang.String s)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • parseMsa

        public static Msa parseMsa​(byte[] bytes)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • parse

        public static java.util.List<MolecularSequence> parse​(java.io.File f)
                                                       throws java.io.IOException
        Throws:
        java.io.IOException
      • parse

        public static java.util.List<MolecularSequence> parse​(java.io.InputStream is)
                                                       throws java.io.IOException
        Throws:
        java.io.IOException