Class HmmerProfileParser


  • public class HmmerProfileParser
    extends java.lang.Object
    A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training note that this class is still currently experimental.
    Author:
    Lachlan Coin
    • Field Detail

      • domain1

        protected java.lang.String domain1
      • hmm

        protected org.biojava.bio.program.hmmer.HmmerProfileParser.HmmerModel hmm
    • Method Detail

      • parse

        public static HmmerProfileHMM parse​(java.io.File inputfile)
        Returns a profile HMM representing the core HMMER hmm
        Parameters:
        inputfile - the file which contains the Profile HMM data, as output by HMMER - e.g. HMM_ls
      • parseFull

        public static FullHmmerProfileHMM parseFull​(java.io.File inputfile)
        Returns the full markov model - including the core model + J,C,N loop states.
        Parameters:
        inputfile - the file which contains the Profile HMM data, as output by HMMER - e.g. HMM_ls
      • parseModel

        public void parseModel​(java.io.File inputFile)