org.biojava.bio.program.hmmer
Class HmmerProfileParser

java.lang.Object
  extended by org.biojava.bio.program.hmmer.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 Summary
protected  Alphabet alph
           
protected  java.lang.String domain1
           
protected  org.biojava.bio.program.hmmer.HmmerProfileParser.HmmerModel hmm
           
 
Constructor Summary
protected HmmerProfileParser(java.lang.String domain)
           
 
Method Summary
 HmmerProfileHMM getModel()
           
protected  HmmerProfileHMM initialiseProfileHMM(int len)
           
static HmmerProfileHMM parse(java.io.File inputfile)
          Returns a profile HMM representing the core HMMER hmm
static FullHmmerProfileHMM parseFull(java.io.File inputfile)
          Returns the full markov model - including the core model + J,C,N loop states.
 void parseModel(java.io.File inputFile)
           
 void setProfileHMM()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

alph

protected Alphabet alph

domain1

protected java.lang.String domain1

hmm

protected org.biojava.bio.program.hmmer.HmmerProfileParser.HmmerModel hmm
Constructor Detail

HmmerProfileParser

protected HmmerProfileParser(java.lang.String domain)
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

initialiseProfileHMM

protected HmmerProfileHMM initialiseProfileHMM(int len)

getModel

public HmmerProfileHMM getModel()

setProfileHMM

public void setProfileHMM()

parseModel

public void parseModel(java.io.File inputFile)