org.biojava.bio.program.hmmer

Class HmmerProfileParser

java.lang.Object

org.biojava.bio.program.hmmer.HmmerProfileParser

public class HmmerProfileParser
extends 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

Fields

Modifier and Type	Field and Description
protected Alphabet	alph
protected String	domain1
protected org.biojava.bio.program.hmmer.HmmerProfileParser.HmmerModel	hmm

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	HmmerProfileParser(String domain)

Method Summary

Modifier and Type	Method and Description
HmmerProfileHMM	getModel()
protected HmmerProfileHMM	initialiseProfileHMM(int len)
static HmmerProfileHMM	parse(File inputfile) Returns a profile HMM representing the core HMMER hmm
static FullHmmerProfileHMM	parseFull(File inputfile) Returns the full markov model - including the core model + J,C,N loop states.
void	parseModel(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 String domain1

hmm

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

Constructor Detail

HmmerProfileParser

protected HmmerProfileParser(String domain)

Method Detail

parse

public static HmmerProfileHMM parse(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(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(File inputFile)