org.biojava.bio.program.hmmer
Class HmmerProfileParser
java.lang.Object
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
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
alph
protected Alphabet alph
domain1
protected java.lang.String domain1
hmm
protected org.biojava.bio.program.hmmer.HmmerProfileParser.HmmerModel hmm
HmmerProfileParser
protected HmmerProfileParser(java.lang.String domain)
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)