Package org.biojava.bio.program.hmmer
Class HmmerProfileParser
java.lang.Object
org.biojava.bio.program.hmmer.HmmerProfileParser
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
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetModel()
protected HmmerProfileHMM
initialiseProfileHMM
(int len) static HmmerProfileHMM
Returns a profile HMM representing the core HMMER hmmstatic FullHmmerProfileHMM
Returns the full markov model - including the core model + J,C,N loop states.void
parseModel
(File inputFile) void
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Field Details
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alph
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domain1
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hmm
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Constructor Details
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HmmerProfileParser
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Method Details
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parse
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
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parseFull
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
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initialiseProfileHMM
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getModel
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setProfileHMM
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parseModel
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