public class HmmerProfileParser
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
protected Alphabet |
alph |
protected java.lang.String |
domain1 |
protected org.biojava.bio.program.hmmer.HmmerProfileParser.HmmerModel |
hmm |
Modifier | Constructor and Description |
---|---|
protected |
HmmerProfileParser(java.lang.String domain) |
Modifier and Type | Method and Description |
---|---|
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() |
protected Alphabet alph
protected java.lang.String domain1
protected org.biojava.bio.program.hmmer.HmmerProfileParser.HmmerModel hmm
public static HmmerProfileHMM parse(java.io.File inputfile)
inputfile
- the file which contains the Profile HMM data, as output by HMMER - e.g. HMM_lspublic static FullHmmerProfileHMM parseFull(java.io.File inputfile)
inputfile
- the file which contains the Profile HMM data, as output by HMMER - e.g. HMM_lsprotected HmmerProfileHMM initialiseProfileHMM(int len)
public HmmerProfileHMM getModel()
public void setProfileHMM()
public void parseModel(java.io.File inputFile)