BiobaseInfernal-0.7.0.1: Infernal data structures and tools

Index

AC2CMBiobase.SElab.CM
ACCBiobase.SElab.Types
accBiobase.SElab.HMM
AccessionBiobase.SElab.Types
accession 
1 (Function)Biobase.SElab.Taxonomy
2 (Function)Biobase.SElab.CM
alignMapBiobase.SElab.HMM
alphBiobase.SElab.HMM
AlphabetBiobase.SElab.HMM
AminoBiobase.SElab.HMM
BBiobase.SElab.CM
BEGLBiobase.SElab.CM
BEGRBiobase.SElab.CM
BIFBiobase.SElab.CM
BitScore 
1 (Type/Class)Biobase.SElab.Types
2 (Data Constructor)Biobase.SElab.Types
ClanBiobase.SElab.Types
Classification 
1 (Type/Class)Biobase.SElab.Types
2 (Data Constructor)Biobase.SElab.Types
classificationBiobase.SElab.Taxonomy
CM 
1 (Type/Class)Biobase.SElab.CM
2 (Data Constructor)Biobase.SElab.CM
CMVersionBiobase.SElab.CM
CoinsBiobase.SElab.HMM
compoBiobase.SElab.HMM
compoLineBiobase.SElab.HMM.Import
csBiobase.SElab.HMM
CustomBiobase.SElab.HMM
DBiobase.SElab.CM
dateBiobase.SElab.HMM
descriptionBiobase.SElab.HMM
DiceBiobase.SElab.HMM
DNABiobase.SElab.HMM
EBiobase.SElab.CM
ELBiobase.SElab.CM
EmitNothingBiobase.SElab.CM
EmitsBiobase.SElab.CM
emitsBiobase.SElab.CM
EmitsPairBiobase.SElab.CM
EmitsSingleBiobase.SElab.CM
ENDBiobase.SElab.CM
finishedHeaderBiobase.SElab.CM.Import
fromFile 
1 (Function)Biobase.SElab.RfamNames.Import
2 (Function)Biobase.SElab.Taxonomy.Import
3 (Function)Biobase.SElab.CM.Import
gatheringBiobase.SElab.CM
headerLinesBiobase.SElab.HMM.Import
headerMapBiobase.SElab.HMM.Import
HMMBiobase.SElab.HMM
hmmBiobase.SElab.CM
HMM3 
1 (Type/Class)Biobase.SElab.HMM
2 (Data Constructor)Biobase.SElab.HMM
ID2CMBiobase.SElab.CM
IDDBiobase.SElab.Types
iddBiobase.SElab.HMM
IdentificationBiobase.SElab.Types
ILBiobase.SElab.CM
illegalStateBiobase.SElab.CM
Infernal10Biobase.SElab.CM
Infernal11Biobase.SElab.CM
insertEBiobase.SElab.HMM
IRBiobase.SElab.CM
isNodeBiobase.SElab.CM.Import
legalHMMBiobase.SElab.HMM.Import
lengBiobase.SElab.HMM
lineParserBiobase.SElab.CM.Import
localBeginBiobase.SElab.CM
localEndBiobase.SElab.CM
makeLocalBiobase.SElab.CM
makeLocalBeginBiobase.SElab.CM
makeLocalEndBiobase.SElab.CM
mapAcRfamNamesBiobase.SElab.RfamNames.Import
mapAcTaxonomyBiobase.SElab.Taxonomy.Import
mapIdRfamNamesBiobase.SElab.RfamNames.Import
mapIdTaxonomyBiobase.SElab.Taxonomy.Import
matchEBiobase.SElab.HMM
MATLBiobase.SElab.CM
MATPBiobase.SElab.CM
MATRBiobase.SElab.CM
mkRfamNameBiobase.SElab.RfamNames.Import
mkTaxonomyBiobase.SElab.Taxonomy.Import
MLBiobase.SElab.CM
modelACBiobase.SElab.RfamNames
modelIDBiobase.SElab.RfamNames
ModelNames 
1 (Type/Class)Biobase.SElab.RfamNames
2 (Data Constructor)Biobase.SElab.RfamNames
MPBiobase.SElab.CM
MRBiobase.SElab.CM
name 
1 (Function)Biobase.SElab.Taxonomy
2 (Function)Biobase.SElab.CM
NegLogProbBiobase.SElab.HMM
nidBiobase.SElab.HMM
NLPBiobase.SElab.HMM
Node 
1 (Type/Class)Biobase.SElab.HMM
2 (Data Constructor)Biobase.SElab.HMM
NodeID 
1 (Type/Class)Biobase.SElab.CM
2 (Data Constructor)Biobase.SElab.CM
nodeIDBiobase.SElab.CM
nodes 
1 (Function)Biobase.SElab.HMM
2 (Function)Biobase.SElab.CM
NodeTypeBiobase.SElab.CM
nodeTypeBiobase.SElab.CM
noiseCutoffBiobase.SElab.CM
nullModelBiobase.SElab.CM
pairBiobase.SElab.CM
parse 
1 (Function)Biobase.SElab.RfamNames.Import
2 (Function)Biobase.SElab.Taxonomy.Import
parseBeginBiobase.SElab.HMM.Import
parseCM1xBiobase.SElab.CM.Import
parseHeaderBiobase.SElab.CM.Import
parseHeadersBiobase.SElab.CM.Import
parseHMM3Biobase.SElab.HMM.Import
parseNodes 
1 (Function)Biobase.SElab.HMM.Import
2 (Function)Biobase.SElab.CM.Import
parseStateBiobase.SElab.CM.Import
parseStatesBiobase.SElab.CM.Import
PfamBiobase.SElab.Types
prob2ScoreBiobase.SElab.Types
readAccessionBiobase.SElab.CM.Import
readAlphBiobase.SElab.HMM.Import
readBitScoreBiobase.SElab.CM.Import
readBooleanBiobase.SElab.HMM.Import
readBS 
1 (Function)Biobase.SElab.HMM.Import
2 (Function)Biobase.SElab.CM.Import
readNLPBiobase.SElab.HMM.Import
rfBiobase.SElab.HMM
RfamBiobase.SElab.Types
RNABiobase.SElab.HMM
ROOTBiobase.SElab.CM
SBiobase.SElab.CM
sathLinesBiobase.SElab.HMM.Import
score2ProbBiobase.SElab.Types
shortenNameBiobase.SElab.Taxonomy
singleBiobase.SElab.CM
SpeciesBiobase.SElab.Types
speciesACBiobase.SElab.RfamNames
speciesIDBiobase.SElab.RfamNames
State 
1 (Type/Class)Biobase.SElab.CM
2 (Data Constructor)Biobase.SElab.CM
StateID 
1 (Type/Class)Biobase.SElab.CM
2 (Data Constructor)Biobase.SElab.CM
stateIDBiobase.SElab.CM
statesBiobase.SElab.CM
StateTypeBiobase.SElab.CM
stateTypeBiobase.SElab.CM
symAlphBiobase.SElab.HMM
Taxonomy 
1 (Type/Class)Biobase.SElab.Taxonomy
2 (Data Constructor)Biobase.SElab.Taxonomy
test 
1 (Function)Biobase.SElab.HMM.Import
2 (Function)Biobase.SElab.CM.Import
transBiobase.SElab.HMM
transHeadersBiobase.SElab.HMM
transitionsBiobase.SElab.CM
trustedCutoffBiobase.SElab.CM
unACCBiobase.SElab.Types
unBitScoreBiobase.SElab.Types
unClassificationBiobase.SElab.Types
unIDDBiobase.SElab.Types
unNodeIDBiobase.SElab.CM
unsortedBiobase.SElab.CM
unStateIDBiobase.SElab.CM
version 
1 (Function)Biobase.SElab.HMM
2 (Function)Biobase.SElab.CM
_accBiobase.SElab.HMM
_accession 
1 (Function)Biobase.SElab.Taxonomy
2 (Function)Biobase.SElab.CM
_alignMapBiobase.SElab.HMM
_alphBiobase.SElab.HMM
_classificationBiobase.SElab.Taxonomy
_compoBiobase.SElab.HMM
_csBiobase.SElab.HMM
_dateBiobase.SElab.HMM
_descriptionBiobase.SElab.HMM
_emitsBiobase.SElab.CM
_gatheringBiobase.SElab.CM
_hmmBiobase.SElab.CM
_iddBiobase.SElab.HMM
_insertEBiobase.SElab.HMM
_lengBiobase.SElab.HMM
_localBeginBiobase.SElab.CM
_localEndBiobase.SElab.CM
_matchEBiobase.SElab.HMM
_modelACBiobase.SElab.RfamNames
_modelIDBiobase.SElab.RfamNames
_name 
1 (Function)Biobase.SElab.Taxonomy
2 (Function)Biobase.SElab.CM
_nidBiobase.SElab.HMM
_nodeIDBiobase.SElab.CM
_nodes 
1 (Function)Biobase.SElab.HMM
2 (Function)Biobase.SElab.CM
_nodeTypeBiobase.SElab.CM
_noiseCutoffBiobase.SElab.CM
_nullModelBiobase.SElab.CM
_pairBiobase.SElab.CM
_rfBiobase.SElab.HMM
_singleBiobase.SElab.CM
_speciesACBiobase.SElab.RfamNames
_speciesIDBiobase.SElab.RfamNames
_stateIDBiobase.SElab.CM
_statesBiobase.SElab.CM
_stateTypeBiobase.SElab.CM
_symAlphBiobase.SElab.HMM
_transBiobase.SElab.HMM
_transHeadersBiobase.SElab.HMM
_transitionsBiobase.SElab.CM
_trustedCutoffBiobase.SElab.CM
_unsortedBiobase.SElab.CM
_version 
1 (Function)Biobase.SElab.HMM
2 (Function)Biobase.SElab.CM