Contents
Index
BiobaseInfernal-0.7.0.1: Infernal data structures and tools
Index
AC2CM
Biobase.SElab.CM
ACC
Biobase.SElab.Types
acc
Biobase.SElab.HMM
Accession
Biobase.SElab.Types
accession
1 (Function)
Biobase.SElab.Taxonomy
2 (Function)
Biobase.SElab.CM
alignMap
Biobase.SElab.HMM
alph
Biobase.SElab.HMM
Alphabet
Biobase.SElab.HMM
Amino
Biobase.SElab.HMM
B
Biobase.SElab.CM
BEGL
Biobase.SElab.CM
BEGR
Biobase.SElab.CM
BIF
Biobase.SElab.CM
BitScore
1 (Type/Class)
Biobase.SElab.Types
2 (Data Constructor)
Biobase.SElab.Types
Clan
Biobase.SElab.Types
Classification
1 (Type/Class)
Biobase.SElab.Types
2 (Data Constructor)
Biobase.SElab.Types
classification
Biobase.SElab.Taxonomy
CM
1 (Type/Class)
Biobase.SElab.CM
2 (Data Constructor)
Biobase.SElab.CM
CMVersion
Biobase.SElab.CM
Coins
Biobase.SElab.HMM
compo
Biobase.SElab.HMM
compoLine
Biobase.SElab.HMM.Import
cs
Biobase.SElab.HMM
Custom
Biobase.SElab.HMM
D
Biobase.SElab.CM
date
Biobase.SElab.HMM
description
Biobase.SElab.HMM
Dice
Biobase.SElab.HMM
DNA
Biobase.SElab.HMM
E
Biobase.SElab.CM
EL
Biobase.SElab.CM
EmitNothing
Biobase.SElab.CM
Emits
Biobase.SElab.CM
emits
Biobase.SElab.CM
EmitsPair
Biobase.SElab.CM
EmitsSingle
Biobase.SElab.CM
END
Biobase.SElab.CM
finishedHeader
Biobase.SElab.CM.Import
fromFile
1 (Function)
Biobase.SElab.RfamNames.Import
2 (Function)
Biobase.SElab.Taxonomy.Import
3 (Function)
Biobase.SElab.CM.Import
gathering
Biobase.SElab.CM
headerLines
Biobase.SElab.HMM.Import
headerMap
Biobase.SElab.HMM.Import
HMM
Biobase.SElab.HMM
hmm
Biobase.SElab.CM
HMM3
1 (Type/Class)
Biobase.SElab.HMM
2 (Data Constructor)
Biobase.SElab.HMM
ID2CM
Biobase.SElab.CM
IDD
Biobase.SElab.Types
idd
Biobase.SElab.HMM
Identification
Biobase.SElab.Types
IL
Biobase.SElab.CM
illegalState
Biobase.SElab.CM
Infernal10
Biobase.SElab.CM
Infernal11
Biobase.SElab.CM
insertE
Biobase.SElab.HMM
IR
Biobase.SElab.CM
isNode
Biobase.SElab.CM.Import
legalHMM
Biobase.SElab.HMM.Import
leng
Biobase.SElab.HMM
lineParser
Biobase.SElab.CM.Import
localBegin
Biobase.SElab.CM
localEnd
Biobase.SElab.CM
makeLocal
Biobase.SElab.CM
makeLocalBegin
Biobase.SElab.CM
makeLocalEnd
Biobase.SElab.CM
mapAcRfamNames
Biobase.SElab.RfamNames.Import
mapAcTaxonomy
Biobase.SElab.Taxonomy.Import
mapIdRfamNames
Biobase.SElab.RfamNames.Import
mapIdTaxonomy
Biobase.SElab.Taxonomy.Import
matchE
Biobase.SElab.HMM
MATL
Biobase.SElab.CM
MATP
Biobase.SElab.CM
MATR
Biobase.SElab.CM
mkRfamName
Biobase.SElab.RfamNames.Import
mkTaxonomy
Biobase.SElab.Taxonomy.Import
ML
Biobase.SElab.CM
modelAC
Biobase.SElab.RfamNames
modelID
Biobase.SElab.RfamNames
ModelNames
1 (Type/Class)
Biobase.SElab.RfamNames
2 (Data Constructor)
Biobase.SElab.RfamNames
MP
Biobase.SElab.CM
MR
Biobase.SElab.CM
name
1 (Function)
Biobase.SElab.Taxonomy
2 (Function)
Biobase.SElab.CM
NegLogProb
Biobase.SElab.HMM
nid
Biobase.SElab.HMM
NLP
Biobase.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
nodeID
Biobase.SElab.CM
nodes
1 (Function)
Biobase.SElab.HMM
2 (Function)
Biobase.SElab.CM
NodeType
Biobase.SElab.CM
nodeType
Biobase.SElab.CM
noiseCutoff
Biobase.SElab.CM
nullModel
Biobase.SElab.CM
pair
Biobase.SElab.CM
parse
1 (Function)
Biobase.SElab.RfamNames.Import
2 (Function)
Biobase.SElab.Taxonomy.Import
parseBegin
Biobase.SElab.HMM.Import
parseCM1x
Biobase.SElab.CM.Import
parseHeader
Biobase.SElab.CM.Import
parseHeaders
Biobase.SElab.CM.Import
parseHMM3
Biobase.SElab.HMM.Import
parseNodes
1 (Function)
Biobase.SElab.HMM.Import
2 (Function)
Biobase.SElab.CM.Import
parseState
Biobase.SElab.CM.Import
parseStates
Biobase.SElab.CM.Import
Pfam
Biobase.SElab.Types
prob2Score
Biobase.SElab.Types
readAccession
Biobase.SElab.CM.Import
readAlph
Biobase.SElab.HMM.Import
readBitScore
Biobase.SElab.CM.Import
readBoolean
Biobase.SElab.HMM.Import
readBS
1 (Function)
Biobase.SElab.HMM.Import
2 (Function)
Biobase.SElab.CM.Import
readNLP
Biobase.SElab.HMM.Import
rf
Biobase.SElab.HMM
Rfam
Biobase.SElab.Types
RNA
Biobase.SElab.HMM
ROOT
Biobase.SElab.CM
S
Biobase.SElab.CM
sathLines
Biobase.SElab.HMM.Import
score2Prob
Biobase.SElab.Types
shortenName
Biobase.SElab.Taxonomy
single
Biobase.SElab.CM
Species
Biobase.SElab.Types
speciesAC
Biobase.SElab.RfamNames
speciesID
Biobase.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
stateID
Biobase.SElab.CM
states
Biobase.SElab.CM
StateType
Biobase.SElab.CM
stateType
Biobase.SElab.CM
symAlph
Biobase.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
trans
Biobase.SElab.HMM
transHeaders
Biobase.SElab.HMM
transitions
Biobase.SElab.CM
trustedCutoff
Biobase.SElab.CM
unACC
Biobase.SElab.Types
unBitScore
Biobase.SElab.Types
unClassification
Biobase.SElab.Types
unIDD
Biobase.SElab.Types
unNodeID
Biobase.SElab.CM
unsorted
Biobase.SElab.CM
unStateID
Biobase.SElab.CM
version
1 (Function)
Biobase.SElab.HMM
2 (Function)
Biobase.SElab.CM
_acc
Biobase.SElab.HMM
_accession
1 (Function)
Biobase.SElab.Taxonomy
2 (Function)
Biobase.SElab.CM
_alignMap
Biobase.SElab.HMM
_alph
Biobase.SElab.HMM
_classification
Biobase.SElab.Taxonomy
_compo
Biobase.SElab.HMM
_cs
Biobase.SElab.HMM
_date
Biobase.SElab.HMM
_description
Biobase.SElab.HMM
_emits
Biobase.SElab.CM
_gathering
Biobase.SElab.CM
_hmm
Biobase.SElab.CM
_idd
Biobase.SElab.HMM
_insertE
Biobase.SElab.HMM
_leng
Biobase.SElab.HMM
_localBegin
Biobase.SElab.CM
_localEnd
Biobase.SElab.CM
_matchE
Biobase.SElab.HMM
_modelAC
Biobase.SElab.RfamNames
_modelID
Biobase.SElab.RfamNames
_name
1 (Function)
Biobase.SElab.Taxonomy
2 (Function)
Biobase.SElab.CM
_nid
Biobase.SElab.HMM
_nodeID
Biobase.SElab.CM
_nodes
1 (Function)
Biobase.SElab.HMM
2 (Function)
Biobase.SElab.CM
_nodeType
Biobase.SElab.CM
_noiseCutoff
Biobase.SElab.CM
_nullModel
Biobase.SElab.CM
_pair
Biobase.SElab.CM
_rf
Biobase.SElab.HMM
_single
Biobase.SElab.CM
_speciesAC
Biobase.SElab.RfamNames
_speciesID
Biobase.SElab.RfamNames
_stateID
Biobase.SElab.CM
_states
Biobase.SElab.CM
_stateType
Biobase.SElab.CM
_symAlph
Biobase.SElab.HMM
_trans
Biobase.SElab.HMM
_transHeaders
Biobase.SElab.HMM
_transitions
Biobase.SElab.CM
_trustedCutoff
Biobase.SElab.CM
_unsorted
Biobase.SElab.CM
_version
1 (Function)
Biobase.SElab.HMM
2 (Function)
Biobase.SElab.CM