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FlowReact Compound Members

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Here is a list of all class members with links to the class documentation for each member:

- a -

addinstance() : MRnaSeq, StructSeq, Sequence, PhenoType
allS : _F_set
alphabet_size : ZScore

- b -

base : _baum
BatchReactor() : BatchReactor
BiEvalSeq() : BiEvalSeq
BiFitReactor() : BiFitReactor
bInnovation : Reactor
bmf_list : _mol
BonusSeq() : BonusSeq
bulge : _E_set

- c -

c_historyFilename : Reactor
c_inFilename : Reactor
c_lineageFilename : Reactor
c_monitorFilename : Reactor
calcSeqFitness() : BiFitReactor, Reactor
calculate_fit() : BiEvalSeq
calculate_fitness() : MRnaSeq, CodeSeq, PseudoSeq, MRnaSeq, PkSequence, CodeSeq, MinorSeq, EvalSeq, StructSeq, Sequence, BonusSeq
calculateZScore() : ZScore
changeTime : BiFitReactor
checkDoubleOption() : CommandLine
checkFitness() : Reactor
checkIntOption() : CommandLine
checkTextOption() : CommandLine
classes : ZScore
cloIter : CommandLine
cloSet : CommandLine
Coax_const : _E_set
CodeSeq() : CodeSeq
col : _baum
ComOp() : ComOp
CrossReactor() : CrossReactor
currform : _mol

- d -

d_currentDumpTime : Reactor
d_currentLogTime : Reactor
d_currentReactivity : Reactor
d_currentStopTime : Reactor
d_currentTime : Reactor
d_outflow : Reactor
d_sumChannel : Reactor
dangle3 : _E_set
dangle5 : _E_set
dangles : _E_set
deep : _E_set
delRNG() : RandomWell
deng : _baum
distance : Sequence
do_flip : _M_set
do_pk : _M_set
down : _baum

- e -

E1 : _mol
e_info : _mol
elostep : _F_set
elotime : _F_set
energy_set : _E_set
EvalSeq() : EvalSeq

- f -

f_info : _mol
F_ninio : _E_set
Factory() : Factory
father : Postorder_list
fillPhenoDiedOutTable() : ProtReactor, RelReactor, ProtReactor, Reactor
fillPhenoProductionTable() : ProtReactor, StructLifeReactor, RelReactor, ProtReactor, Reactor
fillSeqLineageTable() : Reactor
findClo() : CommandLine
fitness : Sequence
found_target : Reactor

- g -

getCharValue() : ComOp
getCurrentCapacity() : Reactor
getEnergy() : PseudoEval
getFitness() : ProtSeq, Sequence, BonusSeq
getFitnessBonus() : BonusSeq
getInFileName() : Reactor
getName() : ComOp
getNr() : PhenoType
getNumValue() : ComOp
getPackedPhenoType() : PhenoType
getPackedSequence() : Sequence
getPhenoType() : MRnaSeq, StructSeq
getPhenoTypeInnovations() : MRnaSeq, StructSeq
getRandom() : RandomWell, RandomNG, PMMMLCG, mtRandom
getScore() : ScoreMatrix
getSequenceList() : Reactor
getSequences_having_phenotype() : PhenoType
getStatus() : PseudoEval
gettmpSequence() : Reactor
getUnpackedPhenoType() : RNAStructure, PhenoType
getUnpackedSequence() : Sequence

- h -

hairpin : _E_set

- i -

initalize() : Reactor
InsDelReactor() : InsDelReactor
insertSequence() : ProtReactor, StructLifeReactor, RelReactor, ProtReactor, Reactor
instances : Sequence
int_bps : _baum
internal_loop : _E_set
isSet() : RandomWell

- j -

james_rule : _E_set
JumpReactor() : JumpReactor

- k -

keyroots : Tree

- l -

left : mtRandom
leftmostleaf : Postorder_list
len : _mol
list_Sequence : Reactor
listIter : Reactor
logML : _E_set
looptype : _baum
lxc : _E_set

- m -

m_info : _mol
MAX_NINIO : _E_set
mC : _F_set
mfe : StructSeq
MinorReactor() : MinorReactor
MinorSeq() : MinorSeq
mismatchH : _E_set
mismatchI : _E_set
MLbase : _E_set
MLclosing : _E_set
MLintern : _E_set
MRnaSeq() : MRnaSeq
mutate : JumpReactor, InsDelReactor, Reactor
mutation() : NoMutReactor, JumpReactor, InsDelReactor, Reactor
mutWay : MRnaSeq, Sequence
my_mol : PseudoEval
my_set : PseudoEval
myturn : _M_set

- n -

n_capacity : Reactor
n_current_capacity : Reactor
n_currentDumpRepl : Reactor
n_dump : Reactor
n_replications : Reactor
n_sequenceInnovations : Reactor
name : ComOp
nCopies : Sequence
nei_cnt : _mol
nei_list : _mol
nerror() : ZScore
new_ninio : _E_set
next : mtRandom, _baum
next_bp : _baum
nFitness : ProtSeq
nGoUp : PopReactor
nMinorFitParents : MinorReactor
nNr : Sequence, PhenoType
no_closingGU : _M_set
no_dang : _baum
noGU : _M_set
NoMutReactor() : NoMutReactor
noS : _F_set
nPhenoTypeInnovations : StructSeq
nPhenoTypes : StructSeq
nSequences_having_phenotype : PhenoType
nStep : PopReactor
Number : DECODE
nummer : _baum

- o -

oldform : _mol
OneLetter : DECODE
operator()() : hash< const ProtSeq *>, eqProtSeq, eqSeq< const MRnaSeq *>, hash< const MRnaSeq *>, eqSeq< const CodeSeq *>, hash< const CodeSeq *>, hash< const RNAStructure *>, eqRNAStructure, hash< const RNAStructure *>, eqRNAStructure, eqSeq< const PseudoSeq *>, hash< const PseudoSeq *>, hash< const ProtSeq *>, eqProtSeq, eqSeq< const MRnaSeq *>, hash< const MRnaSeq *>, eqSeq< const PkSequence *>, hash< const PkSequence *>, eqSeq< const CodeSeq *>, hash< const CodeSeq *>, hash< const RNAStructure *>, eqRNAStructure, eqint, eqSeq< const MinorSeq *>, hash< const MinorSeq *>, JumpMut, eqSeq< const EvalSeq *>, hash< const EvalSeq *>, eqSeq< const BiEvalSeq *>, hash< const BiEvalSeq *>, eqSeq< const StructSeq *>, hash< const StructSeq *>, eqSeq< const Sequence *>, hash< const Sequence *>, SchnablMut, Recombination, PointMut, PointMutBPMatch, hash< const PhenoType *>, eqPhenoType, InsDelPointMut, InsdelMut, hash< const ComOp *>, eqCO, eqSeq< const BonusSeq *>, hash< const BonusSeq *>
operator<< : ThresholdReactor, MinorReactor, Sequence, Reactor, PhenoType
operator==() : Sequence, PhenoType
outflow() : ProtReactor, RelReactor, ProtReactor, Reactor

- p -

paramFile : ZScore
phenoSeq : PhenoType
PhenoType() : PhenoType
pk_com : _baum
pk_flag : _baum
PKEval : PseudoSeq
PkSequence() : PkSequence
PMMMLCG() : PMMMLCG
pointMut() : Mutation
polyProtCoords : ZScore
polyProtSurf : ZScore
PopReactor() : PopReactor
postorder_list : Tree
ppLenght : ZScore
ppLists : ZScore
prev : _baum
prev_bp : _baum
pRNA_sequence : Sequence
ProtReactor() : ProtReactor
ProtSeq() : ProtSeq
protSeqIter : MRnaSeq
protSeqSet : MRnaSeq
pS : _F_set
pSecStructure : StructSeq
pSeq : PseudoEval
PseudoEval() : PseudoEval
PseudoReactor() : PseudoReactor
PseudoSeq() : PseudoSeq
pTarget : Reactor
pTarget2 : BiFitReactor
pVal : ComOp

- r -

ReacFactory() : ReacFactory
reactNr : Reactor
Reactor() : Reactor
readInitalPopulation() : ProtReactor, StepReactor, StartReactor, ProtReactor, Reactor
readPDB() : ZScore
readPolyProt() : ZScore
readPotentials() : ZScore
readTarget() : BiFitReactor, Reactor
registerSetting() : CommandLine
reloadMT() : mtRandom
RelReactor() : RelReactor
removeinstance() : MRnaSeq, StructSeq, Sequence, PhenoType
replication() : ReacFactory, MinorReactor, CrossReactor, Reactor
revalue() : Factory
RNAStructure() : RNAStructure
rng : RandomWell
round : _mol
rseed : PMMMLCG
rwell : Reactor, Mutation

- s -

scoreMatrix() : MRnaSeq
ScoreMatrix() : ScoreMatrix
seed() : RandomWell, RandomNG, PMMMLCG, mtRandom
seq : _mol
seqIter : Reactor
seqSet : Reactor
Sequence() : Sequence
setBonus() : Reactor
setCurrentCapacity() : Reactor
setFitness() : ProtSeq
setFitnessBonus() : BonusSeq
setNr() : PhenoType
setPhenoPointer() : RNAStructure, PhenoType
setRNG() : RandomWell
setup() : ProtReactor, StructLifeReactor, PseudoReactor, PseudoEval, ProtReactor, Reactor
setValue() : ComOp
shallow : _E_set
sign : swString
Sint2 : _E_set
smn : _F_set
smt : _F_set
sons : Postorder_list
SP : ZScore
stack : _E_set
stack_bulge : _E_set
starT : _F_set
startE : _F_set
startform : _mol
startlen : _F_set
StartReactor() : StartReactor
state : mtRandom
status : PseudoEval
step() : StructLifeReactor, StepReactor, StartReactor, RelReactor, PopReactor, NoMutReactor, ReacFactory, Factory, BatchReactor, Reactor
StepReactor() : StepReactor
stoP : _F_set
stopE : _F_set
stopform : _mol
struc : _mol
structIter : StructSeq
StructLifeReactor() : StructLifeReactor
StructSeq() : StructSeq
structSet : StructSeq
surface_classes : ZScore
surfaceParameter : ZScore

- t -

targetCoords : ZScore
targetProtLenght : ZScore
targetSurf : ZScore
temp : PMMMLCG
temperature : _mol
tessPolyProt() : ZScore
tessTarget() : ZScore
TETRA_ENERGY : _E_set
tetra_loop : _E_set
Tetraloops : _E_set
ThreeLetter : DECODE
ThresholdReactor() : ThresholdReactor
timeSeed() : RandomWell, RandomNG, PMMMLCG, mtRandom
tList : ZScore
tmpSequence : Reactor
TR : ZScore
TropZScore : MRnaSeq
type : swString, Postorder_list

- u -

up : _baum

- v -

value : ComOp
vroot : _mol

- w -

weight : swString, Postorder_list
writeDump() : Reactor
writeMonitor() : ThresholdReactor, MinorReactor, Reactor
writeMonitorHeader() : Reactor
writePhenoTypes() : ProtReactor, RelReactor, ProtReactor
writeSequences() : ProtReactor, RelReactor, ProtReactor, Reactor

- z -

Zeit : _mol
ZScore() : ZScore

- ~ -

~ComOp() : ComOp
~Factory() : Factory
~PhenoType() : PhenoType
~PseudoEval() : PseudoEval
~Reactor() : Reactor
~ScoreMatrix() : ScoreMatrix
~Sequence() : Sequence
~ZScore() : ZScore

Generated at Wed May 9 14:01:08 2001 for FlowReact by