Modifier and Type | Method and Description |
---|---|
static double |
Helper.computesNaEquivalent(Environment environment)
computes a sodium equivalent concentration from the different ion concentrations of the Environment object.
|
Modifier and Type | Field and Description |
---|---|
protected Environment |
ApproximativeMode.environment
environment containing the sequences, ion and agent concentrations and the options (default options and
options entered by the user)
|
Modifier and Type | Method and Description |
---|---|
Environment |
OptionManagement.createEnvironment(String[] args)
collects the options entered by the user and creates an Environment from them.
|
Modifier and Type | Method and Description |
---|---|
ThermoResult |
RegisterMethods.computeOtherMeltingCorrections(Environment environment)
corrects the melting temperature if other agents are present in the solution (formamide, DMSO, ...)
|
CorrectionMethod |
RegisterMethods.getIonCorrectionMethod(Environment environment)
This method is called to get the CorrectionMethod which represents the method or model
used for the ion correction in the environment 'environment'.
|
Modifier and Type | Method and Description |
---|---|
protected double |
EntropyCorrection.correctEntropy(Environment environment)
corrects the computed entropy (delta S (Na = 1M)).
|
ThermoResult |
DNADMSOCorrections.correctMeltingResult(Environment environment,
double parameter) |
ThermoResult |
EntropyCorrection.correctMeltingResults(Environment environment) |
boolean |
DNADMSOCorrections.isApplicable(Environment environment) |
boolean |
EntropyCorrection.isApplicable(Environment environment) |
Modifier and Type | Method and Description |
---|---|
static double |
Tan06MagnesiumCorrection.computeFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
static double |
Tan07MagnesiumCorrection.computeFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
Tan06MagnesiumCorrection.correctEntropy(Environment environment) |
protected double |
Tan07MagnesiumCorrection.correctEntropy(Environment environment) |
ThermoResult |
Owczarzy08MagnesiumCorrection.correctMeltingResults(Environment environment) |
protected double |
Owczarzy08MagnesiumCorrection.correctTemperature(Environment environment)
corrects the computed melting temperature depending on the environment.
|
boolean |
Tan06MagnesiumCorrection.isApplicable(Environment environment) |
boolean |
Tan07MagnesiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy08MagnesiumCorrection.isApplicable(Environment environment) |
Modifier and Type | Method and Description |
---|---|
protected double |
Tan07MixedNaMgCorrection.correctEntropy(Environment environment) |
ThermoResult |
Owczarzy08MixedNaMgCorrection.correctMeltingResults(Environment environment) |
boolean |
Tan07MixedNaMgCorrection.isApplicable(Environment environment) |
Modifier and Type | Method and Description |
---|---|
static double |
Tan07SodiumCorrection.calculateFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
static double |
Tan06SodiumCorrection.calculateFreeEnergyPerBaseStack(Environment environment)
represents the function associated with the electrostatic folding free energy per base stack.
|
protected double |
Tan07SodiumCorrection.correctEntropy(Environment environment) |
protected double |
Tan06SodiumCorrection.correctEntropy(Environment environment) |
protected double |
Santalucia98_04SodiumCorrection.correctEntropy(Environment environment) |
protected double |
Ahsen01SodiumCorrection.correctEntropy(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection19.correctMeltingResults(Environment environment) |
ThermoResult |
Santalucia96SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
MarmurSchildkrautDoty98_62SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Tan07SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Tan06SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection22.correctMeltingResults(Environment environment) |
ThermoResult |
FrankKamenetskii71SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Wetmur91SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
SchildkrautLifson65SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection21.correctMeltingResults(Environment environment) |
ThermoResult |
Santalucia98_04SodiumCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Owczarzy04SodiumCorrection20.correctMeltingResults(Environment environment) |
boolean |
Owczarzy04SodiumCorrection19.isApplicable(Environment environment) |
boolean |
Santalucia96SodiumCorrection.isApplicable(Environment environment) |
boolean |
MarmurSchildkrautDoty98_62SodiumCorrection.isApplicable(Environment environment) |
boolean |
Tan07SodiumCorrection.isApplicable(Environment environment) |
boolean |
Tan06SodiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy04SodiumCorrection22.isApplicable(Environment environment) |
boolean |
FrankKamenetskii71SodiumCorrection.isApplicable(Environment environment) |
boolean |
Wetmur91SodiumCorrection.isApplicable(Environment environment) |
boolean |
SchildkrautLifson65SodiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy04SodiumCorrection21.isApplicable(Environment environment) |
boolean |
Santalucia98_04SodiumCorrection.isApplicable(Environment environment) |
boolean |
Ahsen01SodiumCorrection.isApplicable(Environment environment) |
boolean |
Owczarzy04SodiumCorrection20.isApplicable(Environment environment) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
CorrectionMethod.correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
boolean |
CorrectionMethod.isApplicable(Environment environment)
Check if the environment chosen by the user is a applicable with the correction model.
|
boolean |
PatternComputationMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
static double |
NearestNeighborMode.computesHairpinTemperature(Environment environment)
computes the melting temperature of a hairpin loop (when there is more than 4 CNG repeats in a sequence)
|
static double |
NearestNeighborMode.computesMeltingTemperature(Environment environment)
computes the melting temperature for for the Environment 'environment'.
|
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Musielski81DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Escara80DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Cullen76DMSOCorrection.correctMeltingResults(Environment environment) |
ThermoResult |
Ahsen01DMSOCorrection.correctMeltingResults(Environment environment) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
FormamideLinearMethod.correctMeltingResults(Environment environment) |
ThermoResult |
Blake96FormamideCorrection.correctMeltingResults(Environment environment) |
boolean |
FormamideLinearMethod.isApplicable(Environment environment) |
boolean |
Blake96FormamideCorrection.isApplicable(Environment environment) |
Modifier and Type | Method and Description |
---|---|
boolean |
PatternComputation.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Broda05CNGRepeats.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Xia98.computesHybridizationInitiation(Environment environment) |
ThermoResult |
DecomposedInitiation.computesHybridizationInitiation(Environment environment) |
ThermoResult |
Turner06.computesHybridizationInitiation(Environment environment) |
ThermoResult |
CricksNNMethod.computesHybridizationInitiation(Environment environment)
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
|
ThermoResult |
GlobalInitiation.computesHybridizationInitiation(Environment environment) |
ThermoResult |
Santalucia04.computesHybridizationInitiation(Environment environment) |
ThermoResult |
Santalucia96.computesHybridizationInitiation(Environment environment) |
boolean |
Breslauer86.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Freier86.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Xia98.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Sugimoto96.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Sugimoto95.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner06.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia04.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Tanaka04.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
AllawiSantalucia97.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia96.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Znosko071x2Loop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner06InternalLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia04InternalLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Turner99_06LongBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Santalucia04LongBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Sugimoto02RNADanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
SugimotoLongDanglingEndMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Sugimoto02DNADanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
SecondDanglingEndMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Tanaka04SingleBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Serra07SingleBulgeLoop.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Bommarito00SingleDanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Serra06_08SingleDanglingEnd.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
SingleDanglingEndMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Znosko08mm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
ZnoskoMethod.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Watkins11mm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner06mm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99mm.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Sugimoto01Hydroxyadenine.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Asanuma05Azobenzene.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
McTigue04LockedAcid.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Turner99_06tanmm.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99tanmm.isApplicable(Environment environment,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
boolean |
Santalucia05Inosine.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Turner99Wobble.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Znosko07Inosine.isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
Serra12Wobble.isApplicable(Environment environment,
int pos1,
int pos2) |