Modifier and Type | Method and Description |
---|---|
static ThermoResult |
Main.getMeltingResults(String[] args,
OptionManagement optionManager)
Compute the entropy, enthalpy and melting temperature, and return
these results.
|
ThermoResult |
Environment.getResult()
This method is called to get the ThermoResult of Environment.
|
Modifier and Type | Method and Description |
---|---|
void |
Environment.setResult(ThermoResult result)
changes the result ThermoResult of Environment.
|
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Santalucia98.computesThermodynamics() |
ThermoResult |
WetmurDNARNA91.computesThermodynamics() |
ThermoResult |
ApproximativeMode.computesThermodynamics() |
ThermoResult |
Wetmur91.computesThermodynamics() |
ThermoResult |
MarmurChester62_93.computesThermodynamics() |
ThermoResult |
MarmurSchildkrautDoty.computesThermodynamics() |
ThermoResult |
Owen69.computesThermodynamics() |
ThermoResult |
WetmurDNA91.computesThermodynamics() |
ThermoResult |
Ahsen01.computesThermodynamics() |
ThermoResult |
WetmurRNA91.computesThermodynamics() |
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, ...)
|
Modifier and Type | Method and Description |
---|---|
ThermoResult |
DNADMSOCorrections.correctMeltingResult(Environment environment,
double parameter) |
ThermoResult |
EntropyCorrection.correctMeltingResults(Environment environment) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Owczarzy08MagnesiumCorrection.correctMeltingResults(Environment environment) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Owczarzy08MixedNaMgCorrection.correctMeltingResults(Environment environment) |
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
MeltingComputationMethod.computesThermodynamics()
This method is called to compute the melting temperature.
|
ThermoResult |
PatternComputationMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
CorrectionMethod.correctMeltingResults(Environment environment)
This method is called to correct the computed melting temperature.
|
Modifier and Type | Method and Description |
---|---|
ThermoResult |
PatternComputationMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
NearestNeighborMode.computesThermodynamics() |
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) |
Modifier and Type | Method and Description |
---|---|
abstract ThermoResult |
PatternComputation.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
abstract ThermoResult |
PatternComputation.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Broda05CNGRepeats.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Broda05CNGRepeats.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Znosko071x2Loop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Znosko071x2Loop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Turner99_06LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Turner99_06LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Sugimoto02RNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SugimotoLongDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto02DNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Sugimoto02RNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SugimotoLongDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto02DNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Serra05DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SecondDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Serra05DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SecondDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Tanaka04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99_06SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
GlobalSingleBulgeLoopMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra07SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Tanaka04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99_06SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
GlobalSingleBulgeLoopMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra07SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Bommarito00SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06_08SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SingleDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Bommarito00SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06_08SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SingleDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Znosko08mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
ZnoskoMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Watkins11mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Znosko08mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
ZnoskoMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Watkins11mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Sugimoto01Hydroxyadenine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Asanuma05Azobenzene.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
McTigue04LockedAcid.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Sugimoto01Hydroxyadenine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Asanuma05Azobenzene.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
McTigue04LockedAcid.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Turner99_06tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Turner99_06tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Santalucia05Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
InosineNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra12Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Turner99Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Serra12Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Santalucia05Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
InosineNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra12Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Turner99Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Serra12Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
MeltingCalculator.fetchMeltingResults()
Computes and returns the results from MELTING.
|
ThermoResult |
MeltingCalculator.getResults()
Returns the results from MELTING.
|
Modifier and Type | Method and Description |
---|---|
void |
ResultsPanel.displayMeltingResults(ThermoResult results)
Displays the results from the MELTING program.
|
Modifier and Type | Method and Description |
---|---|
void |
MeltingFrame.displayMeltingResults(ThermoResult results)
Displays the MELTING results.
|
void |
OuterFrame.displayMeltingResults(ThermoResult results)
Displays MELTING results on the MELTING frame.
|