- c - Variable in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
-
- calculateFreeEnergyPerBaseStack(Environment) - Static method in class melting.ionCorrection.sodiumCorrections.Tan06SodiumCorrection
-
represents the function associated with the electrostatic folding free energy per base stack.
- calculateFreeEnergyPerBaseStack(Environment) - Static method in class melting.ionCorrection.sodiumCorrections.Tan07SodiumCorrection
-
represents the function associated with the electrostatic folding free energy per base stack.
- calculateNumberOfTerminal(String, String, int, int) - Method in class melting.sequences.NucleotidSequences
-
calculates the number of base pairs (base1, base2) at the postions pos1 and pos2 in the duplex of NucleotidSequences.
- characters(char[], int, int) - Method in class melting.handlers.DataHandler
-
- characters(char[], int, int) - Method in class melting.handlers.EnergyHandler
-
- characters(char[], int, int) - Method in class melting.handlers.ThermoHandler
-
- checkContainer(Container) - Method in class meltinggui.MeltingLayout
-
Checks that a supplied container is the parent container for this layout.
- checkSequence(String) - Static method in class melting.sequences.NucleotidSequences
-
Checks if the String sequence is composed of nucleic acids known by MELTING.
- clearErrors() - Method in class meltinggui.frames.ErrorFrame
-
- clearErrors() - Method in class meltinggui.frames.OuterFrame
-
- CNGMethod - Static variable in class melting.configuration.OptionManagement
-
Option name for the choice of CNG repeats computation method.
- collector - Variable in class melting.patternModels.PatternComputation
-
DataCollect collector : contains the data HasMap with the thermodynamic parameters for the pattern computation.
- ComboBoxDialog - Class in meltinggui.dialogs
-
A dialog with a label and a combo box with various options on it.
- ComboBoxDialog(String, ComboBoxOption[], String) - Constructor for class meltinggui.dialogs.ComboBoxDialog
-
Sets up the dialog.
- ComboBoxOption - Class in meltinggui.widgets
-
An option on a combo box used to select additional MELTING options.
- ComboBoxOption(String, String) - Constructor for class meltinggui.widgets.ComboBoxOption
-
Constructor setting the text to be displayed in the combo box and the text
that would be written to the cmomand line.
- CompatibleMain - Class in melting
-
- CompatibleMain() - Constructor for class melting.CompatibleMain
-
- complementarySelectAll() - Method in class meltinggui.dialogs.SequenceDialog
-
Selects all the text in the "Complementary sequence" text box.
- complementarySequence - Static variable in class melting.configuration.OptionManagement
-
Option name for the complementary sequence (3'5').
- completedNode() - Method in class melting.handlers.NodeHandler
-
if the node is completed, the boolean completed becomes true.
- computeFreeEnergyPerBaseStack(Environment) - Static method in class melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection
-
represents the function associated with the electrostatic folding free energy per base stack.
- computeFreeEnergyPerBaseStack(Environment) - Static method in class melting.ionCorrection.magnesiumCorrections.Tan07MagnesiumCorrection
-
represents the function associated with the electrostatic folding free energy per base stack.
- computeOtherMeltingCorrections(Environment) - Method in class melting.configuration.RegisterMethods
-
corrects the melting temperature if other agents are present in the solution (formamide, DMSO, ...)
- computesHairpinTemperature(Environment) - Static method in class melting.nearestNeighborModel.NearestNeighborMode
-
computes the melting temperature of a hairpin loop (when there is more than 4 CNG repeats in a sequence)
- computesHybridizationInitiation(Environment) - Method in class melting.patternModels.cricksPair.CricksNNMethod
-
computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
- computesHybridizationInitiation(Environment) - Method in class melting.patternModels.cricksPair.DecomposedInitiation
-
- computesHybridizationInitiation(Environment) - Method in class melting.patternModels.cricksPair.GlobalInitiation
-
- computesHybridizationInitiation(Environment) - Method in class melting.patternModels.cricksPair.Santalucia04
-
- computesHybridizationInitiation(Environment) - Method in class melting.patternModels.cricksPair.Santalucia96
-
- computesHybridizationInitiation(Environment) - Method in class melting.patternModels.cricksPair.Turner06
-
- computesHybridizationInitiation(Environment) - Method in class melting.patternModels.cricksPair.Xia98
-
- computesInternalLoopLength(int, int) - Method in class melting.sequences.NucleotidSequences
-
computes the number of nucleic acids in the internal loop between the positions pos1 + 1 and
pos2 - 1 in the duplex ArrayList of the NucleotidSequences object.
- computesMeltingTemperature(Environment) - Static method in class melting.nearestNeighborModel.NearestNeighborMode
-
computes the melting temperature for for the Environment 'environment'.
- computesNaEquivalent(Environment) - Static method in class melting.Helper
-
computes a sodium equivalent concentration from the different ion concentrations of the Environment object.
- computeSodiumEquivalent(double, double, double, double, double) - Method in class melting.ionCorrection.sodiumEquivalence.Ahsen01_NaEquivalent
-
- computeSodiumEquivalent(double, double, double, double, double) - Method in class melting.ionCorrection.sodiumEquivalence.Mitsuhashi96NaEquivalent
-
- computeSodiumEquivalent(double, double, double, double, double) - Method in class melting.ionCorrection.sodiumEquivalence.Peyret00_NaEquivalent
-
- computeSodiumEquivalent(double, double, double, double, double) - Method in interface melting.methodInterfaces.SodiumEquivalentMethod
-
This method is called to convert an initial sodium concentration in a new equivalent sodium concentration
which takes in account the other cation concentrations.
- computesPercentGC() - Method in class melting.sequences.NucleotidSequences
-
computes the percentage of GC base pairs in the duplex of NucleotidSequences.
- computesPercentMismatching() - Method in class melting.sequences.NucleotidSequences
-
Computes the percentage of mismatching base pairs in the duplex of NucleotidSequences.
- computesThermodynamics() - Method in class melting.approximativeMethods.Ahsen01
-
- computesThermodynamics() - Method in class melting.approximativeMethods.ApproximativeMode
-
- computesThermodynamics() - Method in class melting.approximativeMethods.MarmurChester62_93
-
- computesThermodynamics() - Method in class melting.approximativeMethods.MarmurSchildkrautDoty
-
- computesThermodynamics() - Method in class melting.approximativeMethods.Owen69
-
- computesThermodynamics() - Method in class melting.approximativeMethods.Santalucia98
-
- computesThermodynamics() - Method in class melting.approximativeMethods.Wetmur91
-
- computesThermodynamics() - Method in class melting.approximativeMethods.WetmurDNA91
-
- computesThermodynamics() - Method in class melting.approximativeMethods.WetmurDNARNA91
-
- computesThermodynamics() - Method in class melting.approximativeMethods.WetmurRNA91
-
- computesThermodynamics() - Method in interface melting.methodInterfaces.MeltingComputationMethod
-
This method is called to compute the melting temperature.
- computesThermodynamics() - Method in class melting.nearestNeighborModel.NearestNeighborMode
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in interface melting.methodInterfaces.PatternComputationMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cngPatterns.Broda05CNGRepeats
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.AllawiSantalucia97
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Breslauer86
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.CricksNNMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Freier86
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Santalucia04
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Santalucia96
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Sugimoto95
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Sugimoto96
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Tanaka04
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Turner06
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.cricksPair.Xia98
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.InternalLoops.Santalucia04InternalLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.InternalLoops.Turner06InternalLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.InternalLoops.Znosko071x2Loop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.longDanglingEnds.SugimotoLongDanglingEndMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.PatternComputation
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.secondDanglingEnds.SecondDanglingEndMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.secondDanglingEnds.Serra05DoubleDanglingEnd
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.secondDanglingEnds.Serra06DoubleDanglingEnd
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleBulge.GlobalSingleBulgeLoopMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleBulge.Santalucia04SingleBulgeLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleBulge.Serra07SingleBulgeLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleBulge.Tanaka04SingleBulgeLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleBulge.Turner99_06SingleBulgeLoop
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleDanglingEnds.Bommarito00SingleDanglingEnd
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleDanglingEnds.SingleDanglingEndMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleMismatch.AllawiSantaluciaPeyret97_98_99mm
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleMismatch.Turner06mm
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleMismatch.Watkins11mm
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleMismatch.Znosko07mm
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleMismatch.Znosko08mm
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.singleMismatch.ZnoskoMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.specificAcids.Asanuma05Azobenzene
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.specificAcids.LockedAcidNNMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.specificAcids.McTigue04LockedAcid
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.specificAcids.Owczarzy11LockedAcid
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.tandemMismatches.AllawiSantaluciaPeyret97_98_99tanmm
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.tandemMismatches.Turner99_06tanmm
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.wobble.InosineNNMethod
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.wobble.Santalucia05Inosine
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.wobble.Serra12Wobble
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.wobble.Turner99Wobble
-
- computeThermodynamics(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.wobble.Znosko07Inosine
-
- convertToPyr_Pur(String) - Static method in class melting.sequences.NucleotidSequences
-
converts a sequence into a String composed of purine and pyrimidine.
- copy() - Method in class meltinggui.widgets.ComboBoxOption
-
Copies this combo box option to another combo box option.
- correctEntropy(Environment) - Method in class melting.correctionMethods.EntropyCorrection
-
corrects the computed entropy (delta S (Na = 1M)).
- correctEntropy(Environment) - Method in class melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection
-
- correctEntropy(Environment) - Method in class melting.ionCorrection.magnesiumCorrections.Tan07MagnesiumCorrection
-
- correctEntropy(Environment) - Method in class melting.ionCorrection.mixedNaMgCorrections.Tan07MixedNaMgCorrection
-
- correctEntropy(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Ahsen01SodiumCorrection
-
- correctEntropy(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Santalucia98_04SodiumCorrection
-
- correctEntropy(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Tan06SodiumCorrection
-
- correctEntropy(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Tan07SodiumCorrection
-
- CorrectionMethod - Interface in melting.methodInterfaces
-
This interface is implemented by classes which contain methods to correct the melting temperature.
- correctMeltingResult(Environment, double) - Method in class melting.correctionMethods.DNADMSOCorrections
-
- correctMeltingResults(Environment) - Method in class melting.correctionMethods.EntropyCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.mixedNaMgCorrections.Owczarzy08MixedNaMgCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.FrankKamenetskii71SodiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.MarmurSchildkrautDoty98_62SodiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection19
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection20
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection21
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection22
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Santalucia96SodiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Santalucia98_04SodiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.SchildkrautLifson65SodiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Tan06SodiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Tan07SodiumCorrection
-
- correctMeltingResults(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Wetmur91SodiumCorrection
-
- correctMeltingResults(Environment) - Method in interface melting.methodInterfaces.CorrectionMethod
-
This method is called to correct the computed melting temperature.
- correctMeltingResults(Environment) - Method in class melting.otherCorrections.dmsoCorrections.Ahsen01DMSOCorrection
-
- correctMeltingResults(Environment) - Method in class melting.otherCorrections.dmsoCorrections.Cullen76DMSOCorrection
-
- correctMeltingResults(Environment) - Method in class melting.otherCorrections.dmsoCorrections.Escara80DMSOCorrection
-
- correctMeltingResults(Environment) - Method in class melting.otherCorrections.dmsoCorrections.Musielski81DMSOCorrection
-
- correctMeltingResults(Environment) - Method in class melting.otherCorrections.formamideCorrections.Blake96FormamideCorrection
-
- correctMeltingResults(Environment) - Method in class melting.otherCorrections.formamideCorrections.FormamideLinearMethod
-
- correctPositions(int, int, int) - Method in class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctPositions(int, int, int) - Method in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctPositions(int, int, int) - Method in class melting.patternModels.longDanglingEnds.SugimotoLongDanglingEndMethod
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctPositions(int, int, int) - Method in class melting.patternModels.secondDanglingEnds.SecondDanglingEndMethod
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctPositions(int, int, int) - Method in class melting.patternModels.singleBulge.GlobalSingleBulgeLoopMethod
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctPositions(int, int, int) - Method in class melting.patternModels.singleDanglingEnds.SingleDanglingEndMethod
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctPositions(int, int, int) - Method in class melting.patternModels.singleMismatch.ZnoskoMethod
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctPositions(int, int, int) - Method in class melting.patternModels.wobble.InosineNNMethod
-
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
- correctSequences(String, String) - Method in class melting.sequences.NucleotidSequences
-
removes the unnecessary "-" in the String sequence and complementary of NucleotidSequences.
- correctTemperature(Environment) - Method in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
-
corrects the computed melting temperature depending on the environment.
- createEnvironment(String[]) - Method in class melting.configuration.OptionManagement
-
collects the options entered by the user and creates an Environment from them.
- CricksNNMethod - Class in melting.patternModels.cricksPair
-
This class represents the NN nearest neighbor model (adds the thermodynamic energy (enthalpy and entropy) for each Crick's pair composing the duplex).
- CricksNNMethod() - Constructor for class melting.patternModels.cricksPair.CricksNNMethod
-
- Cullen76DMSOCorrection - Class in melting.otherCorrections.dmsoCorrections
-
This class represents the DMSO correction model cul76.
- Cullen76DMSOCorrection() - Constructor for class melting.otherCorrections.dmsoCorrections.Cullen76DMSOCorrection
-