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C

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
 
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