C-Index
Date: 2014-08-08

A B C D E F G H I L M N O P R S T U V W X Z

## 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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