G-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

## G

g - Variable in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
getArgumentType() - Method in class meltinggui.ArgsMessage
  Gets the type of the message.
getAsymmetry() - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the internal loop asymmetry.
getAttribut() - Method in class melting.handlers.ThermoHandler
  This method is called to get the attribut HashMap of the ThermoHandler object.
getAzobenzeneValue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing an azobenzene ("X_C" or "X_T").
getBonus(String, String, String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for a Hairpin loop 'seqLoop' preceded by the base 'base1' and followed by the base 'lastBase'.
getBottomAcid() - Method in class melting.sequences.BasePair
  This method is called to get the nucleic acid "BottomAcid" of BasePair..
getBulgeLoopvalue(String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for a bulge loop of size 'size'.
getC4_3MeltingResult(String) - Static method in class examples.MainTest
  to run melting 4.3 and get the results
getCalculMethod() - Method in class melting.ThermoResult
  Gets the calculation method of the `ThermoResult`.
getClosureValue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the base pair (base1, base2) next to the mismatching base pair.
getCMeltingResult(String) - Static method in class examples.MainTest
  to run melting 4.2 and get the results
getCNGvalue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the CNG pattern 'seq1'.
getCollector() - Method in interface melting.methodInterfaces.PatternComputationMethod
  This method is called to get the DataCollect of the implemented class.
getCollector() - Method in class melting.patternModels.PatternComputation
getCommandLineFlags() - Method in class meltinggui.dialogs.ComboBoxDialog
  Returns the command-line flags corresponding to the user's choice on the combo box.
getCommandLineFlags() - Method in interface meltinggui.dialogs.DialogInterface
  Gets the command-line flags from the dialog.
getCommandLineFlags() - Method in class meltinggui.dialogs.HybridizationDialog
  Returns the command-line flags corresponding to the user's choice of hybridization type.
getCommandLineFlags() - Method in class meltinggui.dialogs.IonConcentrationDialog
  Gets the command line flags the user would have typed in were they using the command line.
getCommandLineFlags() - Method in class meltinggui.dialogs.OligomerConcentrationDialog
  Gets the command-line flags.
getCommandLineFlags() - Method in class meltinggui.dialogs.SequenceDialog
  Gets the command-line flags corresponding to the chosen sequence and complementary sequence.
getCommandLineText() - Method in class meltinggui.ArgsMessage
  Gets the command-line arguments.
getCommandLineText() - Method in class meltinggui.widgets.ComboBoxOption
  Gets the command-line text.
getComplementary(int, int, String) - Method in class melting.sequences.NucleotidSequences
  This method is called to get a substring of the complementary String between the positions pos1 and pos2 in the duplex.
getComplementary() - Method in class melting.sequences.NucleotidSequences
  This method is called to get the encoded complementary String of NucleotidSequences.
getComplementary(int, int) - Method in class melting.sequences.NucleotidSequences
  This method is called to get a substring between two positions of the complementary String.
getComplementaryNNPair(int) - Method in class melting.sequences.NucleotidSequences
  to get the two nucleic acids which are from the complementary sequence (3'5') in the Crick's pair at the position "pos" in the duplex.
getComplementaryNNPairUnlocked(int) - Method in class melting.sequences.NucleotidSequences
  to get the two unlocked nucleic acids which are from the complementary sequence (3'5') in the Crick's pair at the position "pos" in the duplex.
getComplementarySequence(String, String) - Static method in class melting.sequences.NucleotidSequences
  This method is called when we want to get the complementary of NucleotidSequences with the type of hybridization "hybridization".
getComplementaryText() - Method in class meltinggui.dialogs.SequenceDialog
  Gets the complementary sequence text.
getComplementaryTo(String, int, int) - Method in class melting.sequences.NucleotidSequences
  This method is called to get the complementary sequence to the sequence String between the positions pos1 and pos2.
getConcentrations() - Method in class melting.Environment
  This method is called to get the concentrations of Environment.
getCorrectionMethod(String, String) - Method in class melting.configuration.RegisterMethods
  This method is called to get the CorrectionMethod which represents the method 'methodName' entered with the option 'optionName'.
getDanglingSens(String, String) - Static method in class melting.sequences.NucleotidSequences
  this method is called to get the sens of the dangling end for the sequences seq1 and seq2
getDanglingValue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the dangling end present in the duplex composed of seq1 and seq2.
getData() - Method in class melting.DataCollect
  This method is called to get the data of DataCollect.
getData() - Static method in class melting.patternModels.PatternComputation
  This method is called to get the HasMap of DataCollect containing the thermodynamic parameters
getDataFileName(String) - Method in interface melting.methodInterfaces.PatternComputationMethod
getDataFileName(String) - Method in class melting.patternModels.PatternComputation
getDMSO() - Method in class melting.Environment
  This method is called to get the DMSO concentration.
getDNADefaultOptions() - Method in class melting.configuration.OptionManagement
  This method is called to get the DNADefaultOptions of OptionManagement.
getDNTP() - Method in class melting.Environment
  This method is called to get the dNTP concentration.
getDuplex() - Method in class melting.sequences.NucleotidSequences
  This method is called to get the duplex of NucleotidSequences.
getDuplexFrom(String, String) - Static method in class melting.sequences.NucleotidSequences
  This method is called to get the duplex of NucleotidSequences.
getDuplexLength() - Method in class melting.sequences.NucleotidSequences
  This method is called to get the length of the ArrayList duplex of NucleotidSequences.
getEnergy() - Method in class melting.handlers.EnergyHandler
  This method is called to get the energy of EnergyHandler.
getEnergyValueInJ(double) - Method in class melting.ThermoResult
  converts the energyValy double in cal/mol into an energy value in J/mol.
getEnthalpy() - Method in class melting.handlers.ThermoHandler
  This method is called to get the enthalpy double value of the ThermoHandler object.
getEnthalpy() - Method in class melting.Thermodynamics
  This method is called to get the enthalpy of Thermodynamics.
getEntropy() - Method in class melting.handlers.ThermoHandler
  This method is called to get the entropy double value of the ThermoHandler object.
getEntropy() - Method in class melting.Thermodynamics
  This method is called to get the entropy of Thermodynamics.
getEquivalentSequences(String) - Method in class melting.sequences.NucleotidSequences
  This method is called when the same NucleotidSequences is required but with the sequences converted in the new hybridization type "hybridizationType"
getExistingNucleicAcids() - Static method in class melting.sequences.BasePair
  This method is called to get the existingNucleicAcids of BasePair.
getFactor() - Method in class melting.Environment
  This method is called to get the factor of Environment.
getFirstMismatch(String, String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the first non canonical pair in the internal loop.
getFormamide() - Method in class melting.Environment
  This method is called to get the formamide concentration.
getGUThermoResult(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.wobble.Serra12Wobble
getGUThermoResult(NucleotidSequences, int, int, ThermoResult) - Method in class melting.patternModels.wobble.Turner99Wobble
getHairpinLoopvalue(String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for a Hairpin loop of size 'size'.
getHasEnergy() - Method in class melting.handlers.EnergyHandler
  This method is called to get the hasEnergy of EnergyHandler.
getHybridDefaultOptions() - Method in class melting.configuration.OptionManagement
  This method is called to get the hybridDefaultOptions of OptionManagement.
getHybridization() - Method in class melting.Environment
  This method is called to get the hybridization of Environment.
getHydroxyadenosineValue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a hydroxyadenine ("A*").
getInitiation() - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the hybridization initiation.
getInitiation(String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the initiation with the specified type of initiation.
getInitiationBulgevalue(String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the initiation of a bulge loop of size 'size'.
getInitiationLoopValue(String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the initiation of an internal loop with a specified size.
getInitiationLoopValue() - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the initiation of an internal loop.
getInternalLoopType(int, int) - Method in class melting.sequences.NucleotidSequences
  gives the type of the internal loop at the positions pos1 + 1 and pos2 - 1 in the duplex ArrayList of the NucleotidSequences object.
getInternalLoopValue(String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for an internal loop with a specified size.
getInversedSequence(String) - Static method in class melting.sequences.NucleotidSequences
  creates the inverse String of the sequence
getIonCorrectionMethod(Environment) - Method in class melting.configuration.RegisterMethods
  This method is called to get the CorrectionMethod which represents the method or model used for the ion correction in the environment 'environment'.
getK() - Method in class melting.Environment
  This method is called to get the potassium concentration.
getLayoutAlignmentX(Container) - Method in class meltinggui.MeltingLayout
  Returns the alignment along the x axis.
getLayoutAlignmentY(Container) - Method in class meltinggui.MeltingLayout
  Returns the alignment along the y axis.
getLengthAcid() - Method in class melting.sequences.BasePair
  This method is called to get the length of the nucleic acid.
getLoadedData() - Static method in class melting.FileReader
  This method is called to get the loadedData of FileReader.
getLockedAcidValue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a locked nucleic acid ("AL", "TL", "GL" or "CL").
getLoopFistMismatch(int) - Method in class melting.sequences.NucleotidSequences
  This method is called to get the first mismatch of the internal loop at the positions pos1 + 1 and pos2 - 1 in the duplex ArrayList of the NucleotidSequences object.
getMap() - Method in class melting.handlers.DataHandler
  This method is called to get the map of DataHandler.
getMeltingComputationMethod(HashMap<String, String>) - Method in class melting.configuration.RegisterMethods
  This method is called to get the MeltingComputationMethod which represents the method or model for the enthalpy, entropy and melting temperature computation in the HashMap 'optionSet'.
getMeltingResults(String[], OptionManagement) - Static method in class melting.Main
  Compute the entropy, enthalpy and melting temperature, and return these results.
getMeltingTest(String[]) - Static method in class examples.MainTest
  computes the enthalpy, entropy and melting temperature with the options in String [] args.
getMethodCommandLineFlag() - Method in class melting.configuration.MethodText
  Gets the method command line flag.
getMethodName() - Method in class melting.configuration.MethodText
  Gets the method name.
getMethodTextList() - Method in enum melting.configuration.RegisterMethods.MethodType
  Gets a list of the text representations of methods of this type.
getMethodType() - Method in class melting.configuration.RegisterMethods
  Gets an instance of the `MethodType` enum from the current instance of `RegisterMethods`.
getMg() - Method in class melting.Environment
  This method is called to get the magnesium concentration.
getMinimumSize() - Method in class meltinggui.widgets.MeltingTextArea
  Override the `getMinimumSize` method to return the preferred size - these text areas should never be any smaller than their preferred size.
getMismatchParameterValue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the mismatching base pair (base1, base2).
getMismatchValue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the mismatch(es) present in the duplex composed of seq1 and seq2.
getMismatchValue(String, String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the the duplex composed of seq1 and seq2 with the specified type of closing base pairs.
getModifiedAcidName(BasePair) - Method in class melting.sequences.NucleotidSequences
  This method is called to get the name of a specific nucleic acid in the base pair (BasePair object).
getModifiedAcidNames() - Static method in class melting.sequences.NucleotidSequences
  This method is called to get the modifiedAcidNames of NucleotidSequences.
getModifiedvalue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the crick's pair composed of the String seq1 and the String seq2 with one of the sequences containing a specific nucleic acid.
getModifiedvalue(String, String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a specific nucleic acid and a dangling end.
getMRNADefaultOptions() - Method in class melting.configuration.OptionManagement
  This method is called to get the mRNADefaultOptions of OptionManagement.
getNa() - Method in class melting.Environment
  This method is called to get the sodium concentration.
getNaEqMethod(HashMap<String, String>) - Method in class melting.configuration.RegisterMethods
  This method is called to get the SodiumEquivalentMethod which represents the method or model for the sodium equivalence in the HashMap 'optionSet'.
getName() - Method in class melting.approximativeMethods.Ahsen01
  Gets the name of the method.
getName() - Method in class melting.approximativeMethods.MarmurChester62_93
  Gets the full name of the method.
getName() - Method in class melting.approximativeMethods.MarmurSchildkrautDoty
  Gets the full name of the method.
getName() - Method in class melting.approximativeMethods.Owen69
  Gets the full name of the method.
getName() - Method in class melting.approximativeMethods.Santalucia98
  Gets the full name of the method.
getName() - Method in class melting.approximativeMethods.WetmurDNA91
  Gets the full name of the method.
getName() - Method in class melting.approximativeMethods.WetmurDNARNA91
  Gets the full name of the method.
getName() - Method in class melting.approximativeMethods.WetmurRNA91
  Gets the full name of the method.
getName() - Method in class melting.handlers.ThermoHandler
  This method is called to get the name String of the ThermoHandler object.
getName() - Method in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.magnesiumCorrections.Tan07MagnesiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.mixedNaMgCorrections.Owczarzy08MixedNaMgCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.mixedNaMgCorrections.Tan07MixedNaMgCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Ahsen01SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.FrankKamenetskii71SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.MarmurSchildkrautDoty98_62SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection19
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection20
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection21
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection22
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Santalucia96SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Santalucia98_04SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.SchildkrautLifson65SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Tan06SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Tan07SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumCorrections.Wetmur91SodiumCorrection
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumEquivalence.Ahsen01_NaEquivalent
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumEquivalence.Mitsuhashi96NaEquivalent
  Gets the full name of the method.
getName() - Method in class melting.ionCorrection.sodiumEquivalence.Peyret00_NaEquivalent
  Gets the full name of the method.
getName() - Method in interface melting.methodInterfaces.NamedMethod
getName() - Method in class melting.otherCorrections.dmsoCorrections.Ahsen01DMSOCorrection
  Gets the full name of the method.
getName() - Method in class melting.otherCorrections.dmsoCorrections.Cullen76DMSOCorrection
  Gets the full name of the method.
getName() - Method in class melting.otherCorrections.dmsoCorrections.Escara80DMSOCorrection
  Gets the full name of the method.
getName() - Method in class melting.otherCorrections.dmsoCorrections.Musielski81DMSOCorrection
  Gets the full name of the method.
getName() - Method in class melting.otherCorrections.formamideCorrections.Blake96FormamideCorrection
  Gets the full name of the method.
getName() - Method in class melting.otherCorrections.formamideCorrections.FormamideLinearMethod
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cngPatterns.Broda05CNGRepeats
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.AllawiSantalucia97
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Breslauer86
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Freier86
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Santalucia04
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Santalucia96
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Sugimoto95
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Sugimoto96
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Tanaka04
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Turner06
  Gets the full name of the method.
getName() - Method in class melting.patternModels.cricksPair.Xia98
  Gets the full name of the method.
getName() - Method in class melting.patternModels.InternalLoops.Santalucia04InternalLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.InternalLoops.Turner06InternalLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.InternalLoops.Znosko071x2Loop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd
  Gets the full name of the method.
getName() - Method in class melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd
  Gets the full name of the method.
getName() - Method in class melting.patternModels.secondDanglingEnds.Serra05DoubleDanglingEnd
  Gets the full name of the method.
getName() - Method in class melting.patternModels.secondDanglingEnds.Serra06DoubleDanglingEnd
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleBulge.Santalucia04SingleBulgeLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleBulge.Serra07SingleBulgeLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleBulge.Tanaka04SingleBulgeLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleBulge.Turner99_06SingleBulgeLoop
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleDanglingEnds.Bommarito00SingleDanglingEnd
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleMismatch.AllawiSantaluciaPeyret97_98_99mm
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleMismatch.Turner06mm
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleMismatch.Watkins11mm
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleMismatch.Znosko07mm
  Gets the full name of the method.
getName() - Method in class melting.patternModels.singleMismatch.Znosko08mm
  Gets the full name of the method.
getName() - Method in class melting.patternModels.specificAcids.Asanuma05Azobenzene
  Gets the full name of the method.
getName() - Method in class melting.patternModels.specificAcids.LockedAcidNNMethod
  Gets the full name of the method.
getName() - Method in class melting.patternModels.specificAcids.McTigue04LockedAcid
  Gets the full name of the method.
getName() - Method in class melting.patternModels.specificAcids.Owczarzy11LockedAcid
  Gets the full name of the method.
getName() - Method in class melting.patternModels.specificAcids.Owczarzy11SingleMismatchLockedAcid
  Gets the full name of the method.
getName() - Method in class melting.patternModels.specificAcids.Owczarzy11TandemLockedAcid
  Gets the full name of the method.
getName() - Method in class melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine
  Gets the full name of the method.
getName() - Method in class melting.patternModels.tandemMismatches.AllawiSantaluciaPeyret97_98_99tanmm
  Gets the full name of the method.
getName() - Method in class melting.patternModels.tandemMismatches.Turner99_06tanmm
  Gets the full name of the method.
getName() - Method in class melting.patternModels.wobble.Santalucia05Inosine
  Gets the full name of the method.
getName() - Method in class melting.patternModels.wobble.Serra12Wobble
  Gets the full name of the method.
getName() - Method in class melting.patternModels.wobble.Turner99Wobble
  Gets the full name of the method.
getName() - Method in class melting.patternModels.wobble.Znosko07Inosine
  Gets the full name of the method.
getNNPairWithoutHydroxyA(int) - Method in class melting.sequences.NucleotidSequences
  to get the two nucleic acids from each sequence in the Crick's pair at the position "pos" in the duplex.
getNNvalue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics containing the parameters for the crick's pair composed of the String seq1 and the String seq2.
getNucleotides() - Method in class melting.Environment
  This method is called to get the oligomerConcentration of Environment.
getNumberTerminal5TA(int, int) - Method in class melting.sequences.NucleotidSequences
  calculates the number of terminal 5'T3'A in the subduplex between pos1 and pos2
getOptions() - Method in class melting.Environment
  This method is called to get the HashMap options of Environment.
getOptionText() - Method in class meltinggui.widgets.ComboBoxOption
  Gets the option text.
getPatternComputationMethod(String, String) - Method in class melting.configuration.RegisterMethods
  This method is called to get the PatternComputationMethod which represents the method 'methodName' entered with the option 'optionName'.
getPenalty(String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the penalty of type 'type'.
getPenalty(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for a penalty of type 'type' for the specified parameter.
getPosition() - Method in class melting.sequences.BasePair
  This method is called to get the position of BasePair in the duplex.
getPreferredSize() - Method in class meltinggui.widgets.MeltingTextArea
  We override the `getPreferredSize` method in order to produce better resizing behaviour.
getRegister() - Method in class melting.approximativeMethods.ApproximativeMode
getRegister() - Method in interface melting.methodInterfaces.MeltingComputationMethod
  This method is called to get the RegisterMethod of the implemented class.
getRegister() - Method in class melting.nearestNeighborModel.NearestNeighborMode
getResult() - Method in class melting.Environment
  This method is called to get the ThermoResult of Environment.
getResults() - Method in class meltinggui.MeltingCalculator
  Returns the results from MELTING.
getRNADefaultOptions() - Method in class melting.configuration.OptionManagement
  This method is called to get the RNADefaultOptions of OptionManagement.
getSaltIndependentEntropy() - Method in class melting.ThermoResult
  This method is called to get the SaltIndependentEntropy of ThermoResult.
getScreenPosition(Frame) - Method in class meltinggui.frames.FrameScreenPosition
  Fills in the fields from the current screen position of a `Frame` object.
getScreenPosition(JInternalFrame) - Method in class meltinggui.frames.FrameScreenPosition
  Fills in the fields from the current screen position of a `JInternalFrame` object.
getSecondDanglingValue(String, String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the dangling end present in the duplex composed of seq1 and seq2 with the specified sens.
getSequence(int, int, String) - Method in class melting.sequences.NucleotidSequences
  This method is called to get a substring of the sequence String between the positions pos1 and pos2 in the duplex.
getSequence() - Method in class melting.sequences.NucleotidSequences
  This method is called to get the encoded sequence String of NucleotidSequences.
getSequence(int, int) - Method in class melting.sequences.NucleotidSequences
  This method is called to get a substring between two positions of the sequence String.
getSequenceContaining(String, int, int) - Method in class melting.sequences.NucleotidSequences
  this method is called to get the String sequence or complementary of NucleotidSequences.
getSequenceNNPair(int) - Method in class melting.sequences.NucleotidSequences
  to get the two nucleic acids which are from the sequence (5'3') in the Crick's pair at the position "pos" in the duplex.
getSequenceNNPairUnlocked(int) - Method in class melting.sequences.NucleotidSequences
  to get the two unlocked nucleic acids which are from the sequence (5'3') in the Crick's pair at the position "pos" in the duplex.
getSequences() - Method in class melting.Environment
  This method is called to get the sequences NucleotidSequences of Environment.
getSequenceSens(String, int, int) - Method in class melting.sequences.NucleotidSequences
  To get the orientation of the subsequence sequence.
getSequenceText() - Method in class meltinggui.dialogs.SequenceDialog
  Gets the sequence text.
getSingleBulgeLoopvalue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the single bulge (seq1, seq2).
getSingleBulgeNeighbors(int) - Method in class melting.sequences.NucleotidSequences
  This method is called to get the base pairs adjacent to the single bulge loop (unpaired nucleic acid) at the position pos1 in the duplex ArrayList
getSodiumEquivalent(double, double, double, double, double, double) - Method in class melting.ionCorrection.sodiumEquivalence.SodiumEquivalent
  This method is called to get a sodium equivalent concentration when other cations are present.
getsymmetry() - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the symmetry correction.
getTerminal(String) - Method in class melting.DataCollect
  to get the Thermodynamics containing the parameters for the specified type of terminal base pair.
getTerminalMismatchvalue(String, String) - Method in class melting.DataCollect
  to get the Thermodynamics object containing the parameters for the terminal mismatching base pair (seq1, seq2) of a hairpin loop.
getThermo() - Method in class melting.handlers.ThermoHandler
  This method is called to get the Thermodynamics of the ThermoHandler object.
getTm() - Method in class melting.ThermoResult
  This method is called to get the Tm of ThermoResult.
getTopAcid() - Method in class melting.sequences.BasePair
  This method is called to get the nucleic acid "TopAcid" of BasePair.
getTris() - Method in class melting.Environment
  This method is called to get the Tris buffer concentration.
getType() - Method in class melting.handlers.DataHandler
  This method is called to get the type String of DataHandler.
getValue() - Method in class meltinggui.widgets.InputField
  Gets the value from the widget.
getValue(int) - Method in class meltinggui.widgets.InputFieldArray
  Get the value from a particular widget.
getValue() - Method in interface meltinggui.widgets.InputWidgetInterface
  Gets the value given by the user.
getValue() - Method in class meltinggui.widgets.MeltingComboBox
  Gets the command-line text corrseponding to the selected option.
getValue() - Method in class meltinggui.widgets.MeltingTextArea
  Returns the text from the area.
getValue() - Method in class meltinggui.widgets.MeltingTextField
  Returns the text from the field.
gFormula - Static variable in class melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection
  String gFormula : function associated with the electrostatic folding free energy per base stack.
gFormula - Static variable in class melting.ionCorrection.magnesiumCorrections.Tan07MagnesiumCorrection
  String gFormula : function associated with the electrostatic folding free energy per base stack.
gFormula - Static variable in class melting.ionCorrection.mixedNaMgCorrections.Tan07MixedNaMgCorrection
  String gFormula : function associated with the electrostatic folding free energy per base stack.
GlobalInitiation - Class in melting.patternModels.cricksPair
  This class represents one model to compute the initiation enthalpy and entropy.
GlobalInitiation() - Constructor for class melting.patternModels.cricksPair.GlobalInitiation
globalMethod - Static variable in class melting.configuration.OptionManagement
  Option name for the choice of computation method (approximative "-A" or nearest neighbor "-NN").
GlobalSingleBulgeLoopMethod - Class in melting.patternModels.singleBulge
  This class represents one single bulge loop model.
GlobalSingleBulgeLoopMethod() - Constructor for class melting.patternModels.singleBulge.GlobalSingleBulgeLoopMethod
GuiScreenPositions - Class in meltinggui.frames
  The locations on the screen of the GUI and all the components it contains.
GuiScreenPositions(OuterFrame, MeltingFrame, ErrorFrame) - Constructor for class meltinggui.frames.GuiScreenPositions
  Fills in the fields from the frames themselves.

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