- 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
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This method is called to get the RegisterMethod of the implemented class.
- getRegister() - Method in class melting.nearestNeighborModel.NearestNeighborMode
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- getResult() - Method in class melting.Environment
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This method is called to get the ThermoResult of Environment.
- getResults() - Method in class meltinggui.MeltingCalculator
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Returns the results from MELTING.
- getRNADefaultOptions() - Method in class melting.configuration.OptionManagement
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This method is called to get the RNADefaultOptions of OptionManagement.
- getSaltIndependentEntropy() - Method in class melting.ThermoResult
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This method is called to get the SaltIndependentEntropy of ThermoResult.
- getScreenPosition(Frame) - Method in class meltinggui.frames.FrameScreenPosition
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Fills in the fields from the current screen position of a
Frame
object.
- getScreenPosition(JInternalFrame) - Method in class meltinggui.frames.FrameScreenPosition
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Fills in the fields from the current screen position of a
JInternalFrame
object.
- getSecondDanglingValue(String, String, String) - Method in class melting.DataCollect
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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
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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
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This method is called to get the encoded sequence String of NucleotidSequences.
- getSequence(int, int) - Method in class melting.sequences.NucleotidSequences
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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
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this method is called to get the String sequence or complementary of NucleotidSequences.
- getSequenceNNPair(int) - Method in class melting.sequences.NucleotidSequences
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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
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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
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This method is called to get the sequences NucleotidSequences of Environment.
- getSequenceSens(String, int, int) - Method in class melting.sequences.NucleotidSequences
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To get the orientation of the subsequence sequence.
- getSequenceText() - Method in class meltinggui.dialogs.SequenceDialog
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Gets the sequence text.
- getSingleBulgeLoopvalue(String, String) - Method in class melting.DataCollect
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to get the Thermodynamics object containing the parameters for the single bulge (seq1, seq2).
- getSingleBulgeNeighbors(int) - Method in class melting.sequences.NucleotidSequences
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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
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This method is called to get a sodium equivalent concentration when other cations are present.
- getsymmetry() - Method in class melting.DataCollect
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to get the Thermodynamics object containing the parameters for the symmetry correction.
- getTerminal(String) - Method in class melting.DataCollect
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to get the Thermodynamics containing the parameters for the specified type of terminal base pair.
- getTerminalMismatchvalue(String, String) - Method in class melting.DataCollect
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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
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This method is called to get the Thermodynamics of the ThermoHandler object.
- getTm() - Method in class melting.ThermoResult
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This method is called to get the Tm of ThermoResult.
- getTopAcid() - Method in class melting.sequences.BasePair
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This method is called to get the nucleic acid "TopAcid" of BasePair.
- getTris() - Method in class melting.Environment
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This method is called to get the Tris buffer concentration.
- getType() - Method in class melting.handlers.DataHandler
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This method is called to get the type String of DataHandler.
- getValue() - Method in class meltinggui.widgets.InputField
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Gets the value from the widget.
- getValue(int) - Method in class meltinggui.widgets.InputFieldArray
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Get the value from a particular widget.
- getValue() - Method in interface meltinggui.widgets.InputWidgetInterface
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Gets the value given by the user.
- getValue() - Method in class meltinggui.widgets.MeltingComboBox
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Gets the command-line text corrseponding to the selected option.
- getValue() - Method in class meltinggui.widgets.MeltingTextArea
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Returns the text from the area.
- getValue() - Method in class meltinggui.widgets.MeltingTextField
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Returns the text from the field.
- gFormula - Static variable in class melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection
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String gFormula : function associated with the electrostatic folding free energy per base stack.
- gFormula - Static variable in class melting.ionCorrection.magnesiumCorrections.Tan07MagnesiumCorrection
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String gFormula : function associated with the electrostatic folding free energy per base stack.
- gFormula - Static variable in class melting.ionCorrection.mixedNaMgCorrections.Tan07MixedNaMgCorrection
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String gFormula : function associated with the electrostatic folding free energy per base stack.
- GlobalInitiation - Class in melting.patternModels.cricksPair
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This class represents one model to compute the initiation enthalpy and entropy.
- GlobalInitiation() - Constructor for class melting.patternModels.cricksPair.GlobalInitiation
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- globalMethod - Static variable in class melting.configuration.OptionManagement
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Option name for the choice of computation method (approximative "-A" or nearest neighbor "-NN").
- GlobalSingleBulgeLoopMethod - Class in melting.patternModels.singleBulge
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This class represents one single bulge loop model.
- GlobalSingleBulgeLoopMethod() - Constructor for class melting.patternModels.singleBulge.GlobalSingleBulgeLoopMethod
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- GuiScreenPositions - Class in meltinggui.frames
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The locations on the screen of the GUI and all the components it contains.
- GuiScreenPositions(OuterFrame, MeltingFrame, ErrorFrame) - Constructor for class meltinggui.frames.GuiScreenPositions
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Fills in the fields from the frames themselves.