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

I

initialiseAttributes() - Method in class melting.handlers.ThermoHandler
initialises the attribut HashMap of the ThermoHandler object.
initialiseFileName(String) - Method in interface melting.methodInterfaces.PatternComputationMethod
If a file name is entered by the user, the file name of the model becomes the file name entered by the user, otherwise the default file name of the model is used.
initialiseFileName(String) - Method in class melting.patternModels.cngPatterns.Broda05CNGRepeats
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.AllawiSantalucia97
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Breslauer86
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Freier86
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Santalucia04
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Santalucia96
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Sugimoto95
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Sugimoto96
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Tanaka04
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Turner06
 
initialiseFileName(String) - Method in class melting.patternModels.cricksPair.Xia98
 
initialiseFileName(String) - Method in class melting.patternModels.InternalLoops.Santalucia04InternalLoop
 
initialiseFileName(String) - Method in class melting.patternModels.InternalLoops.Turner06InternalLoop
 
initialiseFileName(String) - Method in class melting.patternModels.InternalLoops.Znosko071x2Loop
 
initialiseFileName(String) - Method in class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
 
initialiseFileName(String) - Method in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
 
initialiseFileName(String) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd
 
initialiseFileName(String) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd
 
initialiseFileName(String) - Method in class melting.patternModels.PatternComputation
 
initialiseFileName(String) - Method in class melting.patternModels.secondDanglingEnds.Serra05DoubleDanglingEnd
 
initialiseFileName(String) - Method in class melting.patternModels.secondDanglingEnds.Serra06DoubleDanglingEnd
 
initialiseFileName(String) - Method in class melting.patternModels.singleBulge.Serra07SingleBulgeLoop
 
initialiseFileName(String) - Method in class melting.patternModels.singleBulge.Tanaka04SingleBulgeLoop
 
initialiseFileName(String) - Method in class melting.patternModels.singleDanglingEnds.Bommarito00SingleDanglingEnd
 
initialiseFileName(String) - Method in class melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd
 
initialiseFileName(String) - Method in class melting.patternModels.singleMismatch.AllawiSantaluciaPeyret97_98_99mm
 
initialiseFileName(String) - Method in class melting.patternModels.singleMismatch.Turner06mm
 
initialiseFileName(String) - Method in class melting.patternModels.singleMismatch.Watkins11mm
 
initialiseFileName(String) - Method in class melting.patternModels.singleMismatch.Znosko07mm
 
initialiseFileName(String) - Method in class melting.patternModels.singleMismatch.Znosko08mm
 
initialiseFileName(String) - Method in class melting.patternModels.specificAcids.Asanuma05Azobenzene
 
initialiseFileName(String) - Method in class melting.patternModels.specificAcids.McTigue04LockedAcid
 
initialiseFileName(String) - Method in class melting.patternModels.specificAcids.Owczarzy11LockedAcid
 
initialiseFileName(String) - Method in class melting.patternModels.specificAcids.Owczarzy11SingleMismatchLockedAcid
 
initialiseFileName(String) - Method in class melting.patternModels.specificAcids.Owczarzy11TandemLockedAcid
 
initialiseFileName(String) - Method in class melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine
 
initialiseFileName(String) - Method in class melting.patternModels.tandemMismatches.AllawiSantaluciaPeyret97_98_99tanmm
 
initialiseFileName(String) - Method in class melting.patternModels.tandemMismatches.Turner99_06tanmm
 
initialiseFileName(String) - Method in class melting.patternModels.wobble.Santalucia05Inosine
 
initialiseFileName(String) - Method in class melting.patternModels.wobble.Serra12Wobble
 
initialiseFileName(String) - Method in class melting.patternModels.wobble.Turner99Wobble
 
initialiseFileName(String) - Method in class melting.patternModels.wobble.Znosko07Inosine
 
initialiseLogger() - Method in class melting.configuration.OptionManagement
initialises the meltingLogger.
initialiseModifiedAcidHashmap() - Static method in class melting.sequences.NucleotidSequences
initialises the modifiedAcidNames of NucleotidSequences.
initialiseNucleicAcidList() - Static method in class melting.sequences.BasePair
initialises the existingNucleicAcids of BasePair.
inosineMethod - Static variable in class melting.configuration.OptionManagement
Option name for the choice of inosine computation method.
InosineNNMethod - Class in melting.patternModels.wobble
This class represents the inosine model.
InosineNNMethod() - Constructor for class melting.patternModels.wobble.InosineNNMethod
 
INPUT_GROUP - Static variable in class meltinggui.MeltingLayout
Component group type: input group.
InputField<W extends java.awt.Component & InputWidgetInterface> - Class in meltinggui.widgets
A widget for enter in a value, together with a label to tell you what to enter.
InputField(String, Class<W>) - Constructor for class meltinggui.widgets.InputField
Creates the widgets, and sets them up.
InputFieldArray<W extends java.awt.Component & InputWidgetInterface> - Class in meltinggui.widgets
A vertical array of widgets, each with a label describing what to type in it.
InputFieldArray(String[], Class<W>) - Constructor for class meltinggui.widgets.InputFieldArray
Create the widgets and set them up.
InputWidgetInterface - Interface in meltinggui.widgets
Represents a generic input widget on the frame.
internalLoopMethod - Static variable in class melting.configuration.OptionManagement
Option name for the choice of internal loop computation method.
invalidateLayout(Container) - Method in class meltinggui.MeltingLayout
Invalidates the layout, indicating that any cached information should be discarded.
IonConcentrationDialog - Class in meltinggui.dialogs
A dialog allowing the user to specify the concentration of ions in the solution.
IonConcentrationDialog() - Constructor for class meltinggui.dialogs.IonConcentrationDialog
Set up the dialog.
ionCorrection - Static variable in class melting.configuration.OptionManagement
Option name for the choice of ion correction method.
isApplicable() - Method in class melting.approximativeMethods.Ahsen01
 
isApplicable() - Method in class melting.approximativeMethods.ApproximativeMode
 
isApplicable() - Method in class melting.approximativeMethods.MarmurChester62_93
 
isApplicable() - Method in class melting.approximativeMethods.MarmurSchildkrautDoty
 
isApplicable() - Method in class melting.approximativeMethods.Owen69
 
isApplicable() - Method in class melting.approximativeMethods.Santalucia98
 
isApplicable() - Method in class melting.approximativeMethods.WetmurDNA91
 
isApplicable() - Method in class melting.approximativeMethods.WetmurDNARNA91
 
isApplicable() - Method in class melting.approximativeMethods.WetmurRNA91
 
isApplicable(Environment) - Method in class melting.correctionMethods.DNADMSOCorrections
 
isApplicable(Environment) - Method in class melting.correctionMethods.EntropyCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.magnesiumCorrections.Tan07MagnesiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.mixedNaMgCorrections.Tan07MixedNaMgCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Ahsen01SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.FrankKamenetskii71SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.MarmurSchildkrautDoty98_62SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection19
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection20
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection21
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection22
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Santalucia96SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Santalucia98_04SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.SchildkrautLifson65SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Tan06SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Tan07SodiumCorrection
 
isApplicable(Environment) - Method in class melting.ionCorrection.sodiumCorrections.Wetmur91SodiumCorrection
 
isApplicable(HashMap<String, String>) - Method in class melting.ionCorrection.sodiumEquivalence.SodiumEquivalent
 
isApplicable(Environment) - Method in interface melting.methodInterfaces.CorrectionMethod
Check if the environment chosen by the user is a applicable with the correction model.
isApplicable() - Method in interface melting.methodInterfaces.MeltingComputationMethod
This method is called to check that the options entered by the users are applicable with the used model (class).
isApplicable(Environment, int, int) - Method in interface melting.methodInterfaces.PatternComputationMethod
 
isApplicable(HashMap<String, String>) - Method in interface melting.methodInterfaces.SodiumEquivalentMethod
Check if the model to compute an equivalent sodium cencentration is applicable with the options entered by the user.
isApplicable() - Method in class melting.nearestNeighborModel.NearestNeighborMode
 
isApplicable(Environment) - Method in class melting.otherCorrections.formamideCorrections.Blake96FormamideCorrection
 
isApplicable(Environment) - Method in class melting.otherCorrections.formamideCorrections.FormamideLinearMethod
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cngPatterns.Broda05CNGRepeats
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.AllawiSantalucia97
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Breslauer86
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Freier86
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Santalucia04
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Santalucia96
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Sugimoto95
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Sugimoto96
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Tanaka04
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Turner06
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.cricksPair.Xia98
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.InternalLoops.Santalucia04InternalLoop
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.InternalLoops.Turner06InternalLoop
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.InternalLoops.Znosko071x2Loop
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.longDanglingEnds.SugimotoLongDanglingEndMethod
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.PatternComputation
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.secondDanglingEnds.SecondDanglingEndMethod
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleBulge.Serra07SingleBulgeLoop
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleBulge.Tanaka04SingleBulgeLoop
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleDanglingEnds.Bommarito00SingleDanglingEnd
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleDanglingEnds.SingleDanglingEndMethod
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleMismatch.AllawiSantaluciaPeyret97_98_99mm
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleMismatch.Turner06mm
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleMismatch.Watkins11mm
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleMismatch.Znosko08mm
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.singleMismatch.ZnoskoMethod
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.specificAcids.Asanuma05Azobenzene
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.specificAcids.LockedAcidNNMethod
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.specificAcids.McTigue04LockedAcid
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.specificAcids.Owczarzy11LockedAcid
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.tandemMismatches.AllawiSantaluciaPeyret97_98_99tanmm
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.tandemMismatches.Turner99_06tanmm
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.wobble.Santalucia05Inosine
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.wobble.Serra12Wobble
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.wobble.Turner99Wobble
 
isApplicable(Environment, int, int) - Method in class melting.patternModels.wobble.Znosko07Inosine
 
isAPyrimidineInThePosition(int) - Method in class melting.sequences.NucleotidSequences
to check if there is at least one pyrimidine in the base pair at the position pos of the duplex ArrayList.
isAsymetricInternalLoop(int, int) - Method in class melting.sequences.NucleotidSequences
to check if the internal loop between the positions pos1 + 1 and pos2 - 1 in the duplex ArrayList is asymetric.
isBasePair(String, String, int) - Method in class melting.sequences.NucleotidSequences
To check if the base pair at the position pos in the duplex is (base1, base2) or (base2, base1).
isBasePairEqualTo(String, String) - Method in class melting.sequences.BasePair
Check if the two nucleic acids of the base pair are (base1, base2) or (base2, base1).
isBasePairStrictlyEqualTo(String, String) - Method in class melting.sequences.BasePair
Check if the two nucleic acids of the base pair are (base1, base2).
isBottomBasePyrimidine() - Method in class melting.sequences.BasePair
Check if the nucleic acid represented by BottomAcid is a pyrimidine.
isBulgeLoop(int, int) - Method in class melting.sequences.NucleotidSequences
to check if the pattern between the positions pos1 and pos2 in the duplex is a single or long bulge loop.
isClosingPenaltyNecessary() - Method in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
to check if a penalty for the closing base pairs is necessary.
isClosingPenaltyNecessary() - Method in class melting.patternModels.singleBulge.Turner99_06SingleBulgeLoop
 
isCNGPattern(int, int) - Method in class melting.sequences.NucleotidSequences
to check if the pattern between the positions pos1 and pos2 in the duplex is a CNG repeat pattern.
isComplementaryBasePair() - Method in class melting.sequences.BasePair
To check if the two nucleic acids in the base pair are complementary.
isComplementaryLockedPair() - Method in class melting.sequences.BasePair
To check if the two nucleic acids in the base pair are complementary when one of them is a locked nucleic acid.
isDanglingEnd(int, int) - Method in class melting.sequences.NucleotidSequences
to check if there is at least one dangling end between the positions pos1 and pos2 in the duplex.
isFrequentNucleicAcidTopBase() - Method in class melting.sequences.BasePair
Check if the Nucleic acid TopAcid is a frequent nucleic acid.
isGUSequences(int, int) - Method in class melting.sequences.NucleotidSequences
to check if the pattern between the positions pos1 and pos2 in the duplex is only composed of GU base pairs.
isMeltingInformationOption(String[]) - Method in class melting.configuration.OptionManagement
to check if the user just wants to know some information about melting.
isMismatch(int, int) - Method in class melting.sequences.NucleotidSequences
to check if the pattern between the positions pos1 and pos2 in the duplex is a single mismatch, tandem mismatch or internal loop.
isMismatchPair(int) - Method in class melting.sequences.NucleotidSequences
to check if the base pair at the position pos in the duplex is a mismatch.
isMissingParameters(NucleotidSequences, int, int) - Method in interface melting.methodInterfaces.PatternComputationMethod
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern at the positions pos1 and pos2.
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cngPatterns.Broda05CNGRepeats
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.AllawiSantalucia97
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Breslauer86
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.CricksNNMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Freier86
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Santalucia04
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Santalucia96
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Sugimoto95
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Sugimoto96
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Tanaka04
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Turner06
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.cricksPair.Xia98
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.InternalLoops.Santalucia04InternalLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.InternalLoops.Turner06InternalLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.InternalLoops.Znosko071x2Loop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.longDanglingEnds.SugimotoLongDanglingEndMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.PatternComputation
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.secondDanglingEnds.SecondDanglingEndMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.secondDanglingEnds.Serra05DoubleDanglingEnd
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.secondDanglingEnds.Serra06DoubleDanglingEnd
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleBulge.GlobalSingleBulgeLoopMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleBulge.Santalucia04SingleBulgeLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleBulge.Serra07SingleBulgeLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleBulge.Tanaka04SingleBulgeLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleBulge.Turner99_06SingleBulgeLoop
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleDanglingEnds.Bommarito00SingleDanglingEnd
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleDanglingEnds.SingleDanglingEndMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleMismatch.AllawiSantaluciaPeyret97_98_99mm
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleMismatch.Turner06mm
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleMismatch.Watkins11mm
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.singleMismatch.ZnoskoMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.specificAcids.Asanuma05Azobenzene
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.specificAcids.LockedAcidNNMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.specificAcids.McTigue04LockedAcid
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.specificAcids.Owczarzy11LockedAcid
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.tandemMismatches.AllawiSantaluciaPeyret97_98_99tanmm
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.tandemMismatches.Turner99_06tanmm
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.wobble.InosineNNMethod
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.wobble.Santalucia05Inosine
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.wobble.Serra12Wobble
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.wobble.Turner99Wobble
 
isMissingParameters(NucleotidSequences, int, int) - Method in class melting.patternModels.wobble.Znosko07Inosine
 
isNaEqPossible() - Method in class melting.approximativeMethods.ApproximativeMode
to check if a sodium equivalence is necessary.
isNaEqPossible() - Method in class melting.approximativeMethods.MarmurChester62_93
 
isNoGapInSequence(int, int) - Method in class melting.sequences.NucleotidSequences
to chack if there is no gap (an unpaired nucleic acid) in the duplex between theb positions pos1 and pos2
isOneGCBasePair() - Method in class melting.sequences.NucleotidSequences
To check if there is at least one GC base pair in the duplex of NucleotidSequences.
isPerfectMatchSequence(int, int) - Method in class melting.sequences.NucleotidSequences
to check to check if the sequences between the positions pos1 and pos2 in the duplex are perfectly matching sequences.
isRegisteredNucleicAcid(int) - Method in class melting.sequences.NucleotidSequences
to check if the nucleic acids in the base pair at the position pos in the duplex are existing nucleic acids.
isSelfComplementarity() - Method in class melting.Environment
To check if the sequences are self complementary.
isSelfComplementarySequence(String) - Static method in class melting.sequences.NucleotidSequences
To check if a sequence is self complementary.
isSymmetric(int, int) - Method in class melting.sequences.NucleotidSequences
To check if the String sequence and String complementary are symmetric between the positions pos1 and pos2 in the duplex ArrayList of the NucleotidSequences object.
isTandemMismatchDeltaPPenaltyNecessary(int) - Method in class melting.sequences.NucleotidSequences
to check if there is an AG or GA base pair adjacent to an UC or CU base pair or a CC base pair adjacent to an AA base pair.
isTandemMismatchGGPenaltyNecessary(int) - Method in class melting.sequences.NucleotidSequences
To check if there is a GG base pair adjacent to a AA base pair or a base pair containing a pyrimidine ("C", "T" or "U").
isTopBasePyrimidine() - Method in class melting.sequences.BasePair
Check if the nucleic acid represented by TopAcid is a pyrimidine.
isUnpaired() - Method in class melting.sequences.BasePair
To check if the nucleic acids in the base pair are paired.
isWatsonCrickBottomBase() - Method in class melting.sequences.BasePair
Check if the Nucleic acid BottomAcid is a frequent nucleic acid.
A B C D E F G H I L M N O P R S T U V W X Z