- 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
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To check if a sequence is self complementary.
- isSymmetric(int, int) - Method in class melting.sequences.NucleotidSequences
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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
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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
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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
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Check if the nucleic acid represented by TopAcid is a pyrimidine.
- isUnpaired() - Method in class melting.sequences.BasePair
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To check if the nucleic acids in the base pair are paired.
- isWatsonCrickBottomBase() - Method in class melting.sequences.BasePair
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Check if the Nucleic acid BottomAcid is a frequent nucleic acid.