I-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

## 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.

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