Uses of Class melting.Environment (MELTING Java 5 API)
Date: 2013-10-04

## Uses of Class
melting.Environment

- Packages that use Environment
  Package | Description
  --- | ---
  melting |
  melting.approximativeMethods |
  melting.configuration |
  melting.correctionMethods |
  melting.ionCorrection.magnesiumCorrections |
  melting.ionCorrection.mixedNaMgCorrections |
  melting.ionCorrection.sodiumCorrections |
  melting.methodInterfaces |
  melting.nearestNeighborModel |
  melting.otherCorrections.dmsoCorrections |
  melting.otherCorrections.formamideCorrections |
  melting.patternModels |
  melting.patternModels.cngPatterns |
  melting.patternModels.cricksPair |
  melting.patternModels.InternalLoops |
  melting.patternModels.longBulge |
  melting.patternModels.longDanglingEnds |
  melting.patternModels.secondDanglingEnds |
  melting.patternModels.singleBulge |
  melting.patternModels.singleDanglingEnds |
  melting.patternModels.singleMismatch |
  melting.patternModels.specificAcids |
  melting.patternModels.tandemMismatches |
  melting.patternModels.wobble |

- - ### Uses of Environment in melting

    Methods in melting with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `static double` | Helper.`computesNaEquivalent(Environment environment)` computes a sodium equivalent concentration from the different ion concentrations of the Environment object.

  - ### Uses of Environment in melting.approximativeMethods

    Fields in melting.approximativeMethods declared as Environment
    Modifier and Type | Field and Description
    --- | ---
    `protected Environment` | ApproximativeMode.`environment` environment containing the sequences, ion and agent concentrations and the options (default options and options entered by the user)

  - ### Uses of Environment in melting.configuration

    Methods in melting.configuration that return Environment
    Modifier and Type | Method and Description
    --- | ---
    `Environment` | OptionManagement.`createEnvironment(String[] args)` collects the options entered by the user and creates an Environment from them.

    Methods in melting.configuration with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | RegisterMethods.`computeOtherMeltingCorrections(Environment environment)` corrects the melting temperature if other agents are present in the solution (formamide, DMSO, ...)
    `CorrectionMethod` | RegisterMethods.`getIonCorrectionMethod(Environment environment)` This method is called to get the CorrectionMethod which represents the method or model used for the ion correction in the environment 'environment'.

  - ### Uses of Environment in melting.correctionMethods

    Methods in melting.correctionMethods with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `protected double` | EntropyCorrection.`correctEntropy(Environment environment)` corrects the computed entropy (delta S (Na = 1M)).
    `ThermoResult` | DNADMSOCorrections.`correctMeltingResult(Environment environment, double parameter)`
    `ThermoResult` | EntropyCorrection.`correctMeltingResults(Environment environment)`
    `boolean` | DNADMSOCorrections.`isApplicable(Environment environment)`
    `boolean` | EntropyCorrection.`isApplicable(Environment environment)`

  - ### Uses of Environment in melting.ionCorrection.magnesiumCorrections

    Methods in melting.ionCorrection.magnesiumCorrections with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `static double` | Tan06MagnesiumCorrection.`computeFreeEnergyPerBaseStack(Environment environment)` represents the function associated with the electrostatic folding free energy per base stack.
    `static double` | Tan07MagnesiumCorrection.`computeFreeEnergyPerBaseStack(Environment environment)` represents the function associated with the electrostatic folding free energy per base stack.
    `protected double` | Tan06MagnesiumCorrection.`correctEntropy(Environment environment)`
    `protected double` | Tan07MagnesiumCorrection.`correctEntropy(Environment environment)`
    `ThermoResult` | Owczarzy08MagnesiumCorrection.`correctMeltingResults(Environment environment)`
    `protected double` | Owczarzy08MagnesiumCorrection.`correctTemperature(Environment environment)` corrects the computed melting temperature depending on the environment.
    `boolean` | Tan06MagnesiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Tan07MagnesiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Owczarzy08MagnesiumCorrection.`isApplicable(Environment environment)`

  - ### Uses of Environment in melting.ionCorrection.mixedNaMgCorrections

    Methods in melting.ionCorrection.mixedNaMgCorrections with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `protected double` | Tan07MixedNaMgCorrection.`correctEntropy(Environment environment)`
    `ThermoResult` | Owczarzy08MixedNaMgCorrection.`correctMeltingResults(Environment environment)`
    `boolean` | Tan07MixedNaMgCorrection.`isApplicable(Environment environment)`

  - ### Uses of Environment in melting.ionCorrection.sodiumCorrections

    Methods in melting.ionCorrection.sodiumCorrections with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `static double` | Tan07SodiumCorrection.`calculateFreeEnergyPerBaseStack(Environment environment)` represents the function associated with the electrostatic folding free energy per base stack.
    `static double` | Tan06SodiumCorrection.`calculateFreeEnergyPerBaseStack(Environment environment)` represents the function associated with the electrostatic folding free energy per base stack.
    `protected double` | Tan07SodiumCorrection.`correctEntropy(Environment environment)`
    `protected double` | Tan06SodiumCorrection.`correctEntropy(Environment environment)`
    `protected double` | Santalucia98_04SodiumCorrection.`correctEntropy(Environment environment)`
    `protected double` | Ahsen01SodiumCorrection.`correctEntropy(Environment environment)`
    `ThermoResult` | Owczarzy04SodiumCorrection19.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Santalucia96SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | MarmurSchildkrautDoty98_62SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Tan07SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Tan06SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Owczarzy04SodiumCorrection22.`correctMeltingResults(Environment environment)`
    `ThermoResult` | FrankKamenetskii71SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Wetmur91SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | SchildkrautLifson65SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Owczarzy04SodiumCorrection21.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Santalucia98_04SodiumCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Owczarzy04SodiumCorrection20.`correctMeltingResults(Environment environment)`
    `boolean` | Owczarzy04SodiumCorrection19.`isApplicable(Environment environment)`
    `boolean` | Santalucia96SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | MarmurSchildkrautDoty98_62SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Tan07SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Tan06SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Owczarzy04SodiumCorrection22.`isApplicable(Environment environment)`
    `boolean` | FrankKamenetskii71SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Wetmur91SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | SchildkrautLifson65SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Owczarzy04SodiumCorrection21.`isApplicable(Environment environment)`
    `boolean` | Santalucia98_04SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Ahsen01SodiumCorrection.`isApplicable(Environment environment)`
    `boolean` | Owczarzy04SodiumCorrection20.`isApplicable(Environment environment)`

  - ### Uses of Environment in melting.methodInterfaces

    Methods in melting.methodInterfaces with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | CorrectionMethod.`correctMeltingResults(Environment environment)` This method is called to correct the computed melting temperature.
    `boolean` | CorrectionMethod.`isApplicable(Environment environment)` Check if the environment chosen by the user is a applicable with the correction model.
    `boolean` | PatternComputationMethod.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.nearestNeighborModel

    Methods in melting.nearestNeighborModel with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `static double` | NearestNeighborMode.`computesHairpinTemperature(Environment environment)` computes the melting temperature of a hairpin loop (when there is more than 4 CNG repeats in a sequence)
    `static double` | NearestNeighborMode.`computesMeltingTemperature(Environment environment)` computes the melting temperature for for the Environment 'environment'.

  - ### Uses of Environment in melting.otherCorrections.dmsoCorrections

    Methods in melting.otherCorrections.dmsoCorrections with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Musielski81DMSOCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Escara80DMSOCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Cullen76DMSOCorrection.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Ahsen01DMSOCorrection.`correctMeltingResults(Environment environment)`

  - ### Uses of Environment in melting.otherCorrections.formamideCorrections

    Methods in melting.otherCorrections.formamideCorrections with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | FormamideLinearMethod.`correctMeltingResults(Environment environment)`
    `ThermoResult` | Blake96FormamideCorrection.`correctMeltingResults(Environment environment)`
    `boolean` | FormamideLinearMethod.`isApplicable(Environment environment)`
    `boolean` | Blake96FormamideCorrection.`isApplicable(Environment environment)`

  - ### Uses of Environment in melting.patternModels

    Methods in melting.patternModels with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | PatternComputation.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.cngPatterns

    Methods in melting.patternModels.cngPatterns with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Broda05CNGRepeats.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.cricksPair

    Methods in melting.patternModels.cricksPair with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Xia98.`computesHybridizationInitiation(Environment environment)`
    `ThermoResult` | DecomposedInitiation.`computesHybridizationInitiation(Environment environment)`
    `ThermoResult` | Turner06.`computesHybridizationInitiation(Environment environment)`
    `ThermoResult` | CricksNNMethod.`computesHybridizationInitiation(Environment environment)` computes the enthalpy and entropy for the duplex initiation with the Environment 'environment'.
    `ThermoResult` | GlobalInitiation.`computesHybridizationInitiation(Environment environment)`
    `ThermoResult` | Santalucia04.`computesHybridizationInitiation(Environment environment)`
    `ThermoResult` | Santalucia96.`computesHybridizationInitiation(Environment environment)`
    `boolean` | Breslauer86.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Freier86.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Xia98.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Sugimoto96.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Sugimoto95.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Turner06.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Santalucia04.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Tanaka04.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | AllawiSantalucia97.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Santalucia96.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.InternalLoops

    Methods in melting.patternModels.InternalLoops with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Znosko071x2Loop.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Turner06InternalLoop.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Santalucia04InternalLoop.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.longBulge

    Methods in melting.patternModels.longBulge with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Turner99_06LongBulgeLoop.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Santalucia04LongBulgeLoop.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.longDanglingEnds

    Methods in melting.patternModels.longDanglingEnds with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Sugimoto02RNADanglingEnd.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | SugimotoLongDanglingEndMethod.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Sugimoto02DNADanglingEnd.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.secondDanglingEnds

    Methods in melting.patternModels.secondDanglingEnds with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | SecondDanglingEndMethod.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.singleBulge

    Methods in melting.patternModels.singleBulge with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Tanaka04SingleBulgeLoop.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Serra07SingleBulgeLoop.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.singleDanglingEnds

    Methods in melting.patternModels.singleDanglingEnds with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Bommarito00SingleDanglingEnd.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Serra06_08SingleDanglingEnd.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | SingleDanglingEndMethod.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.singleMismatch

    Methods in melting.patternModels.singleMismatch with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Znosko08mm.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | ZnoskoMethod.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Watkins11mm.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Turner06mm.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | AllawiSantaluciaPeyret97_98_99mm.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.specificAcids

    Methods in melting.patternModels.specificAcids with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Sugimoto01Hydroxyadenine.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Asanuma05Azobenzene.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | McTigue04LockedAcid.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.tandemMismatches

    Methods in melting.patternModels.tandemMismatches with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Turner99_06tanmm.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | AllawiSantaluciaPeyret97_98_99tanmm.`isApplicable(Environment environment, int pos1, int pos2)`

  - ### Uses of Environment in melting.patternModels.wobble

    Methods in melting.patternModels.wobble with parameters of type Environment
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | Santalucia05Inosine.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Turner99Wobble.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Znosko07Inosine.`isApplicable(Environment environment, int pos1, int pos2)`
    `boolean` | Serra12Wobble.`isApplicable(Environment environment, int pos1, int pos2)`