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

## Uses of Class
melting.patternModels.PatternComputation

- Packages that use PatternComputation
  Package | Description
  --- | ---
  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 PatternComputation in melting.patternModels.cngPatterns

    Subclasses of PatternComputation in melting.patternModels.cngPatterns
    Modifier and Type | Class and Description
    --- | ---
    `class` | `Broda05CNGRepeats` This class represents the CNG repeats model bro05.

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

    Subclasses of PatternComputation in melting.patternModels.cricksPair
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AllawiSantalucia97` This class represents the nearest neighbor model all97.
    `class` | `Breslauer86` This class represents the nearest neighbor model bre86.
    `class` | `CricksNNMethod` This class represents the NN nearest neighbor model (adds the thermodynamic energy (enthalpy and entropy) for each Crick's pair composing the duplex).
    `class` | `DecomposedInitiation` This class represents one model to compute the initiation enthalpy and entropy.
    `class` | `Freier86` This class represents the nearest neighbor model fre86.
    `class` | `GlobalInitiation` This class represents one model to compute the initiation enthalpy and entropy.
    `class` | `Santalucia04` This class represents the nearest neighbor model san04.
    `class` | `Santalucia96` This class represents the nearest neighbor model san96.
    `class` | `Sugimoto95` This class represents the nearest neighbor model sug95.
    `class` | `Sugimoto96` This class represents the nearest neighbor model sug96.
    `class` | `Tanaka04` This class represents the nearest neighbor model tan04.
    `class` | `Turner06` This class represents the nearest neighbor model tur06.
    `class` | `Xia98` This class represents the nearest neighbor model xia98.

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

    Subclasses of PatternComputation in melting.patternModels.InternalLoops
    Modifier and Type | Class and Description
    --- | ---
    `class` | `Santalucia04InternalLoop` This class represents the internal loop model san04.
    `class` | `Turner06InternalLoop` This class represents the internal loop model tur06.
    `class` | `Znosko071x2Loop` This class represents the 1x2 internal loop model zno07.

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

    Subclasses of PatternComputation in melting.patternModels.longBulge
    Modifier and Type | Class and Description
    --- | ---
    `class` | `Santalucia04LongBulgeLoop` This class represents the long bulge loop model san04.
    `class` | `Turner99_06LongBulgeLoop` This class represents the long bulge loop model tur06.

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

    Subclasses of PatternComputation in melting.patternModels.longDanglingEnds
    Modifier and Type | Class and Description
    --- | ---
    `class` | `Sugimoto02DNADanglingEnd` This class represents the long dangling end model sugdna02 (for long poly A only).
    `class` | `Sugimoto02RNADanglingEnd` This class represents the long dangling end model sugrna02 (for long poly A only).
    `class` | `SugimotoLongDanglingEndMethod` This class represents the long dangling end model (for long poly A only)from Sugimoto et al. 2002.

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

    Subclasses of PatternComputation in melting.patternModels.secondDanglingEnds
    Modifier and Type | Class and Description
    --- | ---
    `class` | `SecondDanglingEndMethod` This class represents the second dangling end model.
    `class` | `Serra05DoubleDanglingEnd` This class represents the second dangling end model ser05.
    `class` | `Serra06DoubleDanglingEnd` This class represents the second dangling end model ser06.

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

    Subclasses of PatternComputation in melting.patternModels.singleBulge
    Modifier and Type | Class and Description
    --- | ---
    `class` | `GlobalSingleBulgeLoopMethod` This class represents one single bulge loop model.
    `class` | `Santalucia04SingleBulgeLoop` This class represents the single bulge loop model san04.
    `class` | `Serra07SingleBulgeLoop` This class represents the single bulge loop model ser07.
    `class` | `Tanaka04SingleBulgeLoop` This class represents the single bulge loop model tan04.
    `class` | `Turner99_06SingleBulgeLoop` This class represents the single bulge loop model tur06.

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

    Subclasses of PatternComputation in melting.patternModels.singleDanglingEnds
    Modifier and Type | Class and Description
    --- | ---
    `class` | `Bommarito00SingleDanglingEnd` This class represents the single dangling end model bom00.
    `class` | `Serra06_08SingleDanglingEnd` This class represents the single dangling end model ser08.
    `class` | `SingleDanglingEndMethod` This class represents the single dangling end model.

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

    Subclasses of PatternComputation in melting.patternModels.singleMismatch
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AllawiSantaluciaPeyret97_98_99mm` This class represents the single mismatch model allsanpey.
    `class` | `Turner06mm` This class represents the single mismatch model tur06.
    `class` | `Watkins11mm` This class represents the DNA/RNA single mismatch model wat11.
    `class` | `Znosko07mm` This class represents the single mismatch model zno07.
    `class` | `Znosko08mm` This class represents the single mismatch model zno08.
    `class` | `ZnoskoMethod` This class represents the single mismatch model from Znosco et al, 2007, 2008.

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

    Subclasses of PatternComputation in melting.patternModels.specificAcids
    Modifier and Type | Class and Description
    --- | ---
    `class` | `Asanuma05Azobenzene` This class represents the azobenzene (X_C or X_T) model asa05.
    `class` | `McTigue04LockedAcid` This class represents the locked nucleic acid (AL, GL, CL or TL) model mct04.
    `class` | `Sugimoto01Hydroxyadenine` This class represents the hydroxyadenine (A*) model sug01.

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

    Subclasses of PatternComputation in melting.patternModels.tandemMismatches
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AllawiSantaluciaPeyret97_98_99tanmm` This class represents the tandem mismatches model allsanpey.
    `class` | `Turner99_06tanmm` This class represents the tandem mismatches model tur06.

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

    Subclasses of PatternComputation in melting.patternModels.wobble
    Modifier and Type | Class and Description
    --- | ---
    `class` | `InosineNNMethod` This class represents the inosine model.
    `class` | `Santalucia05Inosine` This class represents the inosine model san05.
    `class` | `Serra12Wobble` This class represents the GU base pair model ser12.
    `class` | `Turner99Wobble` This class represents the GU base pair model tur99.
    `class` | `Znosko07Inosine` This class represents the inosine model zno07.