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

## Uses of Class
melting.sequences.NucleotidSequences

- Packages that use NucleotidSequences
  Package | Description
  --- | ---
  melting |
  melting.methodInterfaces |
  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 |
  melting.sequences |

- - ### Uses of NucleotidSequences in melting

    Methods in melting that return NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `NucleotidSequences` | Environment.`getSequences()` This method is called to get the sequences NucleotidSequences of Environment.

  - ### Uses of NucleotidSequences in melting.methodInterfaces

    Methods in melting.methodInterfaces with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | PatternComputationMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | PatternComputationMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)` Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern at the positions pos1 and pos2.

  - ### Uses of NucleotidSequences in melting.patternModels

    Methods in melting.patternModels with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `abstract ThermoResult` | PatternComputation.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | PatternComputation.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.cngPatterns with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Broda05CNGRepeats.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Broda05CNGRepeats.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.cricksPair with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Breslauer86.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Freier86.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Xia98.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Sugimoto96.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Sugimoto95.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Turner06.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | CricksNNMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Santalucia04.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Tanaka04.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | AllawiSantalucia97.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Santalucia96.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Breslauer86.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Freier86.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Xia98.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Sugimoto96.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Sugimoto95.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Turner06.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | CricksNNMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Santalucia04.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Tanaka04.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | AllawiSantalucia97.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Santalucia96.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.InternalLoops with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Znosko071x2Loop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Turner06InternalLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Santalucia04InternalLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Znosko071x2Loop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Turner06InternalLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Santalucia04InternalLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.longBulge with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Turner99_06LongBulgeLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Santalucia04LongBulgeLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Turner99_06LongBulgeLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Santalucia04LongBulgeLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.longDanglingEnds with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Sugimoto02RNADanglingEnd.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | SugimotoLongDanglingEndMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Sugimoto02DNADanglingEnd.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Sugimoto02RNADanglingEnd.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | SugimotoLongDanglingEndMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Sugimoto02DNADanglingEnd.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.secondDanglingEnds with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Serra05DoubleDanglingEnd.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Serra06DoubleDanglingEnd.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | SecondDanglingEndMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Serra05DoubleDanglingEnd.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Serra06DoubleDanglingEnd.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | SecondDanglingEndMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.singleBulge with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Tanaka04SingleBulgeLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Turner99_06SingleBulgeLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Santalucia04SingleBulgeLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | GlobalSingleBulgeLoopMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Serra07SingleBulgeLoop.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Tanaka04SingleBulgeLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Turner99_06SingleBulgeLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Santalucia04SingleBulgeLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | GlobalSingleBulgeLoopMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Serra07SingleBulgeLoop.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.singleDanglingEnds with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Bommarito00SingleDanglingEnd.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Serra06_08SingleDanglingEnd.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | SingleDanglingEndMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Bommarito00SingleDanglingEnd.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Serra06_08SingleDanglingEnd.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | SingleDanglingEndMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.singleMismatch with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Znosko08mm.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | ZnoskoMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Watkins11mm.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Znosko07mm.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Turner06mm.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | AllawiSantaluciaPeyret97_98_99mm.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | ZnoskoMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Watkins11mm.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Turner06mm.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | AllawiSantaluciaPeyret97_98_99mm.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.specificAcids with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Sugimoto01Hydroxyadenine.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Asanuma05Azobenzene.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | McTigue04LockedAcid.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Sugimoto01Hydroxyadenine.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Asanuma05Azobenzene.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | McTigue04LockedAcid.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.tandemMismatches with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Turner99_06tanmm.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | AllawiSantaluciaPeyret97_98_99tanmm.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Turner99_06tanmm.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | AllawiSantaluciaPeyret97_98_99tanmm.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

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

    Methods in melting.patternModels.wobble with parameters of type NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | Santalucia05Inosine.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | InosineNNMethod.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Turner99Wobble.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Znosko07Inosine.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `ThermoResult` | Serra12Wobble.`computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `protected ThermoResult` | Turner99Wobble.`getGUThermoResult(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `protected ThermoResult` | Serra12Wobble.`getGUThermoResult(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)`
    `boolean` | Santalucia05Inosine.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | InosineNNMethod.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Turner99Wobble.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Znosko07Inosine.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`
    `boolean` | Serra12Wobble.`isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)`

  - ### Uses of NucleotidSequences in melting.sequences

    Methods in melting.sequences that return NucleotidSequences
    Modifier and Type | Method and Description
    --- | ---
    `static NucleotidSequences` | NucleotidSequences.`buildSymetricSequences(String seq1, String seq2)` creates a NucleotidSequences with two symmetric sequences String created from the seq1 String an seq2 String.
    `NucleotidSequences` | NucleotidSequences.`getEquivalentSequences(String hybridizationType)` This method is called when the same NucleotidSequences is required but with the sequences converted in the new hybridization type "hybridizationType"

    Constructors in melting.sequences with parameters of type NucleotidSequences
    Constructor and Description
    `NucleotidSequences(String hybridizationType, NucleotidSequences sequences)` Creates a new NucleotidSequences object from a reference nucleotiDSequences object.