Keywords: DeveloppersGuide

### Thermodynamic model for Crick's pairs computation

If it is possible, you directly can create a new class which extends the CricksNNMethod class. (melting.patternModels.cricksPair)
The CrickNNMethod class already implements the following public functions of the PatternComputationMethod interface.: ThermoResult computeThermodynamics(NucleotidSequences sequences,int pos1, int pos2, ThermoResult result), isMissingParameters(NucleotidSequences sequences, int pos1, int pos2), and ThermoResult computesHybridizationInitiation(Environment environment).
A CricksNNMethod can compute the enthalpy and entropy of a perfectly matching structure by adding the thermodynamic parameters of each Crick's base pair. The implemented function isMissingParameters(NucleotidSequences sequences, int pos1, int pos2) can determine if a thermodynamic parameter for one of the Crick's pair is missing. Finally, the implemented function ThermoResult computesHybridizationInitiation(Environment environment) is the base implementation of the hybridization initiation computation and the symetry correction for self complementary sequences.

If the hybridization initiation can be computed with the function public ThermoResult computesHybridizationInitiation(Environment environment) of one of the following classes : DecomposedInitiation or GlobalInitiation, you directly can create a new class which extends DecomposedInitiation or GlobalInitiation.