Keywords: DeveloppersGuide

### Thermodynamic model for single bulge loop computation

If it is possible, you directly can create a new class which extends the GlobalSingleBuleLoop class (melting.patternModels.singleBulge).
The GlobalSingleBuleLoop class already implements the following public functions of the PatternComputationMethod interface.: ThermoResult computeThermodynamics(NucleotidSequences sequences,int pos1, int pos2, ThermoResult result), and isMissingParameters(NucleotidSequences sequences, int pos1, int pos2).
A GlobalSingleBuleLoop can compute the enthalpy and entropy of a single bulge loop by adding the thermodynamic parameters for the trinucleotide containing the single bulge loop. The implemented function isMissingParameters(NucleotidSequences sequences, int pos1, int pos2) can determine if a thermodynamic parameter for the trinucleotide containing the single bulge loop is missing.
Finally, the implemented function int[] correctPositions(int pos1, int pos2, int duplexLength) is necessary to take into account the adjacent base pairs of the single bulge loop.