Refactoring agreed for the next version (v0.1.2; see CHANGELOG.md); this is just intended as a relabelling of existing implementation to make major review easier for the following version (v0.1.3):
[x] Convert teaspoon.adaptation.Methods class members to Static and rename/move to teaspoon.app.utils
[x] Rename variable names in teaspoon.adaptation.Value (and possibly the class itself), generate getters, and move to utils.
[x] Fixed / estimated NR behaviour clarified / automated.
[x] Rename existing methods which achieve different behaviours via overloading:
teaspoon.adaptation.analyseGene.bmAnalysis() vs teaspoon.adaptation.analyseGene.bmAnalysisBootstrap(int)
teaspoon.adaptation.analyseDeepGenome.bmAnalysis() vs teaspoon.adaptation.analyseDeepGenome.bmAnalysisBootstrap(int)
[x] Refactoring to teaspoon.adaptation.BhattMethod:
needPrior behaviour (always true, not necessarily needed)
Refactoring agreed for the next version (v0.1.2; see CHANGELOG.md); this is just intended as a relabelling of existing implementation to make major review easier for the following version (v0.1.3):
teaspoon.adaptation.Methodsclass members to Static and rename/move toteaspoon.app.utilsteaspoon.adaptation.Value(and possibly the class itself), generate getters, and move toutils.teaspoon.adaptation.analyseGene.bmAnalysis()vsteaspoon.adaptation.analyseGene.bmAnalysisBootstrap(int)teaspoon.adaptation.analyseDeepGenome.bmAnalysis()vsteaspoon.adaptation.analyseDeepGenome.bmAnalysisBootstrap(int)teaspoon.adaptation.BhattMethod:execute()/run()/analyse()renamed