- examples
This package contains all the main classes to test the program.
- test
It contains all the experimental Data and sequences to test the program.
- melting
This package contains the general classes used by most classes of the program. It also
contains the main class which runs MELTING.
- approximativeMethods
It contains all the classes which implement an approximative formula to compute the melting
temperature.
- configuration
It contains all the classes which register the option, models and corrections names. It contains
the classes which manage the default options and which map the models and correction names with the
matching classes.
- correctionMethods
It regroups some of the base implementations for ion or denaturing agent corrections.
- exceptions
It contains all the exceptions used in the program.
- handlers
It contains all the Handler classes necessary to parse the XML files.
- ionCorrection
- magnesiumCorrections
It contains all the classes which implement a magnesium correction.
- mixedNaMgCorrections
It contains all the classes which implement a mixed sodium, magnesium correction.
- sodiumCorrections
It contains all the classes which implement a sodium correction.
- sodiumEquivalence
It contains all the classes which implement a formula to compute a sodium-equivalent concentration.
- methodInterfaces
It contains all the interfaces.
- nearestNeighborModel
It contains the class which uses a Nearest-Neighbor approach to compute the enthalpy, entropy and
melting temperature.
- otherCorrections
- dmsoCorrections
It contains all the classes which implement a DMSO correction.
- formamideCorrections
It contains all the classes which implement a formamide correction.
- patternModels
It contains the base implementation of each thermodynamic model.
- cngPatterns
It contains the class which implements a thermodynamic model for CNG repetitions computation.
- cricksPair
It contains the classes which implement a thermodynamic model for Crick's pairs computation.
- InternalLoops
It contains the classes which implement a thermodynamic model for internal loop computation.
- longBulge
It contains the classes which implement a thermodynamic model for long bulge loop computation.
- longDanglingEnds
It contains the classes which implement a thermodynamic model for long dangling end computation.
- secondDanglingEnds
It contains the classes which implement a thermodynamic model for two adjacent dangling end computation.
- singleBulge
It contains the classes which implement a thermodynamic model for single bulge loop computation.
- singleDanglingEnds
It contains the classes which implement a thermodynamic model for single dangling end computation.
- singleMismatch
It contains the classes which implement a thermodynamic model for single mismatch computation.
- specificAcids
It contains the classes which implement a thermodynamic model for specific or modified nucleic acids
computation.
- tandemMismatches
It contains the classes which implement a thermodynamic model for tandem mismatches computation.
- wobble
It contains the classes which implement a thermodynamic model for inosine and GU base pair computation.
- sequences
It contains the classes which allow to represent nucleic acids and sequences and analyze them.
Computational Neurobiology
2009-08-24