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<H1><A NAME="SECTION00030000000000000000">
Package layout</A>
</H1>
<P>
<UL>
<LI><SPAN CLASS="textit">examples</SPAN>
<BR>
This package contains all the main classes to test the program.
<UL>
<LI><SPAN CLASS="textit">test</SPAN>
<BR>
It contains all the experimental Data and sequences to test the program.
</LI>
</UL>
</LI>
<LI><SPAN CLASS="textit">melting</SPAN>
<BR>
This package contains the general classes used by most classes of the program. It also
contains the main class which runs <SMALL>MELTING</SMALL>.
<UL>
<LI><SPAN CLASS="textit">approximativeMethods</SPAN>
<BR>
It contains all the classes which implement an approximative formula to compute the melting
temperature.
</LI>
<LI><SPAN CLASS="textit">configuration</SPAN>
<BR>
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.
</LI>
<LI><SPAN CLASS="textit">correctionMethods</SPAN>
<BR>
It regroups some of the base implementations for ion or denaturing agent corrections.
</LI>
<LI><SPAN CLASS="textit">exceptions</SPAN>
<BR>
It contains all the exceptions used in the program.
</LI>
<LI><SPAN CLASS="textit">handlers</SPAN>
<BR>
It contains all the Handler classes necessary to parse the XML files.
</LI>
<LI><SPAN CLASS="textit">ionCorrection</SPAN>
<BR>
<UL>
<LI><SPAN CLASS="textit">magnesiumCorrections</SPAN>
<BR>
It contains all the classes which implement a magnesium correction.
</LI>
<LI><SPAN CLASS="textit">mixedNaMgCorrections</SPAN>
<BR>
It contains all the classes which implement a mixed sodium, magnesium correction.
</LI>
<LI><SPAN CLASS="textit">sodiumCorrections</SPAN>
<BR>
It contains all the classes which implement a sodium correction.
</LI>
<LI><SPAN CLASS="textit">sodiumEquivalence</SPAN>
<BR>
It contains all the classes which implement a formula to compute a sodium-equivalent concentration.
</LI>
</UL>
</LI>
<LI><SPAN CLASS="textit">methodInterfaces</SPAN>
<BR>
It contains all the interfaces.
</LI>
<LI><SPAN CLASS="textit">nearestNeighborModel</SPAN>
<BR>
It contains the class which uses a Nearest-Neighbor approach to compute the enthalpy, entropy and
melting temperature.
</LI>
<LI><SPAN CLASS="textit">otherCorrections</SPAN>
<BR>
<UL>
<LI><SPAN CLASS="textit">dmsoCorrections</SPAN>
<BR>
It contains all the classes which implement a DMSO correction.
</LI>
<LI><SPAN CLASS="textit">formamideCorrections</SPAN>
<BR>
It contains all the classes which implement a formamide correction.
</LI>
</UL>
</LI>
<LI><SPAN CLASS="textit">patternModels</SPAN>
<BR>
It contains the base implementation of each thermodynamic model.
<UL>
<LI><SPAN CLASS="textit">cngPatterns</SPAN>
<BR>
It contains the class which implements a thermodynamic model for CNG repetitions computation.
</LI>
<LI><SPAN CLASS="textit">cricksPair</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for Crick's pairs computation.
</LI>
<LI><SPAN CLASS="textit">InternalLoops</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for internal loop computation.
</LI>
<LI><SPAN CLASS="textit">longBulge</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for long bulge loop computation.
</LI>
<LI><SPAN CLASS="textit">longDanglingEnds</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for long dangling end computation.
</LI>
<LI><SPAN CLASS="textit">secondDanglingEnds</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for two adjacent dangling end computation.
</LI>
<LI><SPAN CLASS="textit">singleBulge</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for single bulge loop computation.
</LI>
<LI><SPAN CLASS="textit">singleDanglingEnds</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for single dangling end computation.
</LI>
<LI><SPAN CLASS="textit">singleMismatch</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for single mismatch computation.
</LI>
<LI><SPAN CLASS="textit">specificAcids</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for specific or modified nucleic acids
computation.
</LI>
<LI><SPAN CLASS="textit">tandemMismatches</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for tandem mismatches computation.
</LI>
<LI><SPAN CLASS="textit">wobble</SPAN>
<BR>
It contains the classes which implement a thermodynamic model for inosine and GU base pair computation.
</LI>
</UL>
</LI>
<LI><SPAN CLASS="textit">sequences</SPAN>
<BR>
It contains the classes which allow to represent nucleic acids and sequences and analyze them.
</LI>
</UL>
</LI>
</UL>
<P>
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<ADDRESS>
Computational Neurobiology
2009-08-24
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