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<H2><A NAME="SECTION00083000000000000000">
New DMSO and formamide corrections</A>
</H2>
<P>
<SPAN CLASS="textbf">1)</SPAN> Create a new class which implements the CorrectionMethod interface or, if it is adapted for
a new DMSO correction, which extends the DNADMSOCorrections class in the melting.correctionMethods package.
You must create your class int the adapted package : melting.otherCorrections.dmsoCorrections
package if it is a DMSO correction or melting.otherCorrections.formamideCorrections package if
it is a formamide correction.
<BR>
<BR>
If you just implement the CorrectionMethod interface, you have to implement the public methods
<SPAN CLASS="textit">boolean isApplicable(Environment environment)</SPAN> and <SPAN CLASS="textit">ThermoResult correctMeltingResults(Environment environment)</SPAN>
The first method is important to define the conditions of application of the correction and the
second is important to correct the computed melting temperature.
<BR>
<BR>
The DNADMSOCorrections is a base implementation for DMSO corrections and is focused on DNA sequences.
If you extend DNADMSOCorrections, you have to override the public method <SPAN CLASS="textit">boolean isApplicable(Environment environment)</SPAN>
to define the conditions of application of the DMSO correction.
The public method <SPAN CLASS="textit">ThermoResult correctMeltingResults(Environment environment)</SPAN>
has to be implemented to compute the DMSO correction.
<BR>
<BR>
<P>
<SPAN CLASS="textbf">2)</SPAN> Register the correction name and the class which represents it in the RegisterMethods
class (melting.configuration package).
You have to add into one of these functions of RegisterMethods :
<SPAN CLASS="textit">private void initialiseDMSOCorrectionMethod()</SPAN> or <SPAN CLASS="textit">private void initialiseFormamideCorrectionMethod()</SPAN>.
this following line :
<P>
<PRE>
/**
* initialises the DMSOCorrectionMethod HashMap of the
* RegisterMethods object.
*/
private void initialiseDMSOCorrectionMethod(){
[...]
DMSOCorrection.put("DMSOCorrection-Name",
Class-Name.class);
}
/**
* initialises the formamideCorrectionMethod HashMap of the
* RegisterMethods object.
*/
private void initialiseFormamideCorrectionMethod(){
[...]
formamideCorrection.put("formamideCorrection-Name",
Class-Name.class);
}
</PRE>
<P>
<SPAN CLASS="textbf">3)</SPAN> Don't forget to add a <SPAN CLASS="textit">private static String</SPAN> instance variable in your class. This
String represents the correction formula must be printed if the verbose mode is required by the user.
<P>
<PRE>
// Create a private static String which represents the
// correction formula.
private static String correctionFormula = "formula";
[...]
// To print the article reference of the correction
// formula if the verbose mode is required.
OptionManagement.meltingLogger.log(Level.FINE, "article
reference of the formula");
// To print the correction formula (the private static String)
OptionManagement.meltingLogger.log(Level.FINE,
correctionFormula);
[...]
}
</PRE>
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<ADDRESS>
Computational Neurobiology
2009-08-24
</ADDRESS>
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