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<H2><A NAME="SECTION00081000000000000000">
New ion correction</A>
</H2>
<P>
<SPAN CLASS="textbf">1)</SPAN> Create a new class which implements the CorrectionMethod interface or, if it is adapted, which
extends the EntropyCorrection class in the melting.correctionMethods package.
<BR>
<BR>
The class must be created in the adapted package :
melting.ionCorrection.magnesiumCorrection if it is a new magnesium correction,
melting.ionCorrection.mixedNaMgCorrection if it is a new mixed monovalent correction,
magnesium correction or
melting.ionCorrection.sodiumCorrection if it is a new sodium correction.
<BR>
<BR>
<P>
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 ion correction and the
second is important to correct the computed melting temperature.
<BR>
<BR>
<P>
The EntropyCorrection is a base implementation for ion corrections which directly correct the
computed entropy and then compute te melting temperature. If you extend EntropyCorrection, you have to
override the public method <SPAN CLASS="textit">boolean isApplicable(Environment environment)</SPAN> to define the conditions
of application of the ion correction.
<BR>
<BR>
The public method <SPAN CLASS="textit">ThermoResult correctMeltingResults(Environment environment)</SPAN> is already implemented
by EntropyCorrection but you have to override the method <SPAN CLASS="textit">protected double correctEntropy(Environment environment)</SPAN>
to correct the computed entropy.
<BR>
<BR>
<P>
<SPAN CLASS="textbf">2)</SPAN> Register the ion correction name and the class which represents it in the RegisterMethods
class (melting.configuration package).
You have to add into the function <SPAN CLASS="textit">private void initialiseIonCorrectionMethod()</SPAN> of RegisterMethods
this following line :
<P>
<PRE>
private void initialiseIonCorrectionMethod(){
[...]
ionCorrection.put("sodiumCorrection-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 you applied to the computed melting temperature or the
computed entropy and 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 correction");
// To print the correction formula (the private static String)
OptionManagement.meltingLogger.log(Level.FINE,
correctionFormula);
[...]
}
</PRE>
<P>
<SPAN CLASS="textbf">4)</SPAN> In case of sodium corrections, you can use the method <SPAN CLASS="textit">public static computesNaEquivalent(environment)</SPAN>
of the Helper class in melting package to convert the sodium concentration entered by the user
into a sodium equivalent concentration which takes into account the other cations entered
by the user.
<P>
<PRE>
double NaEq = Helper.computesNaEquivalent(environment);
</PRE>
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<ADDRESS>
Computational Neurobiology
2009-08-24
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