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<H2><A NAME="SECTION00092000000000000000">
New denaturing agent species or other species</A>
</H2>
<P>
<SPAN CLASS="textbf">1)</SPAN> If the new species is an ion which can't be included in the algorithm from Owczarzy et al. 2008
or if it is a new denaturing agent, you have to create a new instance variable of RegisterMethods in
the melting.cinfiguration package. The new <SPAN CLASS="textit">private static HashMap<String, Class<? extends CorrectionMethod»</SPAN>
register all the corrections for the new species.
<P>
<PRE>
/**
* HasMap formamideCorrection : contains all the methods for
* the new species correction.
*/
private static HashMap<String, Class<? extends CorrectionMethod>>
newSpeciesCorrection =
new HashMap<String, Class<? extends CorrectionMethod>>();
</PRE>
<P>
<SPAN CLASS="textbf">2)</SPAN> You have to create a new method in RegisterMethods to initialise the new HasMap :
<P>
<PRE>
/**
* initialises the newSpeciesCorrectionMethod HashMap of
* the RegisterMethods object.
*/
private void initialiseNewSpeciesCorrectionMethod(){
[...]
newSpeciesCorrection.put("NewSpeciesCorrection-Name",
ClassName.class);
}
</PRE>
<P>
<SPAN CLASS="textbf">3)</SPAN> You have to create a new option to give the possibility to change the correction
for the new species. You must add a new <SPAN CLASS="textit">public static final String</SPAN> in the
OptionManagement class to register the name of the new option. (melting.configuration package)
<P>
<PRE>
/**
* Option name for to change the default correction for the
* new species.
*/
public static final String newSpeciesOption = "Option-Name";
</PRE>
<P>
<SPAN CLASS="textbf">4)</SPAN> Choose a default new species correction for each type of hybridization in
the following methods of OptionManagement :
<P>
<PRE>
/**
* initialises the DNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialisesDNADefaultOptions() {
[...]
this.DNADefaultOptions.put(newSpeciesOption,
"DNAdefaultCorrection-Name");
}
/**
* initialises the RNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseRNADefaultOptions() {
[...]
this.RNADefaultOptions.put(newSpeciesOption,
"RNAdefaultCorrection-Name");
}
/**
* initialises the hybridDefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseHybridDefaultOptions() {
[...]
this.hybridDefaultOptions.put(newSpeciesOption,
"DNARNAdefaultCorrection-Name");
}
/**
* initialises the mRNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseMRNADefaultOptions() {
[...]
this.mRNADefaultOptions.put(newSpeciesOption,
"mRNAdefaultCorrection-Name");
}
</PRE>
<P>
<SPAN CLASS="textbf">5)</SPAN> You have to register the new option in the HashMap <SPAN CLASS="textit">registerEnvironmentOptions</SPAN>
of OptionManagement. You just have to add the following line into the method
<SPAN CLASS="textit">private void initialiseRegisterEnvironmentOptions()</SPAN> of OptionManagement :
<P>
<PRE>
/**
* Initialises the registerEnvironmentOptions HashMap of the
* OptionManagement object.
*/
private void initialiseRegisterEnvironmentOptions(){
[...]
registerEnvironmentOptions.add(newSpeciesOption);
}
</PRE>
<P>
<SPAN CLASS="textbf">6)</SPAN> You have to register the new species and the new corrections for it in RegisterMethods (melting.configuration package).
You must add the following line to the method <SPAN CLASS="textit">private void initialiseOtherCorrectionMethod()</SPAN> :
<P>
<PRE>
/**
* initialises the otherCorrectionMethod HashMap of the
* RegisterMethods object.
*/
private void initialiseOtherCorrectionMethod(){
[...]
// create a relationship between the new option and
//the corrections registered for the new species.
otherCorrection.put(OptionManagement.newSpeciesOption,
newSpeciesCorrection);
}
</PRE>
<P>
<SPAN CLASS="textbf">7)</SPAN> You have to complete the method <SPAN CLASS="textit">public ThermoResult computeOtherMeltingCorrections(Environment environment)</SPAN>
of RegisterMethods. This method is important to correct the melting temperature if another ion or denaturing agent species
are present :
<P>
<PRE>
public ThermoResult computeOtherMeltingCorrections(Environment
environment){
[...]
// Check if the new species is present in the environment
if (environment.getNewSpecies() > 0){
// Get the correction associated with the option name of the
// new species.
CorrectionMethod newSpeciesCorrection =
getCorrectionMethod(OptionManagement.newSpeciesCorrection,
environment.getOptions().get(OptionManagement.newSpeciesCorrection));
if (newSpeciesCorrection == null){
throw new NoExistingMethodException("There is no implemented
new species correction.");
}
else if (newSpeciesCorrection.isApplicable(environment)){
environment.setResult
(newSpeciesCorrection.correctMeltingResults(environment));
}
else {
throw new MethodNotApplicableException("The new species correction
is not applicable with this environment
(option " + OptionManagement.newSpeciesCorrection + ").");
}
}
</PRE>
<P>
<SPAN CLASS="textbf">8)</SPAN> Create a new class for the new species corrections as it is explained in the section
<SPAN CLASS="textit">How to add new corrections for Na, Mg, K, Tris, DMSO and/or formamide</SPAN>.
<P>
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<ADDRESS>
Computational Neurobiology
2009-08-24
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