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<H1><A NAME="SECTION00070000000000000000">
How to add new nucleic acids</A>
</H1>
<P>
<SPAN CLASS="textbf">1)</SPAN> Add the name to the new nucleic acid in the SpecificAcidNames enum in the melting.sequences
package :
<P>
<PRE>
public enum SpecificAcidNames {
inosine, lockedNucleicAcid, hydroxyadenine, azobenzene,
newNucleicAcidName
}
</PRE>
<P>
<SPAN CLASS="textbf">2)</SPAN> Register the new nucleic acid syntax in the ArrayList <SPAN CLASS="textit">existingNucleicAcids</SPAN>
of BasePair in the melting.sequences package. You just have to add the following line
into the method <SPAN CLASS="textit">public static void initialiseNucleicAcidList()</SPAN> of BasePair :
<P>
<PRE>
/**
* initialises the ArrayList existingNucleicAcids of the
* BasePair class.
*/
public static void initialiseNucleicAcidList(){
[...]
// You have to choose a syntax (String representation)
// of the new nucleic acid in the String sequence.
// It is this syntax which will be recognized by the
// program when it analyzes the sequences.
existingNucleicAcids.add("newAcid-syntax");
}
</PRE>
<P>
<SPAN CLASS="textbf">3)</SPAN> Create a relationship between the nucleic acid syntax in the ArrayList
<SPAN CLASS="textit">existingNucleicAcids</SPAN> of BasePair and the
nucleic acid name registered in the SpecificAcidNames enum. You have to add
the following line into the method <SPAN CLASS="textit">public static void initialiseModifiedAcidHashmap()</SPAN>
of NucleotidSequences in the melting.sequences package :
<P>
<PRE>
/**
* initialises the HasMap modifiedAcidNames of the
* NucleotiSequences class.
*/
public static void initialiseModifiedAcidHashmap(){
[...]
modifiedAcidNames.put("newAcid-syntax",
SpecificAcidNames.newNucleicAcidName);
}
</PRE>
<P>
<SPAN CLASS="textbf">4)</SPAN> Create a new class to manage the computation of the new nucleic acid as it is
explained in the section <SPAN CLASS="textit">How to add new thermodynamic model</SPAN>. (a new nucleic
acid is considered as a new structure in the computation of the enthalpy and entropy of
the Crick's pair containing the new nucleic acid.)
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<ADDRESS>
Computational Neurobiology
2009-08-24
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