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<H1><A NAME="SECTION000100000000000000000">
How to change the default textitMelting options</A>
</H1>
<P>
You can change the default textitMelting options in the OptionManagement class from the
melting.configuration package. There are different default oprions for each type of hybridization.
<P>
<PRE>
/**
* initialises the DNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialisesDNADefaultOptions() {
this.DNADefaultOptions.put(NNMethod, "san04");
this.DNADefaultOptions.put(singleMismatchMethod, "allsanpey");
this.DNADefaultOptions.put(tandemMismatchMethod, "allsanpey");
this.DNADefaultOptions.put(internalLoopMethod, "san04");
this.DNADefaultOptions.put(singleDanglingEndMethod, "bom00");
this.DNADefaultOptions.put(doubleDanglingEndMethod, "sugdna02");
this.DNADefaultOptions.put(singleBulgeLoopMethod, "tan04");
this.DNADefaultOptions.put(longDanglingEndMethod, "sugdna02");
this.DNADefaultOptions.put(longBulgeLoopMethod, "san04");
this.DNADefaultOptions.put(approximativeMode, "wetdna91");
this.DNADefaultOptions.put(DMSOCorrection, "ahs01");
this.DNADefaultOptions.put(formamideCorrection, "bla96");
this.DNADefaultOptions.put(inosineMethod, "san05");
this.DNADefaultOptions.put(hydroxyadenineMethod, "sug01");
this.DNADefaultOptions.put(azobenzeneMethod, "asa05");
this.DNADefaultOptions.put(lockedAcidMethod, "mct04");
this.DNADefaultOptions.put(NaEquivalentMethod, "ahs01");
}
/**
* initialises the RNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseRNADefaultOptions() {
this.RNADefaultOptions.put(NNMethod, "xia98");
this.RNADefaultOptions.put(singleMismatchMethod, "zno07");
this.RNADefaultOptions.put(wobbleBaseMethod, "tur99");
this.RNADefaultOptions.put(tandemMismatchMethod, "tur06");
this.RNADefaultOptions.put(internalLoopMethod, "tur06");
this.RNADefaultOptions.put(singleBulgeLoopMethod, "tur06");
this.RNADefaultOptions.put(longBulgeLoopMethod, "tur06");
this.RNADefaultOptions.put(CNGMethod, "bro05");
this.RNADefaultOptions.put(approximativeMode, "wetrna91");
this.RNADefaultOptions.put(inosineMethod, "zno07");
this.RNADefaultOptions.put(NaEquivalentMethod, "ahs01");
this.RNADefaultOptions.put(DMSOCorrection, "ahs01");
this.RNADefaultOptions.put(formamideCorrection, "bla96");
this.RNADefaultOptions.put(singleDanglingEndMethod, "ser08");
this.RNADefaultOptions.put(doubleDanglingEndMethod, "ser06");
this.RNADefaultOptions.put(longDanglingEndMethod, "sugrna02");
}
/**
* initialises the hybridDefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseHybridDefaultOptions() {
this.hybridDefaultOptions.put(NNMethod, "sug95");
this.hybridDefaultOptions.put(approximativeMode, "Wetdnarna91");
this.hybridDefaultOptions.put(NaEquivalentMethod, "ahs01");
this.hybridDefaultOptions.put(DMSOCorrection, "ahs01");
this.hybridDefaultOptions.put(formamideCorrection, "bla96");
}
/**
* initialises the mRNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseMRNADefaultOptions() {
this.mRNADefaultOptions.put(NNMethod, "tur06");
this.mRNADefaultOptions.put(NaEquivalentMethod, "ahs01");
this.mRNADefaultOptions.put(DMSOCorrection, "ahs01");
this.mRNADefaultOptions.put(formamideCorrection, "bla96");
}
</PRE>
<P>
<BR><HR>
<ADDRESS>
Computational Neurobiology
2009-08-24
</ADDRESS>
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