Keywords: DeveloppersGuide

# How to change the default textitMelting options

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.

    	/**
    	 * 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");

    	}