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<H2><A NAME="SECTION000113000000000000000">
what to change if you add new subnodes or new attributes</A>
</H2>
<P>
The current Handler classes in the package melting.handlers can manage
this type of node hierarchy :
<P>
<PRE>
<data type="strucure-type">
<subnode attribute1="value1" attribute2="value2">
<enthalpy>xx[...]xx.x</enthalpy>
<entropy>xx[...]xx.x</entropy>
</subnode>
[...]
<subnode sequence="AA/TT">
<enthalpy>xx[...]xx.x</enthalpy>
<entropy>xx[...]xx.x</entropy>
</subnode>
</data>
</PRE>
<P>
<SPAN CLASS="textbf">1)</SPAN> You have to register your new attribute in the DataHandler class in the melting.handlers
package. You need to change the method <SPAN CLASS="textit">public void endElement(String uri, String localName, String name)</SPAN>
to build the matching key in the dictionnary which will contain the thermodynamic parameters :
<P>
<PRE>
@Override
public void endElement(String uri, String localName, String name)
throws SAXException {
if (subHandler != null) {
subHandler.endElement(uri, localName, name);
if (subHandler.hasCompletedNode()) {
ThermoHandler handler = (ThermoHandler) subHandler;
String key = name;
if (handler.getAttribut().containsKey("type")) {
key += handler.getAttribut().get("type");
}
[...]
// Add your new attribute here
if (handler.getAttribut().containsKey("newAttribute-Name")) {
key += "subnode-Name" + handler.getAttribut().get("newAttribute-Name");
}
[...]
}
</PRE>
<P>
The dictionnary key for each thermodynamic parameter mostly has the following syntax,
<P>
<SPAN CLASS="textit">Subnode-nameAttribute1Value1Attribute2Value2</SPAN>
<P>
but it can be different for some attributes. (see the method in details)
<BR>
<BR><SPAN CLASS="textbf">2)</SPAN> You have to create (or change) a method in the DataCollect class from the melting package
to more easily get the thermodynamic parameters you need. See the example below :
<P>
<PRE>
/**
* to get the Thermodynamics object containing the parameters
* for the base pair (base1, base2) next to the mismatching
* base pair.
* @param string base1 : from the sequence (5'3')
* @param string base2 : from the complementary sequence (3'5')
* @return Thermodynamics object containing the parameters for
* the base pair (base1, base2) next to the mismatching base pair.
*/
public Thermodynamics getClosureValue(String base1, String base2){
Thermodynamics s = data.get("closure"+"per-"+base1 + "/"
+ base2);
return s;
}
// Your method can be similar to the following method
public Thermodynamics getNewThermodynamicParameter1(arg-1, ..., arg-n){
Thermodynamics s = data.get("node-name"+"attribute-1"+value-1
+[...]+"attribute-n"+value-n);
return s;
}
</PRE>
<P>
<BR><HR>
<ADDRESS>
Computational Neurobiology
2009-08-24
</ADDRESS>
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