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<H1><A NAME="SECTION00060000000000000000">
How to create a new duplex structure</A>
</H1>
<P>
<SPAN CLASS="textbf">1)</SPAN> Create a new package with the name of the structure.
<BR>
<BR>
<P>
<SPAN CLASS="textbf">2)</SPAN> Create a new instance variable
<SPAN CLASS="textit">private static HashMap<String, Class<? extends PatternComputationMethod» newStructureMethod</SPAN>
of the class RegisterMethods in the melting.configuration package.
<P>
<PRE>
/**
* HasMap newStructureMethod : contains all the methods
* for the new structure computation.
*/
private static HashMap<String, Class<? extends
PatternComputationMethod>> newStructureMethod =
new HashMap<String, Class<? extends PatternComputationMethod>>();
</PRE>
<P>
<SPAN CLASS="textbf">3)</SPAN> Create a new method in the RegisterMethod class to initialise the
<SPAN CLASS="textit"><String, Class<? extends PatternComputationMethod» newStructureMethod</SPAN> you created. It must contains
all the relationships between the new model names and the matching implemented class:
<P>
<PRE>
private void initialisenewStructureMethods(){
newStructureMethod.put("model1-Name", classModel1-Name.class);
newStructureMethod.put("model2-Name", classModel2-Name.class);
newStructureMethod.put("model3-Name", classModel3-Name.class);
[...]
}
</PRE>
<P>
<SPAN CLASS="textbf">4)</SPAN> Call this method in the constructor of RegisterMethod :
<P>
<PRE>
public RegisterMethods(){
[...]
initialisenewStructureMethods();
}
</PRE>
<P>
<SPAN CLASS="textbf">5)</SPAN> Create a new <SPAN CLASS="textit">public static final String</SPAN> as instance variable of the OptionManagement
class in the melting.configuration package. This String represents the new option name you choose
to change the default model used to compute the new structure.
<P>
<PRE>
/**
* Option name to choose another method to compute the
* new structure.
*/
public static final String newStructureOption-Name =
"option-name";
</PRE>
<P>
<SPAN CLASS="textbf">6)</SPAN> Fix the default model name to use for each type of hybridization. You have to add
the following lines into the following methods of OptionManagement :
<P>
<PRE>
/**
* initialises the DNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialisesDNADefaultOptions() {
[...]
this.DNADefaultOptions.put(newStructureOption-Name,
"DNA-defaultModel-Name");
}
/**
* initialises the RNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseRNADefaultOptions() {
[...]
this.RNADefaultOptions.put(newStructureOption-Name,
"RNA-defaultModel-Name");
}
/**
* initialises the hybridDefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseHybridDefaultOptions() {
[...]
this.hybridDefaultOptions.put(newStructureOption-Name,
"DNA/RNA-defaultModel-Name");
}
/**
* initialises the mRNADefaultOptions HashMap of the
* OptionManagement object.
*/
private void initialiseMRNADefaultOptions() {
[...]
this.mRNADefaultOptions.put(newStructureOption-Name,
"mRNA-defaultModel-Name");
}
</PRE>
<P>
<SPAN CLASS="textbf">7)</SPAN> Register the new option in the HashMap <SPAN CLASS="textit">registerPatternModels</SPAN> of OptionManagement.
You just have to add this following line into the method <SPAN CLASS="textit">private void initialiseRegisterPatternModels()</SPAN>
of OptionManagement :
<P>
<PRE>
/**
* Initialises the registerPatternModels HashMap of the OptionManagement object.
*/
private void initialiseRegisterPatternModels(){
[...]
registerPatternModels.add(newStructureOption-Name);
}
</PRE>
<P>
<SPAN CLASS="textbf">8)</SPAN> Add in the method <SPAN CLASS="textit">private void initialisePatternModels()</SPAN> of RegsiterMethods the
following line to register the new structure.
<P>
<PRE>
private void initialisePatternModels(){
[...]
// It creates a relationship between the option name
// for the new structure and the HashMap containing
// the models and the class which can compute the new
// structure.
PatternModel.put(OptionManagement.newStructureMethod,
newStructureMethod);
</PRE>
<P>
<SPAN CLASS="textbf">9)</SPAN> Add a new method in the NucleotiSequences class in the melting.sequences package to be abble
to recognize if a structure between two positions in the duplex matches the new structure you created.
<P>
<PRE>
// new method to recognize the new structure in the duplex
public boolean isNewStructure(int pos1, int pos2){
[if the subsequences between the positions pos1 and pos2
in the duplex match the new structure, you must return true.]
}
</PRE>
<P>
<SPAN CLASS="textbf">10)</SPAN> Create a new <SPAN CLASS="textit">private PatternComputationMethod</SPAN> instance variable in the NearestNeighborMode
class in the melting.nearestNeighborMode package. This new instance represents an object PatternComputationMethod
which is a new instance of one of your implemented class which can compute the new structure.
<P>
<PRE>
/**
* PatternComputationMethod newStructureMethod : represents
* the model for new structure computation.
*/
private PatternComputationMethod newStructureMethod;
</PRE>
<P>
<SPAN CLASS="textbf">11)</SPAN> Create a new method in the NearestNeighborMode class to initialise the PatternComputationMethod
newStructureMethod :
<P>
<PRE>
private void initialiseNewStructureMethod(){
// Get the option name (public static final instance
// variable of OptionManagement) which allows to change
// the model to compute the new structure.
String optionName = OptionManagement.newStructureOption-Name;
// Get the model name (model name) which allows to change
// the model to compute the new structure and initialise the
// PatternComputationMethod newStructureMethod.
String methodName = this.environment.getOptions().get(optionName);
this.newStructureMethod = initialiseMethod(optionName, methodName);
}
</PRE>
<P>
<SPAN CLASS="textbf">12)</SPAN> If the new structure you added contains perfectly matching base pairs, maybe you have to
change the method <SPAN CLASS="textit">private int [] getPositionsPattern(int pos1)</SPAN> of the NearestNeighborMode class.
<BR>
<BR>
This method defines the positions of a structure in the duplex (a perfectly matching structure or a
structure composed of non perfectly matching base pairs or composed of modified nucleic acid(s)).
<BR>
<BR>
If you need the adjacent base pairs to the non perfectly matching base pair or the modified nucleic acid,
you can add a method which corrects the positions of the structure in the duplex, in the class computing
the new structure. (see the following example and the Javadoc)
<P>
<PRE>
private int[] correctPositions(int pos1, int pos2,
int duplexLength){
if (pos1 > 0){
pos1 --;
}
if (pos2 < duplexLength - 1){
pos2 ++;
}
int [] positions = {pos1, pos2};
return positions;
}
</PRE>
<P>
<SPAN CLASS="textbf">13)</SPAN> Change the method <SPAN CLASS="textit">private PatternComputationMethod getAppropriatePatternModel(int [] positions)</SPAN>
of NearestNeighborMode to add your new structure initialisation.
<P>
<PRE>
// Method to get the adapted PatternComputationMethod to
// compute the structure defined at the positions int []
// positions.
private PatternComputationMethod getAppropriatePatternModel
(int [] positions){
// if the new structure is always a terminal structure, you
// can change the method here.
if (positions[0] == 0 || positions[1] ==
environment.getSequences().getDuplexLength() - 1){
[...]
// call the NucleotidSequences method to recognize the identity
// of the new structure
else if (environment.getSequences().isNewStructure(positions[0],
positions[1])){
if (this.newStructureMethod == null){
initialiseNewStructureMethod(); // initialise the
//PatternComputationMethod
// newStructureMethod
}
return this.newStructureMethod;
}
}
// if the structure is not always a terminal structure, you can
// change the method here.
[...]
// call the NucleotidSequences method to recognize the identity
// of the new structure
else if (environment.getSequences().isNewStructure(positions[0],
positions[1])){
if (this.newStructureMethod == null){
initialiseNewStructureMethod(); // initialise the
//PatternComputationMethod
// newStructureMethod
}
return this.newStructureMethod;
}
[...]
}
</PRE>
<P>
<SPAN CLASS="textbf">14)</SPAN> Create the new class(es) representing your model(s) for the new structure as it is explained
in the section <SPAN CLASS="textit">How to add new thermodynamic model</SPAN>.
<P>
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<ADDRESS>
Computational Neurobiology
2009-08-24
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