Learning DesignPatterns: The Factory Method Pattern

"The Factory method pattern defines a separate method for creating the objects, which subclasses can then override to specify the derived type of product that will be created"

Example

/** Abstract class for melting temperature calculation */
abstract class TmCalculator
{
public abstract double calcTm(CharSequence s);
}

/** the factory creates two kinds of TmCalculator
1) 2AT4GC
2) Nearest-Neighbor
*/
public class TmCalculatorFactory
{
public TmCalculator create2AT4GC()
{
return new TmCalculator()
{
@Override
public double calcTm(CharSequence s)
{
(...implements ... )
}
};
}

public TmCalculator createNearestNeighbor()
{
return new TmCalculator()
{
@Override
public double calcTm(CharSequence s)
{
(...implements ... )
}
};
}
}

That's it

Pierre

Learning DesignPatterns: The Builder Pattern

largely inspired by Wikipedia:"Builder Pattern is a software design pattern. The intention is to abstract steps of construction of objects so that different implementations of these steps can construct different representations of objects."

Example

/**
* Taxon, the class to be constructed
*/
class Taxon
{
private int id=-1;
private int parent_id=-1;
private String name=null;

public void setId(int id) { this.id=id; }
public void setParentId(int parent_id) { this.parent_id=parent_id; }
public void setName(String name) { this.name=name; }
public int getId() { return this.id;}
public int getParentId() { return this.parent_id;}
public String getName() { return this.name;}
}

/** Abstract interface for creating Taxons */
abstract class TaxonBuilder
{
protected Taxon taxon=new Taxon();

public void createNewTaxon()
{
this.taxon = new Taxon();
}

public Taxon getTaxon()
{
return this.taxon;
}
public abstract void buildId();
public abstract void buildParentId();
public abstract void buildName();
}
/** concrete TaxonBuilder builder for HomoSapiens */
class HomoSapiensBuilder extends TaxonBuilder
{
public void buildId() { super.taxon.setId(9606);}
public void buildParentId() { super.taxon.setParentId(9605);}
public void buildName() { super.taxon.setName("Homo Sapiens");}
}

/** concrete TaxonBuilder builder for Platypus */
class PlatypusBuilder extends TaxonBuilder
{
public void buildId() { super.taxon.setId(9258);}
public void buildParentId() { super.taxon.setParentId(9257);}
public void buildName() { super.taxon.setName("Platypus");}
}

/** constructs a Taxon object by calling its TaxonBuilder */
class TaxonAssembler
{
private TaxonBuilder builder;

public void setTaxonBuilder(TaxonBuilder builder)
{
this.builder=builder;
}

public void assemble()
{
this.builder.createNewTaxon();
this.builder.buildId();
this.builder.buildParentId();
this.builder.buildName();
}
}

public class Test
{
public static void main(String[] args) {
{
TaxonBuilder builder=new PlatypusBuilder();
TaxonAssembler assembler=new TaxonAssembler();
assembler.setBuilder(builder);
assembler.assemble();
Taxon taxon=builder.getTaxon();
}
}

That's it.

Pierre

Learning DesignPatterns: AbstractFactoryPattern

In the very next posts, I'll post my notes about the "Design Patterns". A Design Pattern is a "general reusable solution to a commonly occurring problem in software design". Here, I'll follow the patterns described at http://c2.com/cgi/wiki?DesignPatternsBook and will try to apply them to Bioinformatics. Today I'm starting with the AbstractFactoryPattern.

via Wikipedia:AbstractFactoryPattern provides a way to encapsulate a group of individual factories that have a common theme. In normal usage, the client software creates a concrete implementation of the abstract factory and then uses the generic interfaces to create the concrete objects that are part of the theme.
Use of this pattern makes it possible to interchange concrete classes without changing the code that uses them, even at runtime.

Example

/** the result of a pairwise alignment */
interface Alignment
{
public void print(PrintWriter out);
public double getScore();
}

/** interface for a pairwise alignment */
interface PairwiseAlignment
{
public Alignment align(CharSequence seq1,CharSequence seq2);
}

/** implementation of a global PairwiseAlignment */
class NeedlemanWunsch
implements PairwiseAlignment
{
public Alignment align(CharSequence seq1,CharSequence seq2)
{
(...)
}
}

/** implementation of a local PairwiseAlignment */
class SmithWaterman
implements PairwiseAlignment
{
public Alignment align(CharSequence seq1,CharSequence seq2)
{
(...)
}
}

/** abstract PairwiseAlignmentFactory
* contains an abstract method 'createPairwiseAligner'
* the static function 'newInstance' returns a new 'PairwiseAlignmentFactoryImpl'
*/
abstract class PairwiseAlignmentFactory
{
protected boolean global=true;

protected PairwiseAlignmentFactory()
{
}

public void setGlobal(boolean global)
{
this.global=global;
}

public boolean isGlobal()
{
return this.global;
}

/** abstract. to be implemented */
public abstract PairwiseAlignment createPairwiseAligner();

/** creates a new concrete instance of PairwiseAlignmentFactory */
static public PairwiseAlignmentFactory newInstance()
{
//described later...
return new PairwiseAlignmentFactoryImpl();
}
}

/** a concrete PairwiseAlignmentFactory
* implements createPairwiseAligner()
* instance created by PairwiseAlignment.newInstance()
*/
class PairwiseAlignmentFactoryImpl
extends
{
@Override
public PairwiseAlignment createPairwiseAligner()
{
return isGlobal() ?
new NeedlemanWunsch():
: new SmithWaterman();
}
}

That's it

Pierre