org.forester.phylogeny.factories
Interface PhylogenyFactory

All Known Implementing Classes:

BasicPhylogenyFactory, ParserBasedPhylogenyFactory

public interface PhylogenyFactory

Method Summary

Phylogeny	create() This must be implemented in such a way that it returns an empty Phylogeny.
Phylogeny[]	create(java.lang.Object source, java.lang.Object creator) This must create a Phylogeny from source (e.g.
Phylogeny[]	create(java.lang.Object source, java.lang.Object creator, java.util.List<java.lang.Object> parameters) This must create a Phylogeny from source (e.g.

Method Detail

create

Phylogeny create()

This must be implemented in such a way that it returns an empty Phylogeny.

Returns:

an empty Phylogeny

create

Phylogeny[] create(java.lang.Object source,
                   java.lang.Object creator)
                   throws java.io.IOException

This must create a Phylogeny from source (e.g. an XML file, an alignment, pairwise distances) by using creator (e.g. an XML file parser, an algorithm implementation).

Parameters:

source - a source to create a Phylogeny from

creator - a means to create a Phylogeny

Returns:

a Phylogeny[] based on argument source

Throws:

java.io.IOException

create

Phylogeny[] create(java.lang.Object source,
                   java.lang.Object creator,
                   java.util.List<java.lang.Object> parameters)
                   throws java.io.IOException

This must create a Phylogeny from source (e.g. an XML file, an alignment, pairwise distances) by using creator (e.g. an XML file parser, an algorithm implementation) with parameters listed in parameters.

Parameters:

source - a source to create a Phylogeny from

creator - a means to create a Phylogeny

parameters - a List of parameters for Phylogeny creation

Returns:

a Phylogeny[] based on argument source

Throws:

java.io.IOException