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(Object source, Object creator)
          This must create a Phylogeny from source (e.g.
 Phylogeny[] create(Object source, Object creator, List<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(Object source,
                   Object creator)
                   throws 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:
IOException

create

Phylogeny[] create(Object source,
                   Object creator,
                   List<Object> parameters)
                   throws 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:
IOException