softparsmap
Interface DataSource

All Known Implementing Classes:

AbstractDataSource

public interface DataSource

This interface is responsible of providing the package with data regarding species trees and gene sequences.

Method Summary

PropertyFile	getPropertyFile() Returns the property file.
SequenceData	getSequenceData(GeneLeaf leaf) Returns an instance that implements the interface SequenceData for a given gene leaf.
java.lang.String	getSpeciesName(SpeciesNode speciesNode) Returns the name of the species for a given species node.
SpeciesNode	getSpeciesTree(GeneNode geneTree) Returns the root to a species tree such that all genes found in the gene tree exist in this species tree.
void	initiate() Called by the program ComputeFamilyGroup or ComputeFamilyGroupPair once if the method Compute.initiateDataSource() returns true, else it is not called at all.

Method Detail

getPropertyFile

public PropertyFile getPropertyFile()

Returns the property file.

Returns:

the property file

See Also:

PropertyFile

initiate

public void initiate()

Called by the program ComputeFamilyGroup or ComputeFamilyGroupPair once if the method Compute.initiateDataSource() returns true, else it is not called at all.

getSpeciesTree

public SpeciesNode getSpeciesTree(GeneNode geneTree)

Returns the root to a species tree such that all genes found in the gene tree exist in this species tree.

Parameters:

geneTree - the root of the gene tree

Returns:

the root to the species tree

See Also:

SpeciesNode, GeneNode

getSpeciesName

public java.lang.String getSpeciesName(SpeciesNode speciesNode)

Returns the name of the species for a given species node.

Parameters:

speciesNode - is the species node.

Returns:

the name of the species that is associated with the species node

See Also:

SpeciesNode

getSequenceData

public SequenceData getSequenceData(GeneLeaf leaf)

Returns an instance that implements the interface SequenceData for a given gene leaf.

Parameters:

leaf - the gene leaf.

Returns:

an instance of SequenceData

See Also:

SequenceData