softparsmap
Class DataSourceXmlNcbiTaxonomy

java.lang.Object
  ooc.LinkedTagInstance
      softparsmap.AbstractDataSource
          softparsmap.DataSourceXmlNcbiTaxonomy

All Implemented Interfaces:

DataSource, Dependencies

public class DataSourceXmlNcbiTaxonomy

extends AbstractDataSource

This data source can be used when the sequence database is an XML document. NCBI Taxonomy is used to extract species tree information. It is necessary to construct an index file before using it in different tasks. Run it without arguments to see usage. See the def.xml file for more information.

Constructor Summary

DataSourceXmlNcbiTaxonomy()

Method Summary

java.lang.String	getNcbiNamesColumn(SpeciesNode n, int column)
java.lang.Integer	getNcbiTagId(SpeciesNode n)
SequenceData	getSequenceData(GeneLeaf leaf) Returns an instance that implements the interface SequenceData for a given gene leaf.
java.lang.String	getSpeciesName(SpeciesNode species) 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.
static void	main(java.lang.String[] args)

Methods inherited from class softparsmap.AbstractDataSource

getPropertyFile

Methods inherited from class ooc.LinkedTagInstance

containsKey, get, getAttribute, getAttributeBoolean, getAttributeDouble, getAttributeFloat, getAttributeInteger, getAttributeList, getAttributeRef, getAttributeShort, getAttributeString, getAttributeTag, getChildIterator, getChildIteratorByName, getContainer, getContainerTag, getFirstChildTagByName, getTag, getTagId, getTagInstance, getTagInstance, getTagRef, hasAttributeValue, hasChildTagByName, hasChildTags, hasTag, isMutable, keySet, put, remove, setTag, setupInstance

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DataSourceXmlNcbiTaxonomy

public DataSourceXmlNcbiTaxonomy()

Method Detail

initiate

public void initiate()

Description copied from interface: DataSource

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

getSpeciesName

public java.lang.String getSpeciesName(SpeciesNode species)

Description copied from interface: DataSource

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

Parameters:

species - is the species node.

Returns:

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

See Also:

SpeciesNode

getSpeciesTree

public SpeciesNode getSpeciesTree(GeneNode geneTree)

Description copied from interface: DataSource

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

getSequenceData

public SequenceData getSequenceData(GeneLeaf leaf)

Description copied from interface: DataSource

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

getNcbiTagId

public java.lang.Integer getNcbiTagId(SpeciesNode n)

getNcbiNamesColumn

public java.lang.String getNcbiNamesColumn(SpeciesNode n,
                                           int column)

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception