org.forester.analysis

Class TaxonomyDataManager

java.lang.Object

org.forester.archaeopteryx.tools.RunnableProcess

org.forester.analysis.TaxonomyDataManager

All Implemented Interfaces:

Runnable

public final class TaxonomyDataManager
extends RunnableProcess

Constructor Summary

Constructors

Constructor and Description
TaxonomyDataManager(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy)
TaxonomyDataManager(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy, boolean delete, boolean allow_simple_name)

Method Summary

Modifier and Type	Method and Description
static UniProtTaxonomy	obtainUniProtTaxonomy(String simple_name, org.forester.analysis.TaxonomyDataManager.QUERY_TYPE qt)
static UniProtTaxonomy	obtainUniProtTaxonomy(Taxonomy tax, Object query, org.forester.analysis.TaxonomyDataManager.QUERY_TYPE qt)
void	run()

Methods inherited from class org.forester.archaeopteryx.tools.RunnableProcess

end, start

Methods inherited from class java.lang.Object

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

Constructor Detail

TaxonomyDataManager

public TaxonomyDataManager(MainFrameApplication mf,
                           TreePanel treepanel,
                           Phylogeny phy)

TaxonomyDataManager

public TaxonomyDataManager(MainFrameApplication mf,
                           TreePanel treepanel,
                           Phylogeny phy,
                           boolean delete,
                           boolean allow_simple_name)

Method Detail

obtainUniProtTaxonomy

public static final UniProtTaxonomy obtainUniProtTaxonomy(Taxonomy tax,
                                                          Object query,
                                                          org.forester.analysis.TaxonomyDataManager.QUERY_TYPE qt)
                                                   throws IOException,
                                                          AncestralTaxonomyInferenceException

Throws:

IOException

AncestralTaxonomyInferenceException

obtainUniProtTaxonomy

public static final UniProtTaxonomy obtainUniProtTaxonomy(String simple_name,
                                                          org.forester.analysis.TaxonomyDataManager.QUERY_TYPE qt)
                                                   throws IOException,
                                                          AncestralTaxonomyInferenceException

Throws:

IOException

AncestralTaxonomyInferenceException

run

public void run()