org.forester.sdi

Class SDIutil

java.lang.Object

org.forester.sdi.SDIutil

public class SDIutil
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SDIutil.ALGORITHM
static class	SDIutil.TaxonomyComparisonBase

Constructor Summary

Constructors

Constructor and Description
SDIutil()

Method Summary

Modifier and Type	Method and Description
static SDIutil.TaxonomyComparisonBase	determineTaxonomyComparisonBase(Phylogeny gene_tree)
static Phylogeny	parseSpeciesTree(Phylogeny gene_tree, File species_tree_file, boolean replace_undescores_in_nhx_trees, boolean ignore_quotes_in_nhx_trees, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees)

Methods inherited from class java.lang.Object

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

Constructor Detail

SDIutil

public SDIutil()

Method Detail

determineTaxonomyComparisonBase

public static final SDIutil.TaxonomyComparisonBase determineTaxonomyComparisonBase(Phylogeny gene_tree)
                                                                            throws SDIException

Throws:

SDIException

parseSpeciesTree

public static final Phylogeny parseSpeciesTree(Phylogeny gene_tree,
                                               File species_tree_file,
                                               boolean replace_undescores_in_nhx_trees,
                                               boolean ignore_quotes_in_nhx_trees,
                                               NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees)
                                        throws FileNotFoundException,
                                               PhyloXmlDataFormatException,
                                               IOException,
                                               SDIException

Throws:

FileNotFoundException

PhyloXmlDataFormatException

IOException

SDIException