SDIutil

java.lang.Object

org.forester.sdi.SDIutil

public class SDIutil extends Object

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static enum

SDIutil.ALGORITHM

static enum

SDIutil.TaxonomyComparisonBase
Constructor Summary

Constructors

Constructor

Description

SDIutil()
Method Summary

Modifier and Type

Method

Description

static final SDIutil.TaxonomyComparisonBase

determineTaxonomyComparisonBase(Phylogeny gene_tree)

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)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SDIutil
  
  public SDIutil()
Method Details
- 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