java.lang.Object
- org.forester.sdi.SDIutil

public class SDIutil
extends java.lang.Object

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class SDIutil.ALGORITHM

static class SDIutil.TaxonomyComparisonBase

Constructor Summary

Constructors
Constructor Description

SDIutil()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static SDIutil.TaxonomyComparisonBase`	`determineTaxonomyComparisonBase(Phylogeny gene_tree)`
`static Phylogeny`	`parseSpeciesTree(Phylogeny gene_tree, java.io.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,
                                               java.io.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 java.io.FileNotFoundException,
                                               PhyloXmlDataFormatException,
                                               java.io.IOException,
                                               SDIException

Throws:: java.io.FileNotFoundException; PhyloXmlDataFormatException; java.io.IOException; SDIException

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

Class SDIutil

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SDIutil

Method Detail

determineTaxonomyComparisonBase

parseSpeciesTree