GSDI

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

All Implemented Interfaces:: GSDII

public final class GSDI
extends java.lang.Object
implements GSDII

Constructor Summary

Constructors
Constructor and Description
`GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree)`
`GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`getDuplicationsSum()`
`java.util.Set<PhylogenyNode>`	`getMappedExternalSpeciesTreeNodes()`
`java.util.SortedSet<java.lang.String>`	`getReMappedScientificNamesFromGeneTree()`
`int`	`getSpeciationOrDuplicationEventsSum()`
`int`	`getSpeciationsSum()`
`java.util.List<PhylogenyNode>`	`getStrippedExternalGeneTreeNodes()`
`java.util.List<PhylogenyNode>`	`getStrippedSpeciesTreeNodes()`
`SDIutil.TaxonomyComparisonBase`	`getTaxCompBase()`
`java.lang.String`	`toString()`

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

Constructor Detail

GSDI

public GSDI(Phylogeny gene_tree,
            Phylogeny species_tree,
            boolean most_parsimonious_duplication_model,
            boolean strip_gene_tree,
            boolean strip_species_tree)
     throws SDIException

Throws:: SDIException

GSDI

public GSDI(Phylogeny gene_tree,
            Phylogeny species_tree,
            boolean most_parsimonious_duplication_model,
            boolean strip_gene_tree,
            boolean strip_species_tree,
            boolean transfer_taxonomy)
     throws SDIException

Throws:: SDIException

Method Detail
- getDuplicationsSum
```
public int getDuplicationsSum()
```
- getMappedExternalSpeciesTreeNodes
```
public java.util.Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()
```
  Specified by:
  
  getMappedExternalSpeciesTreeNodes in interface GSDII
- getReMappedScientificNamesFromGeneTree
```
public final java.util.SortedSet<java.lang.String> getReMappedScientificNamesFromGeneTree()
```
  Specified by:
  
  getReMappedScientificNamesFromGeneTree in interface GSDII
- getSpeciationOrDuplicationEventsSum
```
public final int getSpeciationOrDuplicationEventsSum()
```
- getSpeciationsSum
```
public final int getSpeciationsSum()
```
  Specified by:
  
  getSpeciationsSum in interface GSDII
- getStrippedExternalGeneTreeNodes
```
public java.util.List<PhylogenyNode> getStrippedExternalGeneTreeNodes()
```
  Specified by:
  
  getStrippedExternalGeneTreeNodes in interface GSDII
- getStrippedSpeciesTreeNodes
```
public java.util.List<PhylogenyNode> getStrippedSpeciesTreeNodes()
```
  Specified by:
  
  getStrippedSpeciesTreeNodes in interface GSDII
- getTaxCompBase
```
public SDIutil.TaxonomyComparisonBase getTaxCompBase()
```
  Specified by:
  
  getTaxCompBase in interface GSDII
- toString
```
public final java.lang.String toString()
```
  Overrides:
  
  toString in class java.lang.Object

Class GSDI

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

GSDI

GSDI

Method Detail

getDuplicationsSum

getMappedExternalSpeciesTreeNodes

getReMappedScientificNamesFromGeneTree

getSpeciationOrDuplicationEventsSum

getSpeciationsSum

getStrippedExternalGeneTreeNodes

getStrippedSpeciesTreeNodes

getTaxCompBase

toString