java.lang.Object
- org.forester.rio.RIO

public final class RIO
extends java.lang.Object

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class RIO.REROOTING

Field Summary

Fields
Modifier and Type Field Description

static int DEFAULT_RANGE

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static IntMatrix`	`calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort)`
`static RIO`	`executeAnalysis(java.io.File gene_trees_file, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`static RIO`	`executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`static RIO`	`executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`static RIO`	`executeAnalysis(IteratingPhylogenyParser p, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`static RIO`	`executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`static RIO`	`executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`static RIO`	`executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree)`
`static RIO`	`executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`static RIO`	`executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)`
`Phylogeny[]`	`getAnalyzedGeneTrees()`
`BasicDescriptiveStatistics`	`getDuplicationsStatistics()`
`int`	`getExtNodesOfAnalyzedGeneTrees()`	Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).
`SDIutil.TaxonomyComparisonBase`	`getGSDIRtaxCompBase()`
`int`	`getIntNodesOfAnalyzedGeneTrees()`	Returns the numbers of number of int nodes in gene trees analyzed (after stripping).
`java.lang.StringBuilder`	`getLog()`
`Phylogeny`	`getMinDuplicationsGeneTree()`
`IntMatrix`	`getOrthologTable()`
`java.util.List<PhylogenyNode>`	`getRemovedGeneTreeNodes()`
`Phylogeny`	`getSpeciesTree()`

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

Field Detail
- DEFAULT_RANGE
```
public static final int DEFAULT_RANGE
```
  See Also:
  
  Constant Field Values

Method Detail

getAnalyzedGeneTrees

public final Phylogeny[] getAnalyzedGeneTrees()

getDuplicationsStatistics

public final BasicDescriptiveStatistics getDuplicationsStatistics()

getExtNodesOfAnalyzedGeneTrees
```
public final int getExtNodesOfAnalyzedGeneTrees()
```
Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).

Returns:

number of ext nodes in gene trees analyzed (after stripping)

getGSDIRtaxCompBase

public final SDIutil.TaxonomyComparisonBase getGSDIRtaxCompBase()

getIntNodesOfAnalyzedGeneTrees
```
public final int getIntNodesOfAnalyzedGeneTrees()
```
Returns the numbers of number of int nodes in gene trees analyzed (after stripping).

Returns:

number of int nodes in gene trees analyzed (after stripping)

getLog

public final java.lang.StringBuilder getLog()

getMinDuplicationsGeneTree

public final Phylogeny getMinDuplicationsGeneTree()

getOrthologTable

public final IntMatrix getOrthologTable()

getRemovedGeneTreeNodes

public final java.util.List<PhylogenyNode> getRemovedGeneTreeNodes()

getSpeciesTree

public final Phylogeny getSpeciesTree()

calculateOrthologTable

public static final IntMatrix calculateOrthologTable(Phylogeny[] analyzed_gene_trees,
                                                     boolean sort)
                                              throws RIOException

Throws:: RIOException

executeAnalysis

public static final RIO executeAnalysis(java.io.File gene_trees_file,
                                        java.io.File species_tree_file,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        int first,
                                        int last,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(java.io.File gene_trees_file,
                                        Phylogeny species_tree,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(java.io.File gene_trees_file,
                                        Phylogeny species_tree,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        int first,
                                        int last,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(IteratingPhylogenyParser p,
                                        java.io.File species_tree_file,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        int first,
                                        int last,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(IteratingPhylogenyParser p,
                                        Phylogeny species_tree,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(IteratingPhylogenyParser p,
                                        Phylogeny species_tree,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        int first,
                                        int last,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(Phylogeny[] gene_trees,
                                        Phylogeny species_tree)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(Phylogeny[] gene_trees,
                                        Phylogeny species_tree,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

executeAnalysis

public static final RIO executeAnalysis(Phylogeny[] gene_trees,
                                        Phylogeny species_tree,
                                        SDIutil.ALGORITHM algorithm,
                                        RIO.REROOTING rerooting,
                                        java.lang.String outgroup,
                                        int first,
                                        int last,
                                        boolean produce_log,
                                        boolean verbose,
                                        boolean transfer_taxonomy)
                                 throws java.io.IOException,
                                        SDIException,
                                        RIOException

Throws:: java.io.IOException; SDIException; RIOException

Class RIO

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_RANGE

Method Detail

getAnalyzedGeneTrees

getDuplicationsStatistics

getExtNodesOfAnalyzedGeneTrees

getGSDIRtaxCompBase

getIntNodesOfAnalyzedGeneTrees

getLog

getMinDuplicationsGeneTree

getOrthologTable

getRemovedGeneTreeNodes

getSpeciesTree

calculateOrthologTable

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis

executeAnalysis