RapGreen

java.lang.Object
- rapgreen.RapGreen

public class RapGreen
extends java.lang.Object

Entry point of RapGreen program

Field Summary

Fields
Modifier and Type	Field and Description
`static boolean`	`addOutparalogous` static parameter to add outparalogous genes to the stat file
`static boolean`	`debug` Trace
`static int`	`end` Ending point (exclusive) of the input gene tree directory
`static java.io.File[]`	`geneFiles` Input gene files
`static boolean`	`invert` Tax id inversion mod
`static java.io.File`	`outputGene` Output gene file
`static java.io.File`	`outputNHX` Output gene file in NHX format, storing duplications in the NHX zone
`static java.io.File`	`outputPhyloXML` Output phyloXML gene file
`static java.io.File`	`outputReconciled` Output gene file
`static java.io.File`	`outputRerooted` Output rerooted simple gene file
`static java.io.File`	`outputRerootedSpecies` Output rerooted simple gene file
`static java.io.File`	`outputSpecies` Output gene file
`static boolean`	`pipe` Pipe replacement mod
`static java.io.File`	`speciesFile` Input species file
`static int`	`start` Starting point of the input gene tree directory
`static java.io.File`	`stats` Output stats file
`static java.util.Hashtable`	`taxaTranslationTable` Table of taxa translation, for prefixed sequence names
`static java.util.Vector`	`taxaTranslationVector` Vector of taxa translation, for prefixed sequence names
`static boolean`	`verbose` Verbose mod

Constructor Summary

Constructors
Constructor and Description

RapGreen()

Constructors
Constructor and Description
`RapGreen()`

Method Summary

Methods
Modifier and Type Method and Description

static void main(java.lang.String[] args)
- Methods inherited from class java.lang.Object
  clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods
Modifier and Type	Method and Description
`static void`	`main(java.lang.String[] args)`

- Field Detail
  - debug
```
public static boolean debug
```
    Trace
  - geneFiles
```
public static java.io.File[] geneFiles
```
    Input gene files
  - speciesFile
```
public static java.io.File speciesFile
```
    Input species file
  - outputGene
```
public static java.io.File outputGene
```
    Output gene file
  - outputNHX
```
public static java.io.File outputNHX
```
    Output gene file in NHX format, storing duplications in the NHX zone
  - outputSpecies
```
public static java.io.File outputSpecies
```
    Output gene file
  - outputReconciled
```
public static java.io.File outputReconciled
```
    Output gene file
  - outputPhyloXML
```
public static java.io.File outputPhyloXML
```
    Output phyloXML gene file
  - outputRerooted
```
public static java.io.File outputRerooted
```
    Output rerooted simple gene file
  - outputRerootedSpecies
```
public static java.io.File outputRerootedSpecies
```
    Output rerooted simple gene file
  - stats
```
public static java.io.File stats
```
    Output stats file
  - verbose
```
public static boolean verbose
```
    Verbose mod
  - invert
```
public static boolean invert
```
    Tax id inversion mod
  - pipe
```
public static boolean pipe
```
    Pipe replacement mod
  - start
```
public static int start
```
    Starting point of the input gene tree directory
  - end
```
public static int end
```
    Ending point (exclusive) of the input gene tree directory
  - addOutparalogous
```
public static boolean addOutparalogous
```
    static parameter to add outparalogous genes to the stat file
  - taxaTranslationTable
```
public static java.util.Hashtable taxaTranslationTable
```
    Table of taxa translation, for prefixed sequence names
  - taxaTranslationVector
```
public static java.util.Vector taxaTranslationVector
```
    Vector of taxa translation, for prefixed sequence names
- Constructor Detail
  - RapGreen
```
public RapGreen()
```
- Method Detail
  - main
```
public static void main(java.lang.String[] args)
```

Class RapGreen

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

debug

geneFiles

speciesFile

outputGene

outputNHX

outputSpecies

outputReconciled

outputPhyloXML

outputRerooted

outputRerootedSpecies

stats

verbose

invert

pipe

start

end

addOutparalogous

taxaTranslationTable

taxaTranslationVector

Constructor Detail

RapGreen

Method Detail

main