rapgreen

Class SpeciesDictionary

java.lang.Object

rapgreen.SpeciesDictionary

public class SpeciesDictionary
extends java.lang.Object

Species dictionary.

Contains a collection of species, with scientific name, NCBI and TOL code.

Constructor Summary

Constructors

Constructor and Description
SpeciesDictionary() Simple constructor, need to fill tables independantly

Method Summary

Methods

Modifier and Type	Method and Description
void	addSpecies(java.lang.String c, java.lang.String s, java.lang.String n) Add a new species in the dictionary
java.util.Vector	containsScientificNameList(java.lang.String prefix) Get species list containing a parameter prefix, regarding the scientific full name
java.lang.String	get5LettersCode(java.lang.String c) Get the 5 letters code from the numerical code
java.lang.String	getNumericalCode(java.lang.String c) Get the numerical code from the 5 letters code
java.lang.String	getScientificName(java.lang.String c) Get the scientific name from the 5 letters code
java.lang.String	getScientificNameFromNumerical(java.lang.String n) Get the scientific name from the 5 letters code
boolean	isCompatible(java.lang.String taxonParam, java.util.Hashtable allowedConstraints, java.util.Hashtable forbiddenConstraints) Test if a taxon is compatible with a constraint list, regarding a species tree
boolean	isCompatible(Tree treeParam, java.util.Hashtable allowedConstraints, java.util.Hashtable forbiddenConstraints) Test if a all taxa of a gene tree is compatible with a constraint list, regarding a species tree
java.lang.String	next() Get the next species in the iterator
void	parseSpeciesDico(java.io.File speciesFile) Parse a dico file to fill this dictionary
java.util.Vector	prefixList(java.lang.String prefix) Get species list containing a parameter prefix
java.util.Vector	prefixScientificNameList(java.lang.String prefix) Get species list containing a parameter prefix, regarding the scientific full name
void	setSpeciesTree(Tree speciesTree) Link a species tree to a dictionnary
void	start() Starts the iterator

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SpeciesDictionary

public SpeciesDictionary()

Simple constructor, need to fill tables independantly

Method Detail

addSpecies

public void addSpecies(java.lang.String c,
              java.lang.String s,
              java.lang.String n)

Add a new species in the dictionary

Parameters:

c - The 5 letters string, coding for species

s - The scientific name

n - The numerical code

getNumericalCode

public java.lang.String getNumericalCode(java.lang.String c)

Get the numerical code from the 5 letters code

Parameters:

c - The 5 letters string, coding for species

Returns:

The numerical code of the species c

getScientificName

public java.lang.String getScientificName(java.lang.String c)

Get the scientific name from the 5 letters code

Parameters:

c - The 5 letters string, coding for species

Returns:

The scientific name of the species c

get5LettersCode

public java.lang.String get5LettersCode(java.lang.String c)

Get the 5 letters code from the numerical code

Parameters:

c - The numerical code of the species c

Returns:

The 5 letters string, coding for species

getScientificNameFromNumerical

public java.lang.String getScientificNameFromNumerical(java.lang.String n)

Get the scientific name from the 5 letters code

Parameters:

c - The numerical code, coding for species

Returns:

The scientific name of the species c

prefixList

public java.util.Vector prefixList(java.lang.String prefix)

Get species list containing a parameter prefix

Parameters:

prefix - The prefix

Returns:

The species vector

prefixScientificNameList

public java.util.Vector prefixScientificNameList(java.lang.String prefix)

Get species list containing a parameter prefix, regarding the scientific full name

Parameters:

prefix - The prefix

Returns:

The species vector

containsScientificNameList

public java.util.Vector containsScientificNameList(java.lang.String prefix)

Get species list containing a parameter prefix, regarding the scientific full name

Parameters:

prefix - The prefix

Returns:

The species vector

isCompatible

public boolean isCompatible(java.lang.String taxonParam,
                   java.util.Hashtable allowedConstraints,
                   java.util.Hashtable forbiddenConstraints)

Test if a taxon is compatible with a constraint list, regarding a species tree

Parameters:

taxonParam - The taxon to fit in constraints

allowedConstraints - The table of positive constraints

forbiddenConstraints - The table of positive constraints

speciesTree - The reference species tree

Returns:

True or false, regarding compatibility

isCompatible

public boolean isCompatible(Tree treeParam,
                   java.util.Hashtable allowedConstraints,
                   java.util.Hashtable forbiddenConstraints)

Test if a all taxa of a gene tree is compatible with a constraint list, regarding a species tree

Parameters:

taxonParam - The taxon to fit in constraints

allowedConstraints - The table of positive constraints

forbiddenConstraints - The table of positive constraints

speciesTree - The reference species tree

Returns:

True or false, regarding compatibility

start

public void start()

Starts the iterator

setSpeciesTree

public void setSpeciesTree(Tree speciesTree)

Link a species tree to a dictionnary

Parameters:

the - species tree value

parseSpeciesDico

public void parseSpeciesDico(java.io.File speciesFile)

Parse a dico file to fill this dictionary

Parameters:

the - species dictionary

next

public java.lang.String next()

Get the next species in the iterator

Returns:

The next species