Alignments

Class Site

java.lang.Object

Alignments.Site

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

UniqueSite

public class Site
extends java.lang.Object
implements java.io.Serializable

Represents a "site" in an "alignment". Both terms used generously. When comparing sites the site ID is ignored so as to allowed counting of unique sites for caclulation purposes.

Version:

2.0

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites) Creates a site in a alignment with no ambiguous data
Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig) Creates a site in a alignment with ambiguous data
Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig, java.lang.String siteClass) Creates a site in a alignment with ambiguous data and with the given class.
Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, java.lang.String siteClass) Creates a site in a alignment with no ambiguous data and with the given class.
Site(Site s) Creates a copy of a site
Site(java.lang.String id, java.util.LinkedHashMap<java.lang.String,java.lang.String> sites) Creates a site in a alignment with no ambiguous data
Site(java.lang.String id, java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig) Creates a site in a alignment with ambiguous data
Site(java.lang.String id, java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig, java.lang.String siteClass) Creates a site in a alignment with ambiguous data and with the given class.
Site(java.lang.String id, java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, java.lang.String siteClass) Creates a site in a alignment with no ambiguous data and with the given class.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
Ambiguous	getAmbiguous() Gets the information about ambiguous states for this site
java.util.Set<java.lang.String>	getCharacter(java.lang.String taxa) Gets the possible characters for a given taxa.
java.lang.String	getID() Gets the ID of the site
java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>	getInitialNodeLikelihoods(Tree t, java.util.Map<java.lang.String,java.lang.Integer> map) Gets initial node likelihoods based on the site and tree.
int	getNum() Get the number of taxa
java.lang.String	getRawCharacter(java.lang.String taxa) Gets the raw charcater for a given taxa.
java.lang.String	getSiteClass() Gets the class of this site
java.util.Set<java.lang.String>	getTaxa() Get the set of taxa
int	hashCode()
Site	limitToTaxa(java.util.Collection<java.lang.String> limit) Returns a new Site which is the same as this one except it is limited to certain taxa
Site	recode(java.util.Map<java.lang.String,java.lang.String> recode) Recodes the site and returns it
Site	recode(java.util.Map<java.lang.String,java.lang.String> recode, Ambiguous ambig) Recodes the alignment and returns it and also allows the definition of new ambiguous states
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Site

public Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites)

Creates a site in a alignment with no ambiguous data

Parameters:

sites - Map from taxa name to state

Site

public Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
    java.lang.String siteClass)

Creates a site in a alignment with no ambiguous data and with the given class. Note that either all sites in an alignment must have a class or none should.

Parameters:

sites - Map from taxa name to state

siteClass - The class of this site

Site

public Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
    Ambiguous ambig)

Creates a site in a alignment with ambiguous data

Parameters:

sites - Map from taxa name to state

ambig - Description of ambiguous data

Site

public Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
    Ambiguous ambig,
    java.lang.String siteClass)

Creates a site in a alignment with ambiguous data and with the given class. Note that either all sites in an alignment must have a class or none should.

Parameters:

sites - Map from taxa name to state

ambig - Description of ambiguous data

siteClass - The class of this site

Site

public Site(java.lang.String id,
    java.util.LinkedHashMap<java.lang.String,java.lang.String> sites)

Creates a site in a alignment with no ambiguous data

Parameters:

id - An ID for the site

sites - Map from taxa name to state

Site

public Site(java.lang.String id,
    java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
    java.lang.String siteClass)

Creates a site in a alignment with no ambiguous data and with the given class. Note that either all sites in an alignment must have a class or none should.

Parameters:

id - An ID for the site

sites - Map from taxa name to state

siteClass - The class of this site

Site

public Site(java.lang.String id,
    java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
    Ambiguous ambig)

Creates a site in a alignment with ambiguous data

Parameters:

id - An ID for the site

sites - Map from taxa name to state

ambig - Description of ambiguous data

Site

public Site(java.lang.String id,
    java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
    Ambiguous ambig,
    java.lang.String siteClass)

Creates a site in a alignment with ambiguous data and with the given class. Note that either all sites in an alignment must have a class or none should.

Parameters:

id - An ID for the site

sites - Map from taxa name to state

ambig - Description of ambiguous data

siteClass - The class of this site

Site

public Site(Site s)

Creates a copy of a site

Parameters:

s - The site to copy

Method Detail

getCharacter

public java.util.Set<java.lang.String> getCharacter(java.lang.String taxa)

Gets the possible characters for a given taxa. This returns a set as it takes into account ambiguous data. For example if N is defined to be A, C, T or G then this function will return a set containing A, C, T and G if the raw data contains a N

Parameters:

taxa - Taxa to return the character for

Returns:

The character for the given taxa

getRawCharacter

public java.lang.String getRawCharacter(java.lang.String taxa)
                                 throws AlignmentException

Gets the raw charcater for a given taxa. This no account of ambiguous data and will just return the raw character

Parameters:

taxa - Taxa to return the character for

Returns:

The character for the given taxa

Throws:

AlignmentException - If the passed taxa name is not valid

getNum

public int getNum()

Get the number of taxa

Returns:

The number of taxa

getTaxa

public java.util.Set<java.lang.String> getTaxa()

Get the set of taxa

Returns:

Set containing taxa names

getSiteClass

public java.lang.String getSiteClass()

Gets the class of this site

Returns:

The class of this site

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

getID

public java.lang.String getID()

Gets the ID of the site

Returns:

The ID

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getInitialNodeLikelihoods

public java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> getInitialNodeLikelihoods(Tree t,
                                                                                      java.util.Map<java.lang.String,java.lang.Integer> map)
                                                                                        throws SiteLikelihood.LikelihoodException

Gets initial node likelihoods based on the site and tree. Done like this as creating the node likelihoods is time consuming whereas copying them once initialised is not. As they only need to be initialised once for each site this saves time as they then need only be copied for each likelihood calculation.

Parameters:

t - The tree

map - A map from state to position in array

Returns:

An Map of NodeLikelihoods which can be used to initialise likelihood calculations

Throws:

SiteLikelihood.LikelihoodException - Thrown if all states are initialised to a zero likelihood

recode

public Site recode(java.util.Map<java.lang.String,java.lang.String> recode)

Recodes the site and returns it

Parameters:

recode - A map from original state to new state, e.g. to recode DNA to RY it would contains A -> R, G -> R, C -> Y, T -> Y

Returns:

A recoded site

recode

public Site recode(java.util.Map<java.lang.String,java.lang.String> recode,
          Ambiguous ambig)

Recodes the alignment and returns it and also allows the definition of new ambiguous states

Parameters:

recode - A map from original state to new state, e.g. to recode DNA to RY it would contains A -> R, G -> R, C -> Y, T -> Y

ambig - The new ambiguous states

Returns:

A recoded site

limitToTaxa

public Site limitToTaxa(java.util.Collection<java.lang.String> limit)

Returns a new Site which is the same as this one except it is limited to certain taxa

Parameters:

limit - The taxa to limit the new site to

Returns:

The limited site

getAmbiguous

public Ambiguous getAmbiguous()

Gets the information about ambiguous states for this site

Returns:

Information about the ambiguous states