Alignments

Class Alignment

java.lang.Object

Alignments.Alignment

All Implemented Interfaces:

java.lang.Iterable<Site>

public class Alignment
extends java.lang.Object
implements java.lang.Iterable<Site>

Represents an "alignment", used very loosely. Classes should extend this to represent the different types of alignment, e.g. DuplicationAlignment, FastaAlignment.

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
Alignment(java.util.List<Site> data) Creates an alignment

Method Summary

Methods

Modifier and Type	Method and Description
double	averageLength(java.util.Set<java.lang.String> gaps) Returns the average length of the sequences
boolean	check(java.util.Map<java.lang.String,?> map) Checks whether the map contains an entry for every class in the alignment
boolean	equals(java.lang.Object o)
int	getClassSize(java.lang.String cl) Gets the size of a class, that is how many sites belong to the given class
int	getLength() Gets the length of the aligmnet
int	getNumber() Gets the number of taxa in the alignment
double	getRawFreq(java.lang.String character) Gets the frequency of a raw character
Site	getSite(int s) Returns the site at a given position in the alignment
java.util.List<java.lang.String>	getSiteClasses() Returns a list of site classes in the same order as the sites in the alignment.
java.util.Set<java.lang.String>	getTaxa() Gets the names of the taxa in the aligment
java.util.List<UniqueSite>	getUniqueSites() Returns a list of unique sites in the aligment.
boolean	hasClasses() Checks whether the sites in this alignment have classes
int	hashCode()
java.util.Iterator<Site>	iterator()
Alignment	limitToTaxa(java.util.Collection<java.lang.String> limit) Returns a new Alignment which is the same as this one except it is limited to certain taxa
Alignment	recode(java.util.Map<java.lang.String,java.lang.String> recode) Recodes the alignment and returns it
Alignment	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

Methods inherited from class java.lang.Object

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

Constructor Detail

Alignment

public Alignment(java.util.List<Site> data)
          throws AlignmentException

Creates an alignment

Parameters:

data - A list of sites in the alignment

Throws:

AlignmentException - Thrown if the sites passed have different taxa

Method Detail

getLength

public int getLength()

Gets the length of the aligmnet

Returns:

The length of the alignment

averageLength

public double averageLength(java.util.Set<java.lang.String> gaps)

Returns the average length of the sequences

Parameters:

gaps - The set of gap characters (i.e. characters to be ignored when coutning length)

Returns:

The average sequence length

getNumber

public int getNumber()

Gets the number of taxa in the alignment

Returns:

The number of taxa in the alignment

getUniqueSites

public java.util.List<UniqueSite> getUniqueSites()

Returns a list of unique sites in the aligment. Useful for calculating likelihoods as each site pattern only has to be calculated once.

Returns:

A set of unique sites

getSite

public Site getSite(int s)

Returns the site at a given position in the alignment

Parameters:

s - The site to be returned

Returns:

The site at posiiton s

getTaxa

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

Gets the names of the taxa in the aligment

Returns:

List of taxa names

iterator

public java.util.Iterator<Site> iterator()

Specified by:

iterator in interface java.lang.Iterable<Site>

check

public boolean check(java.util.Map<java.lang.String,?> map)

Checks whether the map contains an entry for every class in the alignment

Parameters:

map - The map

Returns:

Whether the map has an entry for every class

recode

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

Recodes the alignment 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 alignment

recode

public Alignment 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 ambiiguous states

Returns:

A recoded alignment

limitToTaxa

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

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

Parameters:

limit - The taxa to limit the new alignment to

Returns:

The limited alignment

getRawFreq

public double getRawFreq(java.lang.String character)

Gets the frequency of a raw character

Parameters:

character - The character to get the frequency for

Returns:

The frequency of that chaacter

getClassSize

public int getClassSize(java.lang.String cl)

Gets the size of a class, that is how many sites belong to the given class

Parameters:

cl - The class

Returns:

How many sites are in that class

getSiteClasses

public java.util.List<java.lang.String> getSiteClasses()

Returns a list of site classes in the same order as the sites in the alignment. Used in confidence testing to simulate an alignment similar to this one.

Returns:

List of site classes

hasClasses

public boolean hasClasses()

Checks whether the sites in this alignment have classes

Returns:

Whether the sites have clases

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object