Package org.biojava.bio.alignment

Class SimpleAlignment

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.alignment.SimpleAlignment

All Implemented Interfaces:

Serializable, Alignment, SymbolList, Changeable

Direct Known Subclasses:

AlignmentPair

public class SimpleAlignment
extends AbstractSymbolList
implements Alignment, Serializable

A simple implementation of an Alignment.

This is a simple-stupid implementation that is made from a set of same-lengthed SymbolList objects each with an associated label. It does not handle differently lengthed sequences and doesn't contain any gap-editing concepts.

Author:

Matthew Pocock, Greg Cox, Nimesh Singh

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment

Alignment.SymbolListIterator

Field Summary

Fields inherited from interface org.biojava.bio.alignment.Alignment

CONTENT

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor	Description
SimpleAlignment(Map<String,SymbolList> labelToResList)	Generate an alignment from a list of SymbolLists.

Method Summary

Modifier and Type	Method	Description
protected void	finalize()
Alphabet	getAlphabet()	The alphabet that this SymbolList is over.
List<String>	getLabels()	The list of SymbolLists in the alignment.
int	getScore()
int	length()	The number of symbols in this SymbolList.
void	setScore(int score)
Alignment	subAlignment(Set<String> labels, Location loc)	Make a view onto this alignment.
Symbol	symbolAt(int index)	Return the symbol at index, counting from 1.
Symbol	symbolAt(String label, int column)	Retrieve a symbol by label and column.
SymbolList	symbolListForLabel(String label)	Retrieve a single row of the alignment by label.
Iterator<SymbolList>	symbolListIterator()	Creates an Iterator over the SymbolLists in the alignment.

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList

edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.symbol.SymbolList

edit, iterator, seqString, subList, subStr, toList

Constructor Detail

SimpleAlignment

public SimpleAlignment(Map<String,SymbolList> labelToResList)
                throws IllegalArgumentException

Generate an alignment from a list of SymbolLists.

The SymbolLists must all be of the same length.

Parameters:

labelToResList - the label-to-symbol list mapping

Throws:

IllegalArgumentException - if the SymbolLists are not the same length

Method Detail

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolList

The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

symbolAt

public Symbol symbolAt(int index)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

index - the offset into this SymbolList

Returns:

the Symbol at that index

getLabels

public List<String> getLabels()

Description copied from interface: Alignment

The list of SymbolLists in the alignment.

The index in the list is the same as the index in the alignment. Each SymbolList object will only be in the alignment once. However, a single underlying SymbolList may have more than one view within an alignment, each represented by a different GappedSymbolList.

Specified by:

getLabels in interface Alignment

Returns:

the List of all SymbolLists in the alignment

symbolAt

public Symbol symbolAt(String label,
                       int column)

Description copied from interface: Alignment

Retrieve a symbol by label and column.

Specified by:

symbolAt in interface Alignment

Parameters:

label - the SymbolList to retrieve from

column - the index of the column to retrieve

Returns:

the symbol in the symbol list associated with the label at the given column

subAlignment

public Alignment subAlignment(Set<String> labels,
                              Location loc)
                       throws NoSuchElementException

Description copied from interface: Alignment

Make a view onto this alignment.

If labels is null, then each label will be kept. Otherwise, only those in labels will be kept. If loc is null, then the entire length of the alignment will be kept. If loc is not null, then only the columns within the location will be kept.

Specified by:

subAlignment in interface Alignment

Parameters:

labels - the Set of sequences to include by label

loc - the Location to include

Returns:

a sub Alignment

Throws:

NoSuchElementException - if labels contains any item that is not a label

symbolListForLabel

public SymbolList symbolListForLabel(String label)
                              throws NoSuchElementException

Description copied from interface: Alignment

Retrieve a single row of the alignment by label.

Specified by:

symbolListForLabel in interface Alignment

Parameters:

label - the object from which to retrieve the symbol list

Returns:

a SymbolList that contains each token in a row of the alignment

Throws:

NoSuchElementException - if there is no row for 'label'

symbolListIterator

public Iterator<SymbolList> symbolListIterator()

Description copied from interface: Alignment

Creates an Iterator over the SymbolLists in the alignment. This should be similar to iterating over the labels and then fetching each SymbolList, but the order is not guaranteed to be the same.

Specified by:

symbolListIterator in interface Alignment

Returns:

an Iterator

getScore

public int getScore()

Returns:

setScore

public void setScore(int score)

Parameters:

score -