org.biojava.bio.alignment

Interface Alignment

All Superinterfaces:

Changeable, SymbolList

All Known Subinterfaces:

ARAlignment, StatePath, UnequalLengthAlignment

All Known Implementing Classes:

AbstractULAlignment, AbstractULAlignment.SubULAlignment, AlignmentPair, FlexibleAlignment, RelabeledAlignment, SimilarityPairFeature.EmptyPairwiseAlignment, SimpleAlignment, SimpleStatePath

public interface Alignment
extends SymbolList

An alignment containing multiple SymbolLists.

The alignment can be thought of as a rectangular array of Symbols. Each row is indexed by a label and each column is indexed by offset (counting from 1).

Alternatively, it can be thought of as a SymbolList where each Symbol is a list of Symbols in that column.

To create gapped alignments, use SymbolLists with gaps. The most flexible way to do this will be to leverage GappedSymbolList objects.

Since:

1.1

Author:

Matthew Pocock, Nimesh Singh

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	Alignment.SymbolListIterator Iterator implementation looping over symbol lists in an alignment using the labels.

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	CONTENT Signals that SymbolLists will be added to or removed from an alignment.

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

EDIT, EMPTY_LIST

Method Summary

Methods

Modifier and Type	Method and Description
List<String>	getLabels() The list of SymbolLists in the alignment.
Alignment	subAlignment(Set<String> labels, Location loc) Make a view onto this alignment.
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 interface org.biojava.bio.symbol.SymbolList

edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

CONTENT

static final ChangeType CONTENT

Signals that SymbolLists will be added to or removed from an alignment. The ChangeEvent will record Object[] { label, symbolList } in previous if it is being removed, in current if it is being added and in both if the SymbolList for a given name is swapped.

Method Detail

getLabels

List<String> getLabels()

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.

Returns:

the List of all SymbolLists in the alignment

symbolAt

Symbol symbolAt(String label,
              int column)
                throws NoSuchElementException

Retrieve a symbol by label and column.

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

Throws:

NoSuchElementException - if there is no row for 'label'

symbolListForLabel

SymbolList symbolListForLabel(String label)
                              throws NoSuchElementException

Retrieve a single row of the alignment by label.

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'

subAlignment

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

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.

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

symbolListIterator

Iterator<SymbolList> symbolListIterator()

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.

Returns:

an Iterator