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
static class Alignment.SymbolListIterator
          Iterator implementation looping over symbol lists in an alignment using the labels.
 
Field Summary
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
 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


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