org.biojava.bio.alignment

Interface ARAlignment

All Superinterfaces:

Alignment, Changeable, SymbolList

All Known Implementing Classes:

FlexibleAlignment

public interface ARAlignment
extends Alignment

ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.

Author:

David Waring

Nested Class Summary

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

Alignment.SymbolListIterator

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	ADD_LABEL
static ChangeType	REMOVE_LABEL

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

CONTENT

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

EDIT, EMPTY_LIST

Method Summary

Methods

Modifier and Type	Method and Description
void	addSequence(AlignmentElement ae)
void	removeSequence(java.lang.Object label)

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

getLabels, subAlignment, symbolAt, symbolListForLabel, symbolListIterator

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

ADD_LABEL

static final ChangeType ADD_LABEL

REMOVE_LABEL

static final ChangeType REMOVE_LABEL

Method Detail

addSequence

void addSequence(AlignmentElement ae)
                 throws ChangeVetoException,
                        BioException

Throws:

ChangeVetoException

BioException

removeSequence

void removeSequence(java.lang.Object label)
                    throws ChangeVetoException

Throws:

ChangeVetoException