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 inherited from class org.biojava.bio.symbol.Alignment
Alignment.SymbolListIterator
 
Nested classes inherited from class org.biojava.bio.symbol.SymbolList
SymbolList.EmptySymbolList
 
Field Summary
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
 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

public static final ChangeType ADD_LABEL

REMOVE_LABEL

public static final ChangeType REMOVE_LABEL
Method Detail

addSequence

public void addSequence(AlignmentElement ae)
                 throws ChangeVetoException,
                        BioException
Throws:
ChangeVetoException
BioException

removeSequence

public void removeSequence(java.lang.Object label)
                    throws ChangeVetoException
Throws:
ChangeVetoException