Package org.biojava.bio.seq.impl

Class NewAssembledSymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.seq.impl.NewAssembledSymbolList

All Implemented Interfaces:

SymbolList, Changeable

public class NewAssembledSymbolList
extends AbstractSymbolList

Support class for applications which need to patch together sections of sequence into a single SymbolList. This class isn't intended for direct use in user code -- instead, it is a helper for people implementing the full BioJava assembly model. See SimpleAssembly for an example.

Since:

1.1

Author:

Thomas Down, Greg Cox, Matthew Pocock, David Huen (support for overlapped features)

Nested Class Summary

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

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Field Summary

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

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor	Description
NewAssembledSymbolList()

Method Summary

Modifier and Type	Method	Description
Alphabet	getAlphabet()	The alphabet that this SymbolList is over.
Set	getComponentLocationSet()
int	length()	The number of symbols in this SymbolList.
void	putComponent(ComponentFeature f)
void	removeComponent(ComponentFeature f)
void	setLength(int len)
SymbolList	subList(int start, int end)	Return a new SymbolList for the symbols start to end inclusive.
Symbol	symbolAt(int pos)	Return the symbol at index, counting from 1.

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

edit, equals, hashCode, iterator, seqString, 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, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

NewAssembledSymbolList

public NewAssembledSymbolList()

Method Detail

setLength

public void setLength(int len)

putComponent

public void putComponent(ComponentFeature f)

removeComponent

public void removeComponent(ComponentFeature f)

getComponentLocationSet

public Set getComponentLocationSet()

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.

Returns:

the alphabet

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Returns:

the length

symbolAt

public Symbol symbolAt(int pos)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Parameters:

pos - the offset into this SymbolList

Returns:

the Symbol at that index

subList

public SymbolList subList(int start,
                          int end)

Description copied from interface: SymbolList

Return a new SymbolList for the symbols start to end inclusive.

The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

Specified by:

subList in interface SymbolList

Overrides:

subList in class AbstractSymbolList

Parameters:

start - the first symbol of the new SymbolList

end - the last symbol (inclusive) of the new SymbolList