org.biojava.bio.seq.impl

Class AssembledSymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.seq.impl.AssembledSymbolList

All Implemented Interfaces:

SymbolList, Changeable

public class AssembledSymbolList
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

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 and Description
AssembledSymbolList()

Method Summary

Methods

Modifier and Type	Method and 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	putComponent(Location l, SymbolList sl)
void	removeComponent(Location loc)
void	setLength(int len)
SymbolList	subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
String	subStr(int start, int end) Return a region of this symbol list as a String.
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, 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

AssembledSymbolList

public AssembledSymbolList()

Method Detail

setLength

public void setLength(int len)

putComponent

public void putComponent(ComponentFeature f)

putComponent

public void putComponent(Location l,
                SymbolList sl)

Throws:

IllegalArgumentException - if sl would introduce a circularity into the tree of components

removeComponent

public void removeComponent(Location loc)

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

subStr

public String subStr(int start,
            int end)

Description copied from interface: SymbolList

Return a region of this symbol list as a String.

This should use the same rules as seqString.

Specified by:

subStr in interface SymbolList

Overrides:

subStr in class AbstractSymbolList

Parameters:

start - the first symbol to include

end - the last symbol to include

Returns:

the string representation