Package org.biojava.bio.symbol

Class SimpleSymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.symbol.SimpleSymbolList

All Implemented Interfaces:

Serializable, EventListener, SymbolList, Changeable, ChangeListener

public class SimpleSymbolList
extends AbstractSymbolList
implements ChangeListener, Serializable

Basic implementation of SymbolList. This is currently backed by a normal Java array.

SimpleSymbolList is now editable. edit() has been implemented in a way that edits are relatively inefficient, but symbolAt() is very efficient.

A new constructor SimpleSymbolList(SymbolParser,String) has been added so you can now simply turn a String into a SymbolList. This is mostly to provide a simple way to create a SymbolList for people just trying to get their feet wet. So here is an example.

String seqString = "gaattc"; FiniteAlphabet dna = (FiniteAlphabet) AlphabetManager.alphabetForName("DNA"); SymbolParser parser = dna.getTokenization("token"); SymbolList mySl = new SimpleSymbolList (parser,seqString); System.out.println("Look at my sequence " + mySl.seqString());

with the right parser you should be able to make a protein sequence from the String "AspAlaValIleAsp"

subList() is implemented such that subLists are views of the original until such time as the underlying SymbolList is edited in a way that would modify the subList, at which point the subList gets its own array of Symbols and does not reflect the edit to the original. When subList() is called on another subList (which is a veiw SimpleSymbolList) the new SimpleSymbolList is a view of the original, not the subList.

Author:

Thomas Down, David Waring, David Huen (another constructor), George Waldon

See Also:

Serialized Form

Nested Class Summary

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

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Nested classes/interfaces inherited from interface org.biojava.utils.ChangeListener

ChangeListener.AlwaysVetoListener, ChangeListener.ChangeEventRecorder, ChangeListener.LoggingListener

Field Summary

Fields inherited from interface org.biojava.utils.ChangeListener

ALWAYS_VETO, LOG_TO_OUT

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

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor	Description
SimpleSymbolList(SymbolTokenization parser, String seqString)	Construct a SymbolList from a string.
SimpleSymbolList(Alphabet alpha)	Construct an empty SimpleSymbolList.
SimpleSymbolList(Alphabet alpha, List rList)	Construct a SymbolList containing the symbols in the specified list.
SimpleSymbolList(Symbol[] symbols, int length, Alphabet alphabet)	Construct a SimpleSymbolList given the Symbol array that backs it.
SimpleSymbolList(SymbolList sl)	Construct a copy of an existing SymbolList.

Method Summary

Modifier and Type	Method	Description
void	addSymbol(Symbol sym)	Add a new Symbol to the end of this list.
void	edit(Edit edit)	Apply and edit to the SymbolList as specified by Edit.
protected void	finalize()
Alphabet	getAlphabet()	Get the alphabet of this SymbolList.
Symbol[]	getSymbolArray()	Return the Java Symbol[] array that backs this object.
int	length()	Get the length of this SymbolList.
void	postChange(ChangeEvent cev)	Called when a change has just taken place.
void	preChange(ChangeEvent cev)	On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols
SymbolList	subList(int start, int end)	create a subList of the original, this will be a view until either the original symbolList or the sublist is edited
Symbol	symbolAt(int pos)	Find a symbol at a specified offset in the SymbolList.

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

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, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleSymbolList

public SimpleSymbolList(Alphabet alpha)

Construct an empty SimpleSymbolList.

Parameters:

alpha - The alphabet of legal symbols in this list.

SimpleSymbolList

public SimpleSymbolList(Alphabet alpha,
                        List rList)
                 throws IllegalSymbolException

Construct a SymbolList containing the symbols in the specified list.

Parameters:

alpha - The alphabet of legal symbols for this list.

rList - A Java List of symbols.

Throws:

IllegalSymbolException - if a Symbol is not in the specified alphabet.

ClassCastException - if rList contains objects which do not implement Symbol.

SimpleSymbolList

public SimpleSymbolList(SymbolTokenization parser,
                        String seqString)
                 throws IllegalSymbolException

Construct a SymbolList from a string.

Parameters:

parser - A SymbolParser for whatever your string is -- e.g. alphabet.getParser("token").

seqString - A Java List of symbols.

Throws:

IllegalSymbolException - if a Symbol is not in the specified alphabet.

SimpleSymbolList

public SimpleSymbolList(SymbolList sl)

Construct a copy of an existing SymbolList.

Parameters:

sl - the list to copy.

SimpleSymbolList

public SimpleSymbolList(Symbol[] symbols,
                        int length,
                        Alphabet alphabet)

Construct a SimpleSymbolList given the Symbol array that backs it. Used primarily with the chunked SymbolList builder but could be used elsewhere too.

Method Detail

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

getAlphabet

public Alphabet getAlphabet()

Get the alphabet of this SymbolList.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

length

public int length()

Get the length of this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

symbolAt

public Symbol symbolAt(int pos)

Find a symbol at a specified offset in the SymbolList.

Specified by:

symbolAt in interface SymbolList

Parameters:

pos - Position in biological coordinates (1..length)

Returns:

the Symbol at that index

subList

public SymbolList subList(int start,
                          int end)

create a subList of the original, this will be a view until either the original symbolList or the sublist is edited

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

edit

public void edit(Edit edit)
          throws IndexOutOfBoundsException,
                 IllegalAlphabetException,
                 ChangeVetoException

Apply and edit to the SymbolList as specified by Edit.

edit() is now supported using the ChangeEvent system. SubLists do NOT reflect edits.

Specified by:

edit in interface SymbolList

Overrides:

edit in class AbstractSymbolList

Parameters:

edit - the Edit to perform

Throws:

IndexOutOfBoundsException - if the edit does not lie within the SymbolList

IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet

ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

preChange

public void preChange(ChangeEvent cev)
               throws ChangeVetoException

On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols

Specified by:

preChange in interface ChangeListener

Parameters:

cev - An event encapsulating the change which is about to take place.

Throws:

ChangeVetoException - Description of Exception

postChange

public void postChange(ChangeEvent cev)

Description copied from interface: ChangeListener

Called when a change has just taken place.

This method is the place to perform any behavior in response to the change event.

Specified by:

postChange in interface ChangeListener

Parameters:

cev - An event encapsulating the change which has occured.

addSymbol

public void addSymbol(Symbol sym)
               throws IllegalSymbolException,
                      ChangeVetoException

Add a new Symbol to the end of this list.

Parameters:

sym - Symbol to add

Throws:

IllegalSymbolException - if the Symbol is not in this list's alphabet

ChangeVetoException

getSymbolArray

public Symbol[] getSymbolArray()

Return the Java Symbol[] array that backs this object. primarily used to accelerate reconstruction of symbol lists in the packed chunked symbol list implementation.