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 Details
- 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 Details
- 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.

Class SimpleSymbolList

Nested Class Summary

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

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

Field Summary

Fields inherited from interface org.biojava.utils.ChangeListener

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

Constructor Summary

Method Summary

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

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Constructor Details

SimpleSymbolList

SimpleSymbolList

SimpleSymbolList

SimpleSymbolList

SimpleSymbolList

Method Details

finalize

getAlphabet

length

symbolAt

subList

edit

preChange

postChange

addSymbol

getSymbolArray