org.biojava.bio.symbol

Class DummySymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.symbol.DummySymbolList

All Implemented Interfaces:

Serializable, SymbolList, Changeable

public class DummySymbolList
extends AbstractSymbolList
implements Serializable

Symbol list which just consists of non-informative symbols. A DummySymbolList can be constructed over any Alphabet, and may be of any length. Calls to the symbolAt method will always return the non-informative symbol for the alphabet in question (i.e. 'n' for DNA, 'X' for protein, etc.). If you wish to work with Feature objects, but don't have the actual sequence data available, you can construct a SimpleSequence from a DummySequence, and create features. on that.

Since:

1.2

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

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
DummySymbolList(Alphabet alpha, int length, Symbol sym)
DummySymbolList(FiniteAlphabet alpha, int length)

Method Summary

Methods

Modifier and Type	Method and Description
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
int	length() The number of symbols in this SymbolList.
Symbol	symbolAt(int i) Return the symbol at index, counting from 1.

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

edit, equals, hashCode, iterator, seqString, subList, 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

DummySymbolList

public DummySymbolList(FiniteAlphabet alpha,
               int length)

DummySymbolList

public DummySymbolList(Alphabet alpha,
               int length,
               Symbol sym)
                throws IllegalSymbolException

Throws:

IllegalSymbolException

Method Detail

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.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

symbolAt

public Symbol symbolAt(int i)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

i - the offset into this SymbolList

Returns:

the Symbol at that index