org.biojava.bio.symbol
Class DummySymbolList

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.symbol.AbstractSymbolList
          extended by org.biojava.bio.symbol.DummySymbolList
All Implemented Interfaces:
java.io.Serializable, SymbolList, Changeable

public class DummySymbolList
extends AbstractSymbolList
implements java.io.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.).

Since:
1.2
Author:
Thomas Down, Matthew Pocock
See Also:
Serialized Form
For general use:
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.

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