Package 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
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:
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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
ConstructorsConstructorDescriptionDummySymbolList(Alphabet alpha, int length, Symbol sym) DummySymbolList(FiniteAlphabet alpha, int length) -
Method Summary
Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toStringMethods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, waitMethods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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DummySymbolList
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DummySymbolList
- Throws:
IllegalSymbolException
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Method Details
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getAlphabet
Description copied from interface:SymbolListThe alphabet that this SymbolList is over.Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == truefor each symbol that is within this sequence.- Specified by:
getAlphabetin interfaceSymbolList- Returns:
- the alphabet
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length
Description copied from interface:SymbolListThe number of symbols in this SymbolList.- Specified by:
lengthin interfaceSymbolList- Returns:
- the length
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symbolAt
Description copied from interface:SymbolListReturn the symbol at index, counting from 1.- Specified by:
symbolAtin interfaceSymbolList- Parameters:
i- the offset into this SymbolList- Returns:
- the Symbol at that index
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