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:
- 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.).
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
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 java.lang.Object |
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
DummySymbolList
public DummySymbolList(FiniteAlphabet alpha,
int length)
DummySymbolList
public DummySymbolList(Alphabet alpha,
int length,
Symbol sym)
throws IllegalSymbolException
- Throws:
IllegalSymbolException
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