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.).
- 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.
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. |
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