org.biojava.bio.symbol
Class PackedDnaSymbolList
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbolList
org.biojava.bio.symbol.PackedDnaSymbolList
- All Implemented Interfaces:
- Changeable, java.io.Serializable, SymbolList
- public class PackedDnaSymbolList
- extends AbstractSymbolList
- implements java.io.Serializable
a class that implements storage of symbols
in packed form (2 symbols per byte).
- Since:
- 1.2
- Author:
- David Huen
- See Also:
- Serialized Form
Method Summary |
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
byte[] |
getArray()
returns the byte array backing the SymbolList. |
int |
length()
The number of symbols in this SymbolList. |
Symbol |
symbolAt(int index)
Return the symbol at index, counting from 1. |
Methods inherited from class java.lang.Object |
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait |
PackedDnaSymbolList
public PackedDnaSymbolList(SymbolList symList)
throws BioException,
IllegalAlphabetException
- constructor taking another symbol list.
PackedDnaSymbolList
public PackedDnaSymbolList(int length,
byte[] byteArray)
throws BioException
- constructor taking a byte array previously
created by another PackedDnaSymbolList object.
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
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
symbolAt
public Symbol symbolAt(int index)
- Description copied from interface:
SymbolList
- Return the symbol at index, counting from 1.
- Specified by:
symbolAt
in interface SymbolList
- Parameters:
index
- the offset into this SymbolList
- Returns:
- the Symbol at that index
getArray
public byte[] getArray()
- returns the byte array backing the SymbolList.
(can be written out and stored).