org.biojava.bio.symbol

Interface AlphabetIndex

All Superinterfaces:

Changeable

public interface AlphabetIndex
extends Changeable

Map between Symbols and index numbers.

The Symbols will all come from a single finite alphabet. The indices will range from 0 to getAlphabet().size()-1 inclusive with each symbol having a unique index. The resulting table can be used to look up array indices by symbol, which in many cases will be more efficient than performing a Map operation on, for example, a HashMap.

An index should do whatever is necessary to stay synchronized with its alphabet. It may chose to modify the index table with the alphabet, or to veto all changes to the alphabet that would invalidate the indexing scheme.

Since:

1.1

Author:

Thomas Down, Matthew pocock

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	INDEX Indicates that the index is changing, probably due to the underlying alphabet changing.

Method Summary

Methods

Modifier and Type	Method and Description
FiniteAlphabet	getAlphabet() Retrieve the alphabet that this indexes.
int	indexForSymbol(Symbol s) Return the unique index for a symbol.
Symbol	symbolForIndex(int i) Retrieve the symbol for an index.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

INDEX

static final ChangeType INDEX

Indicates that the index is changing, probably due to the underlying alphabet changing.

The previous & changed fields should be arrays of symbols in the order they are indexed in the unmodified and modified indices respectively.

Method Detail

getAlphabet

FiniteAlphabet getAlphabet()

Retrieve the alphabet that this indexes.

Returns:

the FiniteAlphabet that is indexed by this object

indexForSymbol

int indexForSymbol(Symbol s)
                   throws IllegalSymbolException

Return the unique index for a symbol.

Parameters:

s - the Symbol to index

Returns:

the unique index for the symbol

Throws:

IllegalSymbolException - if s is not a member of the indexed alphabet, or if the indexer only indexes the AtomicSymbols within an alphabet and s was not attomic.

symbolForIndex

Symbol symbolForIndex(int i)
                      throws IndexOutOfBoundsException

Retrieve the symbol for an index.

Parameters:

i - the index of the symbol

Returns:

the symbol at that index

Throws:

IndexOutOfBoundsException - if i is negative or >= getAlphabet().size()