AlphabetIndex (biojava-legacy 1.9.5 API)

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 Description

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

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	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()