Interface AlphabetIndex
- All Superinterfaces:
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
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final ChangeType
Indicates that the index is changing, probably due to the underlying alphabet changing. -
Method Summary
Modifier and TypeMethodDescriptionRetrieve the alphabet that this indexes.int
Return the unique index for a symbol.symbolForIndex
(int i) Retrieve the symbol for an index.Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Field Details
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INDEX
Indicates that the index is changing, probably due to the underlying alphabet changing.
The previous invalid input: '&' changed fields should be arrays of symbols in the order they are indexed in the unmodified and modified indices respectively.
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Method Details
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getAlphabet
Retrieve the alphabet that this indexes.- Returns:
- the FiniteAlphabet that is indexed by this object
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indexForSymbol
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.
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symbolForIndex
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()
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