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java.lang.Object | +--org.biojava.bio.symbol.Alphabet.EmptyAlphabet
The class that implements Alphabet and is empty.
Inner classes inherited from class org.biojava.bio.symbol.Alphabet |
Alphabet.EmptyAlphabet |
Fields inherited from interface org.biojava.bio.symbol.Alphabet |
EMPTY_ALPHABET |
Constructor Summary | |
Alphabet.EmptyAlphabet()
|
Method Summary | |
boolean |
contains(Symbol s)
Returns whether or not this Alphabet contains the symbol. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
java.lang.String |
getName()
Get the name of the alphabet. |
SymbolParser |
getParser(java.lang.String name)
Get a parser by name. |
java.util.Iterator |
iterator()
Retrieve an Iterator over the Symbols in this FiniteAlphabet. |
int |
size()
The number of symbols in the alphabet. |
SymbolList |
symbols()
A list of symbols that make up this alphabet. |
void |
validate(Symbol res)
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public Alphabet.EmptyAlphabet()
Method Detail |
public java.lang.String getName()
public Annotation getAnnotation()
public boolean contains(Symbol s)
An alphabet contains an ambiguity symbol iff the ambiguity symbol's getMemberAlphabet() returns an alphabe that is a propper sub-set of this alphabet. That means that every one of the symbols that could mach the ambiguity symbol is also a member of this alphabet.
r
- the Symbol to checkpublic void validate(Symbol res) throws IllegalSymbolException
This function is used all over the code to validate symbols as they enter a method. Also, the code is littered with catches for IllegalSymbolException. There is a preferred style of handling this, which should be covererd in the package documentation.
r
- the Symbol to validatepublic SymbolParser getParser(java.lang.String name) throws java.util.NoSuchElementException
The parser returned is guaranteed to return Symbols and SymbolLists that conform to this alphabet.
Every alphabet should have a SymbolParser under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolParser under the name 'name' that uses symbol names to identify symbols. Any other names may also be defined, but the behaviour of that parser is not defined here.
name
- the name of the parserpublic int size()
public java.util.Iterator iterator()
Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.
public SymbolList symbols()
Subsequent calls to this method are not required to return either the same symbol list, or even a symbol list with the symbols in the same order.
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