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The set of AtomicSymbols which can be concatanated together to make a SymbolList.
A non-atomic symbol is considered to be contained within this alphabet if all of the atomic symbols that it could match are members of this alphabet.
The alphabet concept may need to be widened to include alphabets that extend others, or checks to see if two alphabets are equivalent, or other set-wise operations. As yet, I have baulked at this as it may make Alphabet too heavy to easily implement.
Inner Class Summary | |
static class |
Alphabet.EmptyAlphabet
The class that implements Alphabet and is empty. |
Field Summary | |
static Alphabet |
EMPTY_ALPHABET
A really useful static alphabet that is always empty. |
Method Summary | |
boolean |
contains(Symbol r)
Returns whether or not this Alphabet contains the symbol. |
java.lang.String |
getName()
Get the name of the alphabet. |
SymbolParser |
getParser(java.lang.String name)
Get a parser by name. |
void |
validate(Symbol r)
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. |
Methods inherited from interface org.biojava.bio.Annotatable |
getAnnotation |
Field Detail |
public static final Alphabet EMPTY_ALPHABET
Method Detail |
public java.lang.String getName()
public boolean contains(Symbol r)
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 r) 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, BioException
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 parser
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