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The set of AtomicSymbols which can be concatenated 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.
Nested Class Summary |
Nested classes inherited from class org.biojava.bio.Annotatable |
Annotatable.AnnotationForwarder |
Field Summary | |
static Alphabet |
EMPTY_ALPHABET
A really useful static alphabet that is always empty. |
static ChangeType |
PARSERS
This signals that the available parsers have changed. |
static ChangeType |
SYMBOLS
This ChangeType indicates that some symbols have been added or removed from the alphabet. |
Fields inherited from interface org.biojava.bio.Annotatable |
ANNOTATION |
Method Summary | |
boolean |
contains(Symbol s)
Returns whether or not this Alphabet contains the symbol. |
java.util.List |
getAlphabets()
Return an ordered List of the alphabets which make up a compound alphabet. |
Symbol |
getAmbiguity(java.util.Set syms)
Get a symbol that represents the set of symbols in syms. |
Symbol |
getGapSymbol()
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet. |
java.lang.String |
getName()
Get the name of the alphabet. |
Symbol |
getSymbol(java.util.List rl)
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols. |
SymbolTokenization |
getTokenization(java.lang.String name)
Get a SymbolTokenization by name. |
void |
validate(Symbol s)
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. |
Methods inherited from interface org.biojava.bio.Annotatable |
getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
public static final ChangeType SYMBOLS
This ChangeType indicates that some symbols have been added or removed from the alphabet. The current and previous fields should indicate what symbols were there originally, and what they have been replaced with.
If the alphabet wishes to propagate that the symbol has changed state, then previous and current should be null, but the chainedEvent property should rever to the ChangeEvent on the unerlying Symbol.
public static final ChangeType PARSERS
public static final Alphabet EMPTY_ALPHABET
Method Detail |
public java.lang.String getName()
public java.util.List getAlphabets()
public Symbol getSymbol(java.util.List rl) throws IllegalSymbolException
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
The symbol at i in the list must be a member of the i'th alphabet in getAlphabets. If all of the symbols in rl are atomic, then the resulting symbol will also be atomic. If any one of them is an ambiguity symbol then the resulting symbol will be the appropriate ambiguity symbol.
rl
- A list of Symbol instances
IllegalSymbolException
- if the members of rl are
not Symbols over the alphabets returned from
getAlphabets
public Symbol getAmbiguity(java.util.Set syms) throws IllegalSymbolException
Get a symbol that represents the set of symbols in syms.
Syms must be a set of Symbol instances each of which is contained within this alphabet. This method is used to retrieve ambiguity symbols.
syms
- the Set of Symbols that will be found in getMatches of the
returned symbol
IllegalSymbolException
public Symbol getGapSymbol()
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
In general, this will be a BasisSymbol that represents a list of AlphabetManager.getGapSymbol() the same length as the getAlphabets list.
public boolean contains(Symbol s)
Returns whether or not this Alphabet contains the symbol.
An alphabet contains an ambiguity symbol iff the ambiguity symbol's getMatches() returns an alphabet that is a proper sub-set of this alphabet. That means that every one of the symbols that could match the ambiguity symbol is also a member of this alphabet.
s
- the Symbol to check
public void validate(Symbol s) throws IllegalSymbolException
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
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.
s
- the Symbol to validate
IllegalSymbolException
- if r is not contained in this alphabetpublic SymbolTokenization getTokenization(java.lang.String name) throws BioException
Get a SymbolTokenization by name.
The parser returned is guaranteed to return Symbols and SymbolLists that conform to this alphabet.
Every alphabet should have a SymbolTokenzation under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolTokenization under the name 'name' that uses symbol names to identify symbols. Any other names may also be defined, but the behaviour of the returned SymbolTokenization is not defined here.
name
- the name of the parser
java.util.NoSuchElementException
- if the name is unknown
BioException
- if for any reason the tokenization could not be built
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