- Enclosing class:
public static class DoubleAlphabet.SubDoubleAlphabet extends Unchangeable implements Alphabet, SerializableA class to represent a contiguous range of double symbols.
- Matthew Pocock
- See Also:
- Serialized Form
All Methods Instance Methods Concrete Methods Modifier and Type Method Description
contains(Symbol s)Returns whether or not this Alphabet contains the symbol.
getAlphabets()Return an ordered List of the alphabets which make up a compound alphabet.
getAmbiguity(Set syms)Get a symbol that represents the set of symbols in syms.
getAnnotation()Should return the associated annotation object.
getGapSymbol()Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
getName()Get the name of the alphabet.
getSymbol(List rl)Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
getTokenization(String name)Get a SymbolTokenization by name.
readResolve()To prevent duplication of a what should be a single instance of an existing alphabet.
validate(Symbol sym)Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
Methods inherited from class org.biojava.utils.Unchangeable
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
protected Object readResolve() throws ObjectStreamExceptionTo prevent duplication of a what should be a single instance of an existing alphabet. This method was written as protected so that subclasses even from other packages will inherit it. It should only be overridden with care.
getNameGet the name of the alphabet.
public Annotation getAnnotation()Description copied from interface:
AnnotatableShould return the associated annotation object.
public List getAlphabets()Return an ordered List of the alphabets which make up a compound alphabet. For simple alphabets, this will return a singleton list of itself. The returned list should be immutable.
public Symbol getSymbol(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.
public DoubleAlphabet.DoubleSymbol getSymbol(double val) throws IllegalSymbolException
public Symbol getAmbiguity(Set syms)
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.
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.
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.
public void validate(Symbol sym) 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.
public SymbolTokenization getTokenization(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 behavior of the returned SymbolTokenization is not defined here.
A SymbolTokenization under the name 'default' should be defined for all sequences, that determines the behavior when printing out a sequence. Standard behavior is to define the 'token' SymbolTokenization as default if it exists, else to define the 'name' SymbolTokenization as the default, but others are possible.