Class AbstractAlphabet

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractAlphabet
All Implemented Interfaces:
Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable
Direct Known Subclasses:
IntegerAlphabet.SubIntegerAlphabet, SimpleAlphabet, SingletonAlphabet

public abstract class AbstractAlphabet extends AbstractChangeable implements FiniteAlphabet, Serializable

An abstract implementation of Alphabet.

This provides the frame-work for maintaining the SymbolParser invalid input: '<'-> name mappings and also for the ChangeListeners.

This class is for developers to derive from, not for use directly.

Since:
1.1
Author:
Matthew Pocock, Greg Cox, Francois Pepin, Mark Schreiber
See Also:
  • Field Details

  • Constructor Details

  • Method Details

    • readResolve

      To 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.
      Throws:
      ObjectStreamException
    • putTokenization

      public void putTokenization(String name, SymbolTokenization parser)

      Assigns a symbol parser to a String object.

      Afterwards, the parser can be retrieved using the getTokenization(Sting name) method.

    • getTokenization

      Description copied from interface: Alphabet

      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.

      Specified by:
      getTokenization in interface Alphabet
      Parameters:
      name - the name of the parser
      Returns:
      a parser for that name
      Throws:
      NoSuchElementException - if the name is unknown
      BioException - if for any reason the tokenization could not be built
    • getAmbiguity

      public final Symbol getAmbiguity(Set syms) throws IllegalSymbolException
      Description copied from interface: Alphabet

      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.

      Specified by:
      getAmbiguity in interface Alphabet
      Parameters:
      syms - the Set of Symbols that will be found in getMatches of the returned symbol
      Returns:
      a Symbol (possibly fly-weighted) for the Set of symbols in syms
      Throws:
      IllegalSymbolException
    • getAmbiguityImpl

      Backend for getAmbiguity, called when it is actually necessarly to create a new symbol. By default, calls AlphabetManager.createSymbol.
      Throws:
      IllegalSymbolException
      Since:
      1.3
    • getSymbol

      public final Symbol getSymbol(List syms) throws IllegalSymbolException
      Description copied from interface: Alphabet

      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.

      Specified by:
      getSymbol in interface Alphabet
      Parameters:
      syms - A list of Symbol instances
      Throws:
      IllegalSymbolException - if the members of rl are not Symbols over the alphabets returned from getAlphabets
    • getSymbolImpl

      protected abstract AtomicSymbol getSymbolImpl(List symList) throws IllegalSymbolException
      Throws:
      IllegalSymbolException
    • addSymbolImpl

      Throws:
      IllegalSymbolException
      ChangeVetoException
    • addSymbol

      Description copied from interface: FiniteAlphabet
      Adds a symbol to this alphabet.

      If the symbol matches more than one AtomicSymbol, then each symbol matching it will be added.

      Specified by:
      addSymbol in interface FiniteAlphabet
      Parameters:
      s - the Symbol to add
      Throws:
      IllegalSymbolException - if the symbol is null, or if for any reason it can't be added
      ChangeVetoException - if either the alphabet doesn't allow symbols to be added, or the change was vetoed
    • contains

      public final boolean contains(Symbol sym)
      Description copied from interface: Alphabet

      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.

      Specified by:
      contains in interface Alphabet
      Parameters:
      sym - the Symbol to check
      Returns:
      boolean true if the Alphabet contains the symbol and false otherwise
    • getGapSymbol

      public final Symbol getGapSymbol()
      Description copied from interface: Alphabet

      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.

      Specified by:
      getGapSymbol in interface Alphabet
      Returns:
      the appropriate gap Symbol instance
    • validate

      public final void validate(Symbol sym) throws IllegalSymbolException
      Description copied from interface: Alphabet

      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.

      Specified by:
      validate in interface Alphabet
      Parameters:
      sym - the Symbol to validate
      Throws:
      IllegalSymbolException - if r is not contained in this alphabet
    • containsImpl

      protected abstract boolean containsImpl(AtomicSymbol s)
    • toString

      public String toString()
      Overrides:
      toString in class Object