AlphabetManager (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojava.bio.symbol.AlphabetManager

```
public final class AlphabetManager
extends Object
```
Utility methods for working with Alphabets. Also acts as a registry for well-known alphabets.
The alphabet interfaces themselves don't give you a lot of help in actually getting an alphabet instance. This is where the AlphabetManager comes in handy. It helps out in serialization, generating derived alphabets and building CrossProductAlphabet instances. It also contains limited support for parsing complex alphabet names back into the alphabets.

Author:

Matthew Pocock, Thomas Down, Mark Schreiber, George Waldon (alternate tokenization)

Constructor Summary

Constructors
Constructor and Description

AlphabetManager()

Constructors
Constructor and Description
`AlphabetManager()`

Method Summary

Methods
Modifier and Type	Method and Description
`static Alphabet`	`alphabetForName(String name)` Retrieve the alphabet for a specific name.
`static Iterator`	`alphabets()` Get an iterator over all alphabets known.
`static Symbol`	`createSymbol(Annotation annotation, List symList, Alphabet alpha)` Generates a new Symbol instance that represents the tuple of Symbols in symList.
`static Symbol`	`createSymbol(Annotation annotation, Set symSet, Alphabet alpha)` Generates a new Symbol instance that represents the tuple of Symbols in symList.
`static Symbol`	`createSymbol(char token, Annotation annotation, List symList, Alphabet alpha)` Deprecated. use the new version, without the token argument
`static Symbol`	`createSymbol(char token, Annotation annotation, Set symSet, Alphabet alpha)` Deprecated. use the three-arg version of this method instead.
`static AtomicSymbol`	`createSymbol(char token, String name, Annotation annotation)` Deprecated. Use the two-arg version of this method instead.
`static AtomicSymbol`	`createSymbol(String name)` Generate a new AtomicSymbol instance with a name and an Empty Annotation.
`static AtomicSymbol`	`createSymbol(String name, Annotation annotation)` Generate a new AtomicSymbol instance with a name and Annotation.
`static List`	`factorize(Alphabet alpha, Set symSet)` Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.
`static Alphabet`	`generateCrossProductAlphaFromName(String name)` Generates a new CrossProductAlphabet from the give name.
`static Symbol`	`getAllAmbiguitySymbol(FiniteAlphabet alpha)` Return the ambiguity symbol which matches all symbols in a given alphabet.
`static Set`	`getAllSymbols(FiniteAlphabet alpha)` Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.
`static AlphabetIndex`	`getAlphabetIndex(FiniteAlphabet alpha)` Get an indexer for a specified alphabet.
`static AlphabetIndex`	`getAlphabetIndex(Symbol[] syms)` Get an indexer for an array of symbols.
`static Alphabet`	`getCrossProductAlphabet(List aList)` Retrieve a CrossProductAlphabet instance over the alphabets in aList.
`static Alphabet`	`getCrossProductAlphabet(List aList, Alphabet parent)` Retrieve a CrossProductAlphabet instance over the alphabets in aList.
`static Alphabet`	`getCrossProductAlphabet(List aList, String name)` Attempts to create a cross product alphabet and register it under a name.
`static Symbol`	`getGapSymbol()` Get the special `gap' Symbol.
`static Symbol`	`getGapSymbol(List alphas)` Get the gap symbol appropriate to this list of alphabets.
`static AlphabetManager`	`instance()` Deprecated. all AlphabetManager methods have become static
`static void`	`loadAlphabets(InputSource is)` Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.
`static void`	`registerAlphabet(String[] names, Alphabet alphabet)` Register and Alphabet by more than one name.
`static void`	`registerAlphabet(String name, Alphabet alphabet)` Register an alphabet by name.
`static boolean`	`registered(String name)` Has an Alphabet been registered by that name
`static Set`	`registrations()` A set of names under which Alphabets have been registered.
`static Symbol`	`symbolForLifeScienceID(LifeScienceIdentifier lsid)` Retreives the Symbol for the LSID
`static Symbol`	`symbolForName(String name)` Deprecated. use symbolForLifeScienceID() instead

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - AlphabetManager
```
public AlphabetManager()
```
- Method Detail
  - instance
```
public static AlphabetManager instance()
```
    Deprecated. all AlphabetManager methods have become static
    
    Retrieve the singleton instance.
    
    Returns:
    the AlphabetManager instance
  - getAllAmbiguitySymbol
```
public static Symbol getAllAmbiguitySymbol(FiniteAlphabet alpha)
```
    Return the ambiguity symbol which matches all symbols in a given alphabet.
    
    Parameters:
    alpha - The alphabet
    
    Returns:
    the ambiguity symbol
    Since:
    
    1.2
  - getAllSymbols
```
public static Set getAllSymbols(FiniteAlphabet alpha)
```
    Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols. Warning, this method can return large sets!
    
    Parameters:
    alpha - The alphabet
    
    Returns:
    The set of symbols that are members of alpha
    Since:
    
    1.2
  - alphabetForName
```
public static Alphabet alphabetForName(String name)
                                throws NoSuchElementException
```
    Retrieve the alphabet for a specific name.
    
    Parameters:
    name - the name of the alphabet
    
    Returns:
    the alphabet object
    
    Throws:
    
    NoSuchElementException - if there is no alphabet by that name
  - symbolForName
```
public static Symbol symbolForName(String name)
                            throws NoSuchElementException
```
    Deprecated. use symbolForLifeScienceID() instead
    
    Retrieve the symbol represented a String object
    
    Parameters:
    name - of the string whose symbol you want to get
    
    Returns:
    The Symbol
    
    Throws:
    
    NoSuchElementException - if the string name is invalid.
  - symbolForLifeScienceID
```
public static Symbol symbolForLifeScienceID(LifeScienceIdentifier lsid)
```
    Retreives the Symbol for the LSID
    
    Parameters:
    lsid - the URN for the Symbol
    
    Returns:
    a reference to the Symbol
  - registerAlphabet
```
public static void registerAlphabet(String name,
                    Alphabet alphabet)
```
    Register an alphabet by name.
    
    Parameters:
    name - the name by which it can be retrieved
    alphabet - the Alphabet to store
  - registerAlphabet
```
public static void registerAlphabet(String[] names,
                    Alphabet alphabet)
```
    Register and Alphabet by more than one name. This allows aliasing of an alphabet with two or more names. It is equivalent to calling registerAlphabet(String name, Alphabet alphabet) several times.
    
    Parameters:
    names - the names by which it can be retrieved
    alphabet - the Alphabet to store
    Since:
    
    1.4
  - registrations
```
public static Set registrations()
```
    A set of names under which Alphabets have been registered.
    
    Returns:
    a Set of Strings
  - registered
```
public static boolean registered(String name)
```
    Has an Alphabet been registered by that name
    
    Parameters:
    name - the name of the alphabet
    
    Returns:
    true if it has or false otherwise
  - alphabets
```
public static Iterator alphabets()
```
    Get an iterator over all alphabets known.
    
    Returns:
    an Iterator over Alphabet objects
  - getGapSymbol
```
public static Symbol getGapSymbol()
```
    Get the special `gap' Symbol.
    
    The gap symbol is a Symbol that has an empty alphabet of matches. As such , ever alphabet contains gap, as there is no symbol that matches gap, so there is no case where an alphabet doesn't contain a symbol that matches gap.
    
    Gap can be thought of as an empty sub-space within the space of all possible symbols. If you are working in a cross-product alphabet, you should chose whether to use gap to represent 'no symbol', or a basis symbol of the appropriate size built entirely of gaps to represent 'no symbol in each of the slots'. Perhaps this could be explained better.
    
    Returns:
    the system-wide symbol that represents a gap
  - getGapSymbol
```
public static Symbol getGapSymbol(List alphas)
```
    Get the gap symbol appropriate to this list of alphabets.
    
    The gap symbol with have the same shape a the alphabet list. It will be as long as the list, and if any of the alphabets in the list have a dimension greater than 1, it will also insert the appropriate gap there.
    
    Parameters:
    alphas - List of alphabets
    
    Returns:
    the appropriate gap symbol for the alphabet list
  - createSymbol
```
public static AtomicSymbol createSymbol(String name,
                        Annotation annotation)
```
    Generate a new AtomicSymbol instance with a name and Annotation.
    
    Use this method if you wish to create an AtomicSymbol instance. Initially it will not be a member of any alphabet.
    
    Parameters:
    name - the String returned by getName()
    annotation - the Annotation returned by getAnnotation()
    
    Returns:
    a new AtomicSymbol instance
  - createSymbol
```
public static AtomicSymbol createSymbol(String name)
```
    Generate a new AtomicSymbol instance with a name and an Empty Annotation.
    
    Use this method if you wish to create an AtomicSymbol instance. Initially it will not be a member of any alphabet.
    
    Parameters:
    name - the String returned by getName()
    
    Returns:
    a new AtomicSymbol instance
  - createSymbol
```
public static AtomicSymbol createSymbol(char token,
                        String name,
                        Annotation annotation)
```
    Deprecated. Use the two-arg version of this method instead.
    
    Generate a new AtomicSymbol instance with a token, name and Annotation.
    
    Use this method if you wish to create an AtomicSymbol instance. Initially it will not be a member of any alphabet.
    
    Parameters:
    token - the Char token returned by getToken() (ignpred as of BioJava 1.2)
    name - the String returned by getName()
    annotation - the Annotation returned by getAnnotation()
    
    Returns:
    a new AtomicSymbol instance
  - createSymbol
```
public static Symbol createSymbol(char token,
                  Annotation annotation,
                  List symList,
                  Alphabet alpha)
                           throws IllegalSymbolException
```
    Deprecated. use the new version, without the token argument
    
    Generates a new Symbol instance that represents the tuple of Symbols in symList.
    
    This method is most useful for writing Alphabet implementations. It should not be invoked by casual users. Use alphabet.getSymbol(List) instead.
    
    Parameters:
    annotation - The annotation bundle for the symbol
    token - the Symbol's token [ignored since 1.2]
    symList - a list of Symbol objects
    alpha - the Alphabet that this Symbol will reside in
    
    Returns:
    a Symbol that encapsulates that List
    
    Throws:
    
    IllegalSymbolException - If the Symbol cannot be made
  - createSymbol
```
public static Symbol createSymbol(Annotation annotation,
                  List symList,
                  Alphabet alpha)
                           throws IllegalSymbolException
```
    Generates a new Symbol instance that represents the tuple of Symbols in symList. This will attempt to return the same symbol for the same list.
    
    This method is most useful for writing Alphabet implementations. It should not be invoked by casual users. Use alphabet.getSymbol(List) instead.
    
    Parameters:
    annotation - The annotation bundle for the Symbol
    symList - a list of Symbol objects
    alpha - the Alphabet that this Symbol will reside in
    
    Returns:
    a Symbol that encapsulates that List
    
    Throws:
    
    IllegalSymbolException - If the Symbol cannot be made
  - createSymbol
```
public static Symbol createSymbol(char token,
                  Annotation annotation,
                  Set symSet,
                  Alphabet alpha)
                           throws IllegalSymbolException
```
    Deprecated. use the three-arg version of this method instead.
    
    Generates a new Symbol instance that represents the tuple of Symbols in symList.
    
    This method is most useful for writing Alphabet implementations. It should not be invoked by users. Use alphabet.getSymbol(Set) instead.
    
    Parameters:
    token - the Symbol's token [ignored since 1.2]
    annotation - the Symbol's Annotation
    symSet - a Set of Symbol objects
    alpha - the Alphabet that this Symbol will reside in
    
    Returns:
    a Symbol that encapsulates that List
    
    Throws:
    
    IllegalSymbolException - If the Symbol cannot be made
  - createSymbol
```
public static Symbol createSymbol(Annotation annotation,
                  Set symSet,
                  Alphabet alpha)
                           throws IllegalSymbolException
```
    Generates a new Symbol instance that represents the tuple of Symbols in symList.
    
    This method is most useful for writing Alphabet implementations. It should not be invoked by users. Use alphabet.getSymbol(Set) instead.
    
    Parameters:
    annotation - the Symbol's Annotation
    symSet - a Set of Symbol objects
    alpha - the Alphabet that this Symbol will reside in
    
    Returns:
    a Symbol that encapsulates that List
    
    Throws:
    
    IllegalSymbolException - If the Symbol cannot be made
  - generateCrossProductAlphaFromName
```
public static Alphabet generateCrossProductAlphaFromName(String name)
```
    Generates a new CrossProductAlphabet from the give name.
    
    Parameters:
    name - the name to parse
    
    Returns:
    the associated Alphabet
  - getCrossProductAlphabet
```
public static Alphabet getCrossProductAlphabet(List aList)
```
    Retrieve a CrossProductAlphabet instance over the alphabets in aList.
    
    If all of the alphabets in aList implements FiniteAlphabet then the method will return a FiniteAlphabet. Otherwise, it returns a non-finite alphabet.
    
    If you call this method twice with a list containing the same alphabets, it will return the same alphabet. This promotes the re-use of alphabets and helps to maintain the 'flyweight' principal for finite alphabet symbols.
    
    The resulting alphabet cpa will be retrievable via AlphabetManager.alphabetForName(cpa.getName())
    
    Parameters:
    aList - a list of Alphabet objects
    
    Returns:
    a CrossProductAlphabet that is over the alphabets in aList
  - getCrossProductAlphabet
```
public static Alphabet getCrossProductAlphabet(List aList,
                               String name)
                                        throws IllegalAlphabetException
```
    Attempts to create a cross product alphabet and register it under a name.
    
    Parameters:
    aList - A list of alphabets
    name - The name which the new alphabet will be registered under.
    
    Returns:
    The CrossProductAlphabet
    
    Throws:
    
    IllegalAlphabetException - If the Alphabet cannot be made or a different alphabet is already registed under this name.
  - getCrossProductAlphabet
```
public static Alphabet getCrossProductAlphabet(List aList,
                               Alphabet parent)
```
    Retrieve a CrossProductAlphabet instance over the alphabets in aList.
    
    This method is most usefull for implementors of cross-product alphabets, allowing them to safely build the matches alphabets for ambiguity symbols.
    
    If all of the alphabets in aList implements FiniteAlphabet then the method will return a FiniteAlphabet. Otherwise, it returns a non-finite alphabet.
    
    If you call this method twice with a list containing the same alphabets, it will return the same alphabet. This promotes the re-use of alphabets and helps to maintain the 'flyweight' principal for finite alphabet symbols.
    
    The resulting alphabet cpa will be retrievable via AlphabetManager.alphabetForName(cpa.getName())
    
    Parameters:
    aList - a list of Alphabet objects
    parent - a parent alphabet
    
    Returns:
    a CrossProductAlphabet that is over the alphabets in aList
  - factorize
```
public static List factorize(Alphabet alpha,
             Set symSet)
                      throws IllegalSymbolException
```
    Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet. If the symbol can't be represented by a single list of BasisSymbol instances, return null.
    
    This method is most useful for implementers of Alphabet and Symbol. It probably should not be invoked by users.
    
    Parameters:
    symSet - the Set of AtomicSymbol instances
    alpha - the Alphabet instance that the Symbols are from
    
    Returns:
    a List of BasisSymbols
    
    Throws:
    
    IllegalSymbolException - In practice it should not. If it does it probably indicates a subtle bug somewhere in AlphabetManager
  - loadAlphabets
```
public static void loadAlphabets(InputSource is)
                          throws SAXException,
                                 IOException,
                                 BioException
```
    Load additional Alphabets, defined in XML format, into the AlphabetManager's registry. These can the be retrieved by calling alphabetForName.
    
    Parameters:
    is - an InputSource encapsulating the document to be parsed
    
    Throws:
    
    IOException - if there is an error accessing the stream
    
    SAXException - if there is an error while parsing the document
    
    BioException - if a problem occurs when creating the new Alphabets.
    Since:
    
    1.3
  - getAlphabetIndex
```
public static AlphabetIndex getAlphabetIndex(FiniteAlphabet alpha)
```
    Get an indexer for a specified alphabet.
    
    Parameters:
    alpha - The alphabet to index
    
    Returns:
    an AlphabetIndex instance
    Since:
    
    1.1
  - getAlphabetIndex
```
public static AlphabetIndex getAlphabetIndex(Symbol[] syms)
                                      throws IllegalSymbolException,
                                             BioException
```
    Get an indexer for an array of symbols.
    
    Parameters:
    syms - the Symbols to index in that order
    
    Returns:
    an AlphabetIndex instance
    
    Throws:
    
    IllegalSymbolException
    
    BioException
    Since:
    
    1.1

Class AlphabetManager

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AlphabetManager

Method Detail

instance

getAllAmbiguitySymbol

getAllSymbols

alphabetForName

symbolForName

symbolForLifeScienceID

registerAlphabet

registerAlphabet

registrations

registered

alphabets

getGapSymbol

getGapSymbol

createSymbol

createSymbol

createSymbol

createSymbol

createSymbol

createSymbol

createSymbol

generateCrossProductAlphaFromName

getCrossProductAlphabet

getCrossProductAlphabet

getCrossProductAlphabet

factorize

loadAlphabets

getAlphabetIndex

getAlphabetIndex