Class IntegerAlphabet
- All Implemented Interfaces:
Serializable
,Annotatable
,Alphabet
,Changeable
An efficient implementation of an Alphabet over the infinite set of integer values.
This class can be used to represent lists of integer numbers as a SymbolList with the alphabet IntegerAlphabet. These lists can then be annotated with features, or fed into dynamic-programming algorithms, or processed as per any other SymbolList object.
Object identity should be used to decide if two IntegerSymbol objects are the same. IntegerAlphabet ensures that all IntegerSymbol instances are canonicalized.
- Author:
- Matthew Pocock, Mark Schreiber, Thomas Down
- See Also:
-
Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
A single int value.static class
A class to represent a finite contiguous subset of the infinite IntegerAlphabetNested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic IntegerAlphabet
The singleton instance of the IntegerAlphabet class.Fields inherited from interface org.biojava.bio.symbol.Alphabet
EMPTY_ALPHABET, PARSERS, SYMBOLS
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
-
Method Summary
Modifier and TypeMethodDescriptionboolean
Returns whether or not this Alphabet contains the symbol.static SymbolList
fromArray
(int[] iArray) Retrieve a SymbolList view of an array of integers.Return an ordered List of the alphabets which make up a compound alphabet.getAmbiguity
(Set symSet) Get a symbol that represents the set of symbols in syms.Should return the associated annotation object.Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.static IntegerAlphabet
Retrieve the single IntegerAlphabet instance.getName()
Get the name of the alphabet.getSubAlphabet
(int min, int max) Construct a finite contiguous subset of theIntegerAlphabet
.getSymbol
(int val) Retrieve the Symbol for an int.Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.getTokenization
(String name) Creates a new parser (Mark Schreiber 3 May 2001).void
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
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
-
Field Details
-
INSTANCE
The singleton instance of the IntegerAlphabet class.
-
-
Method Details
-
getSubAlphabet
public static IntegerAlphabet.SubIntegerAlphabet getSubAlphabet(int min, int max) throws IllegalArgumentException Construct a finite contiguous subset of theIntegerAlphabet
. Useful for making CrossProductAlphabets with otherFiniteAlphabet
s.- Parameters:
min
- the lower bound of the Alphabetmax
- the upper bound of the Alphabet- Returns:
- A FiniteAlphabet from min to max inclusive.
- Throws:
IllegalArgumentException
- if max invalid input: '<' min
-
fromArray
Retrieve a SymbolList view of an array of integers.The returned object is a view onto the underlying array, and does not copy it. Changes made to the original array will alter the symulting SymbolList.
- Parameters:
iArray
- the array of integers to view- Returns:
- a SymbolList over the IntegerAlphabet that represent the values in iArray
-
getInstance
Retrieve the single IntegerAlphabet instance.- Returns:
- the singleton IntegerAlphabet instance
-
getSymbol
Retrieve the Symbol for an int.- Parameters:
val
- the int to view- Returns:
- a IntegerSymbol embodying val
-
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 interfaceAlphabet
- Returns:
- the appropriate gap Symbol instance
-
getAnnotation
Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
-
getAlphabets
Description copied from interface:Alphabet
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.- Specified by:
getAlphabets
in interfaceAlphabet
- Returns:
- a List of alphabets
-
getSymbol
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 interfaceAlphabet
- Parameters:
symList
- A list of Symbol instances- Throws:
IllegalSymbolException
- if the members of rl are not Symbols over the alphabets returned fromgetAlphabets
-
getAmbiguity
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 interfaceAlphabet
- Parameters:
symSet
- 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
-
contains
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.
-
validate
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 interfaceAlphabet
- Parameters:
s
- the Symbol to validate- Throws:
IllegalSymbolException
- if r is not contained in this alphabet
-
getName
Description copied from interface:Alphabet
Get the name of the alphabet. -
getTokenization
Creates a new parser (Mark Schreiber 3 May 2001).- Specified by:
getTokenization
in interfaceAlphabet
- Parameters:
name
- Currently only "token" is supported. You may also use "default" as a synonym of "token"- Returns:
- an IntegerParser.
-