Class DoubleAlphabet
- All Implemented Interfaces:
Serializable
,Annotatable
,Alphabet
,Changeable
An efficient implementation of an Alphabet over the infinite set of double values.
This class can be used to represent lists of floating-point numbers as a SymbolList with the alphabet DoubleAlphabet. 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 DoubleResidue objects are the same. DoubleAlphabet ensures that all DoubleAlphabet instances are canonicalized.
- Author:
- Matthew Pocock, Thomas Down
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
A range of double values.static class
A single double value.static class
A class to represent a contiguous range of double symbols.Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
FieldsFields inherited from interface org.biojava.bio.symbol.Alphabet
EMPTY_ALPHABET, PARSERS, SYMBOLS
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Method Summary
Modifier and TypeMethodDescriptionboolean
Returns whether or not this Alphabet contains the symbol.static SymbolList
fromArray
(double[] dArray) Retrieve a SymbolList view of an array of doubles.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.Should return the associated annotation object.Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.static DoubleAlphabet
Retrieve the single DoubleAlphabet instance.getName()
Get the name of the alphabet.getSubAlphabet
(double min, double max) getSymbol
(double val) Retrieve the Symbol for a double.getSymbol
(double minVal, double maxVal) Retrieve the symbol for a range of doubles.Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.getTokenization
(String name) Get a SymbolTokenization by name.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
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Field Details
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INSTANCE
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Method Details
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fromArray
Retrieve a SymbolList view of an array of doubles.
The returned object is a view onto the underlying array, and does not copy it. Changes made to the original array will alter the resulting SymbolList.
- Parameters:
dArray
- the array of doubles to view- Returns:
- a SymbolList over the DoubleAlphabet that represent the values in dArray
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getInstance
Retrieve the single DoubleAlphabet instance.- Returns:
- the singleton DoubleAlphabet instance
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getSymbol
Retrieve the Symbol for a double.- Parameters:
val
- the double to view- Returns:
- a DoubleSymbol embodying val
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getSymbol
Retrieve the symbol for a range of doubles.- Parameters:
minVal
- the minimum valuemaxVal
- that maximum value- Returns:
- a DoubleRange containing all doubles between min and max value.
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getSubAlphabet
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getAnnotation
Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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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.
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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
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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
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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
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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:
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
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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
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getName
Description copied from interface:Alphabet
Get the name of the alphabet. -
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 interfaceAlphabet
- Parameters:
name
- the name of the parser- Returns:
- a parser for that name
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