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java.lang.Objectorg.biojava.utils.Unchangeable
org.biojava.bio.symbol.DoubleAlphabet
public final class DoubleAlphabet
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.
Nested Class Summary | |
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static class |
DoubleAlphabet.DoubleRange
A range of double values. |
static class |
DoubleAlphabet.DoubleSymbol
A single double value. |
static class |
DoubleAlphabet.SubDoubleAlphabet
A class to represent a contiguous range of double symbols. |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary | |
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static DoubleAlphabet |
INSTANCE
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Fields inherited from interface org.biojava.bio.symbol.Alphabet |
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EMPTY_ALPHABET, PARSERS, SYMBOLS |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Method Summary | |
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boolean |
contains(Symbol s)
Returns whether or not this Alphabet contains the symbol. |
static SymbolList |
fromArray(double[] dArray)
Retrieve a SymbolList view of an array of doubles. |
List |
getAlphabets()
Return an ordered List of the alphabets which make up a compound alphabet. |
Symbol |
getAmbiguity(Set syms)
Get a symbol that represents the set of symbols in syms. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
Symbol |
getGapSymbol()
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet. |
static DoubleAlphabet |
getInstance()
Retrieve the single DoubleAlphabet instance. |
String |
getName()
Get the name of the alphabet. |
static DoubleAlphabet.SubDoubleAlphabet |
getSubAlphabet(double min,
double max)
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DoubleAlphabet.DoubleSymbol |
getSymbol(double val)
Retrieve the Symbol for a double. |
DoubleAlphabet.DoubleRange |
getSymbol(double minVal,
double maxVal)
Retrieve the symbol for a range of doubles. |
Symbol |
getSymbol(List symList)
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols. |
SymbolTokenization |
getTokenization(String name)
Get a SymbolTokenization by name. |
void |
validate(Symbol s)
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. |
Methods inherited from class org.biojava.utils.Unchangeable |
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addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
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public static DoubleAlphabet INSTANCE
Method Detail |
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public static SymbolList fromArray(double[] dArray)
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.
dArray
- the array of doubles to view
public static DoubleAlphabet getInstance()
public DoubleAlphabet.DoubleSymbol getSymbol(double val)
val
- the double to view
public DoubleAlphabet.DoubleRange getSymbol(double minVal, double maxVal)
minVal
- the minimum valuemaxVal
- that maximum value
public static DoubleAlphabet.SubDoubleAlphabet getSubAlphabet(double min, double max)
public Annotation getAnnotation()
Annotatable
getAnnotation
in interface Annotatable
public boolean contains(Symbol s)
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.
contains
in interface Alphabet
s
- the Symbol to check
public void validate(Symbol s) throws IllegalSymbolException
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.
validate
in interface Alphabet
s
- the Symbol to validate
IllegalSymbolException
- if r is not contained in this alphabetpublic List getAlphabets()
Alphabet
getAlphabets
in interface Alphabet
public Symbol getGapSymbol()
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.
getGapSymbol
in interface Alphabet
public Symbol getAmbiguity(Set syms) throws IllegalSymbolException
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.
getAmbiguity
in interface Alphabet
syms
- the Set of Symbols that will be found in getMatches of the
returned symbol
IllegalSymbolException
public Symbol getSymbol(List symList) throws IllegalSymbolException
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.
getSymbol
in interface Alphabet
symList
- A list of Symbol instances
IllegalSymbolException
- if the members of rl are
not Symbols over the alphabets returned from
getAlphabets
public String getName()
Alphabet
getName
in interface Alphabet
public SymbolTokenization getTokenization(String name)
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 behaviour 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.
getTokenization
in interface Alphabet
name
- the name of the parser
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