Package org.biojava.bio.seq
Class NucleotideTools
java.lang.Object
org.biojava.bio.seq.NucleotideTools
Useful functionality for processing nucleotide sequences.
- Author:
- Matthew Pocock, Keith James (docs)
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Method Summary
Modifier and TypeMethodDescriptionstatic AtomicSymbol
a()
static Symbol
b()
static AtomicSymbol
c()
static Symbol
complement
(Symbol sym) Complement the symbol.static SymbolList
complement
(SymbolList list) Retrieve a complement view of list.static ReversibleTranslationTable
Get a translation table for complementing Nucleotide symbols.static SymbolList
createNucleotide
(String nucleotide) Return a new Nucleotide SymbolList for nucleotide.static Sequence
createNucleotideSequence
(String nucleotide, String name) Return a new Nucleotide Sequence for nucleotide.static Symbol
d()
static Symbol
forIndex
(int index) Return the symbol for an index - compatible withindex
.static Symbol
forSymbol
(char token) Retrieve the symbol for a symbol.static AtomicSymbol
g()
static FiniteAlphabet
Return the Nucleotide alphabet.static Symbol
h()
static int
Return an integer index for a symbol - compatible withforIndex
.static Symbol
k()
static Symbol
m()
static Symbol
n()
static char
nucleotideToken
(Symbol sym) Get a single-character token for a Nucleotide symbolstatic Symbol
r()
static SymbolList
reverseComplement
(SymbolList list) Retrieve a reverse-complement view of list.static Symbol
s()
static AtomicSymbol
t()
static AtomicSymbol
u()
static Symbol
v()
static Symbol
w()
static Symbol
y()
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Method Details
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a
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g
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c
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t
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u
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r
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y
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m
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k
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s
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w
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b
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d
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h
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v
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n
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getNucleotide
Return the Nucleotide alphabet.- Returns:
- a flyweight version of the Nucleotide alphabet
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createNucleotide
Return a new Nucleotide SymbolList for nucleotide.- Parameters:
nucleotide
- a String to parse into Nucleotide- Returns:
- a SymbolList created form nucleotide
- Throws:
IllegalSymbolException
- if nucleotide contains any non-Nucleotide characters
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createNucleotideSequence
public static Sequence createNucleotideSequence(String nucleotide, String name) throws IllegalSymbolException Return a new Nucleotide Sequence for nucleotide.- Parameters:
nucleotide
- a String to parse into Nucleotidename
- a String to use as the name- Returns:
- a Sequence created form nucleotide
- Throws:
IllegalSymbolException
- if nucleotide contains any non-Nucleotide characters
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index
Return an integer index for a symbol - compatible withforIndex
.The index for a symbol is stable accross virtual machines invalid input: '&' invocations.
- Parameters:
sym
- the Symbol to index- Returns:
- the index for that symbol
- Throws:
IllegalSymbolException
- if sym is not a member of the Nucleotide alphabet
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forIndex
Return the symbol for an index - compatible withindex
.The index for a symbol is stable accross virtual machines invalid input: '&' invocations.
- Parameters:
index
- the index to look up- Returns:
- the symbol at that index
- Throws:
IndexOutOfBoundsException
- if index is not between 0 and 3
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complement
Complement the symbol.- Parameters:
sym
- the symbol to complement- Returns:
- a Symbol that is the complement of sym
- Throws:
IllegalSymbolException
- if sym is not a member of the Nucleotide alphabet
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forSymbol
Retrieve the symbol for a symbol.- Parameters:
token
- the char to look up- Returns:
- the symbol for that char
- Throws:
IllegalSymbolException
- if the char does not belong to {a, g, c, t, u}
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complement
Retrieve a complement view of list.- Parameters:
list
- the SymbolList to complement- Returns:
- a SymbolList that is the complement
- Throws:
IllegalAlphabetException
- if list is not a complementable alphabet
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reverseComplement
Retrieve a reverse-complement view of list.- Parameters:
list
- the SymbolList to complement- Returns:
- a SymbolList that is the complement
- Throws:
IllegalAlphabetException
- if list is not a complementable alphabet
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complementTable
Get a translation table for complementing Nucleotide symbols.- Since:
- 1.1
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nucleotideToken
Get a single-character token for a Nucleotide symbol- Throws:
IllegalSymbolException
- ifsym
is not a member of the Nucleotide alphabet
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