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java.lang.Objectorg.biojava.bio.seq.NucleotideTools
public final class NucleotideTools
Useful functionality for processing nucleotide sequences.
Method Summary | |
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static 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 |
complementTable()
Get a translation table for complementing Nucleotide symbols. |
static SymbolList |
createNucleotide(java.lang.String nucleotide)
Return a new Nucleotide SymbolList for nucleotide. |
static Sequence |
createNucleotideSequence(java.lang.String nucleotide,
java.lang.String name)
Return a new Nucleotide Sequence for nucleotide. |
static Symbol |
d()
|
static Symbol |
forIndex(int index)
Return the symbol for an index - compatible with index . |
static Symbol |
forSymbol(char token)
Retrieve the symbol for a symbol. |
static AtomicSymbol |
g()
|
static FiniteAlphabet |
getNucleotide()
Return the Nucleotide alphabet. |
static Symbol |
h()
|
static int |
index(Symbol sym)
Return an integer index for a symbol - compatible with forIndex . |
static Symbol |
k()
|
static Symbol |
m()
|
static Symbol |
n()
|
static char |
nucleotideToken(Symbol sym)
Get a single-character token for a Nucleotide symbol |
static 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()
|
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static AtomicSymbol a()
public static AtomicSymbol g()
public static AtomicSymbol c()
public static AtomicSymbol t()
public static AtomicSymbol u()
public static Symbol r()
public static Symbol y()
public static Symbol m()
public static Symbol k()
public static Symbol s()
public static Symbol w()
public static Symbol b()
public static Symbol d()
public static Symbol h()
public static Symbol v()
public static Symbol n()
public static FiniteAlphabet getNucleotide()
public static SymbolList createNucleotide(java.lang.String nucleotide) throws IllegalSymbolException
nucleotide
- a String to parse into Nucleotide
IllegalSymbolException
- if nucleotide contains
any non-Nucleotide characterspublic static Sequence createNucleotideSequence(java.lang.String nucleotide, java.lang.String name) throws IllegalSymbolException
nucleotide
- a String to parse into Nucleotidename
- a String to use as the name
IllegalSymbolException
- if nucleotide contains
any non-Nucleotide characterspublic static int index(Symbol sym) throws IllegalSymbolException
forIndex
.
The index for a symbol is stable accross virtual machines & invocations.
sym
- the Symbol to index
IllegalSymbolException
- if sym is not a member of the Nucleotide
alphabetpublic static Symbol forIndex(int index) throws java.lang.IndexOutOfBoundsException
index
.
The index for a symbol is stable accross virtual machines & invocations.
index
- the index to look up
java.lang.IndexOutOfBoundsException
- if index is not between 0 and 3public static Symbol complement(Symbol sym) throws IllegalSymbolException
sym
- the symbol to complement
IllegalSymbolException
- if sym is not a member of the Nucleotide alphabetpublic static Symbol forSymbol(char token) throws IllegalSymbolException
token
- the char to look up
IllegalSymbolException
- if the char does not belong to {a, g, c, t, u}public static SymbolList complement(SymbolList list) throws IllegalAlphabetException
list
- the SymbolList to complement
IllegalAlphabetException
- if list is not a complementable alphabetpublic static SymbolList reverseComplement(SymbolList list) throws IllegalAlphabetException
list
- the SymbolList to complement
IllegalAlphabetException
- if list is not a complementable alphabetpublic static ReversibleTranslationTable complementTable()
public static char nucleotideToken(Symbol sym) throws IllegalSymbolException
IllegalSymbolException
- if sym
is not a member of the Nucleotide alphabet
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