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java.lang.Objectorg.biojava.bio.seq.DNATools
Useful functionality for processing DNA sequences.
Constructor Summary | |
DNATools()
|
Method Summary | |
static AtomicSymbol |
a()
|
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 DNA symbols. |
static SymbolList |
createDNA(java.lang.String dna)
Return a new DNA SymbolList for dna. |
static Sequence |
createDNASequence(java.lang.String dna,
java.lang.String name)
Return a new DNA Sequence for dna. |
static GappedSequence |
createGappedDNASequence(java.lang.String dna,
java.lang.String name)
Get a new dna as a GappedSequence |
static char |
dnaToken(Symbol sym)
Get a single-character token for a DNA symbol |
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 |
getCodonAlphabet()
Gets the (DNA x DNA x DNA) Alphabet |
static FiniteAlphabet |
getDNA()
Return the DNA alphabet. |
static int |
index(Symbol sym)
Return an integer index for a symbol - compatible with forIndex . |
static Symbol |
n()
|
static SymbolList |
reverseComplement(SymbolList list)
Retrieve a reverse-complement view of list. |
static AtomicSymbol |
t()
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public DNATools()
Method Detail |
public static AtomicSymbol a()
public static AtomicSymbol g()
public static AtomicSymbol c()
public static AtomicSymbol t()
public static Symbol n()
public static FiniteAlphabet getDNA()
public static FiniteAlphabet getCodonAlphabet()
public static SymbolList createDNA(java.lang.String dna) throws IllegalSymbolException
dna
- a String to parse into DNA
IllegalSymbolException
- if dna contains
any non-DNA characterspublic static Sequence createDNASequence(java.lang.String dna, java.lang.String name) throws IllegalSymbolException
dna
- a String to parse into DNAname
- a String to use as the name
IllegalSymbolException
- if dna contains
any non-DNA characterspublic static GappedSequence createGappedDNASequence(java.lang.String dna, java.lang.String name) throws IllegalSymbolException
IllegalSymbolException
public 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 DNA
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 DNA alphabetpublic static Symbol forSymbol(char token) throws IllegalSymbolException
token
- the char to look up
IllegalSymbolException
- if the char is not a valid IUB dna codepublic 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 dnaToken(Symbol sym) throws IllegalSymbolException
IllegalSymbolException
- if sym
is not a member of the DNA alphabet
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