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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--org.biojava.bio.seq.DNATools
Usefull functionality for processing DNA sequences.
Constructor Summary | |
DNATools()
|
Method Summary | |
static Symbol |
a()
|
static Symbol |
c()
|
static Symbol |
complement(Symbol sym)
Complement the symbol. |
static SymbolList |
complement(SymbolList list)
Retrieve a complement view of list. |
static SymbolList |
createDNA(java.lang.String dna)
Return a new DNA SymbolList for dna. |
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 Symbol |
g()
|
static FiniteAlphabet |
getDNA()
Return the DNA alphabet. |
static int |
index(Symbol res)
Return an integer index for a symbol - compatible with forIndex. |
static SymbolList |
reverseComplement(SymbolList list)
Retrieve a reverse-complement view of list. |
static Symbol |
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 Symbol a()
public static Symbol g()
public static Symbol c()
public static Symbol t()
public static FiniteAlphabet getDNA()
public static SymbolList createDNA(java.lang.String dna) throws IllegalSymbolException
dna
- a String to parse into DNApublic static int index(Symbol res) throws IllegalSymbolException
The index for a symbol is stable accross virtual machines & invokations.
res
- the Symbol to indexpublic static Symbol forIndex(int index) throws java.lang.IndexOutOfBoundsException
The index for a symbol is stable accross virtual machines & invokations.
index
- the index to look uppublic static Symbol complement(Symbol sym) throws IllegalSymbolException
sym
- the symbol to complementpublic static Symbol forSymbol(char token) throws IllegalSymbolException
token
- the char to look uppublic static SymbolList complement(SymbolList list) throws IllegalAlphabetException
list
- the ResidueList to complementpublic static SymbolList reverseComplement(SymbolList list) throws IllegalAlphabetException
list
- the ResidueList to complement
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