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java.lang.Objectorg.biojava.bio.symbol.MotifTools
public class MotifTools
MotifTools
contains utility methods for sequence
motifs.
Constructor Summary | |
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MotifTools()
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Method Summary | |
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static java.lang.String |
createRegex(SymbolList motif)
createRegex creates a regular expression which
matches the SymbolList . |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MotifTools()
Method Detail |
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public static java.lang.String createRegex(SymbolList motif)
createRegex
creates a regular expression which
matches the SymbolList
. Ambiguous
Symbol
s are simply transformed into character
classes. For example the nucleotide sequence "AAGCTT" becomes
"A{2}GCT{2}" and "CTNNG" is expanded to
"CT[ABCDGHKMNRSTVWY]{2}G". The character class is generated
using the getMatches
method of an ambiguity symbol
to obtain the alphabet of AtomicSymbol
s it
matches, followed by calling getAllSymbols
on this
alphabet, removal of any gap symbols and then tokenization of
the remainder. The ordering of the tokens in a character class
is by ascending numerical order of their tokens as determined
by Arrays.sort(char [])
.
The Alphabet
of the SymbolList
must be finite and must have a character token type. Regular
expressions may be generated for any such
SymbolList
, not just DNA, RNA and protein.
motif
- a SymbolList
.
String
regular expression.
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