Package org.biojava.utils.regex
Class Search
- java.lang.Object
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- org.biojava.utils.regex.Search
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Nested Class Summary
Nested Classes Modifier and Type Class Description static interface
Search.Listener
Interface for a class that will recieve match information from this class.
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Constructor Summary
Constructors Constructor Description Search(FiniteAlphabet alfa)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addPattern(String patternString, boolean overlap)
add a search pattern to the searches to be conducted by this object.void
addPattern(String label, String patternString, boolean overlap)
add a search pattern to the searches to be conducted by this object.char
charValue(Symbol sym)
void
clearPatterns()
remove all patterns from the pattern cache.void
search(SymbolList seq)
search the Sequence with the patterns already registered with this object.void
search(SymbolList seq, int loLimit, int hiLimit)
search part of the SymbolList with the patterns already registered with this object.void
setListener(Search.Listener listener)
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Constructor Detail
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Search
public Search(FiniteAlphabet alfa)
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Method Detail
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setListener
public void setListener(Search.Listener listener)
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addPattern
public void addPattern(String patternString, boolean overlap) throws RegexException, IllegalAlphabetException
add a search pattern to the searches to be conducted by this object.- Parameters:
patternString
- String representation of the pattern.overlap
- if true, the search continues at the base following the start to the previous hit. If false, it continues at the base after the existing hit.- Throws:
RegexException
- if the requested pattern is not validIllegalAlphabetException
- if the requested pattern is not valid
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addPattern
public void addPattern(String label, String patternString, boolean overlap) throws RegexException, IllegalAlphabetException
add a search pattern to the searches to be conducted by this object.- Parameters:
patternString
- String representation of the pattern.overlap
- if true, the search continues at the base following the start to the previous hit. If false, it continues at the base after the existing hit.- Throws:
RegexException
- if the requested pattern is not validIllegalAlphabetException
- if the requested pattern is not valid
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clearPatterns
public void clearPatterns()
remove all patterns from the pattern cache.
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charValue
public char charValue(Symbol sym) throws IllegalSymbolException
- Throws:
IllegalSymbolException
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search
public void search(SymbolList seq)
search the Sequence with the patterns already registered with this object.
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search
public void search(SymbolList seq, int loLimit, int hiLimit)
search part of the SymbolList with the patterns already registered with this object.- Parameters:
loLimit
- low limit of search range.hiLimit
- high limit of search range.
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