Package org.biojava.utils.regex
Class Search
java.lang.Object
org.biojava.utils.regex.Search
A utility class to make searching a Sequence with many regex patterns
easier.
- Since:
- 1.4
- Author:
- David Huen
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic interface
Interface for a class that will recieve match information from this class. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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
void
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 Details
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Search
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Method Details
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setListener
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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
remove all patterns from the pattern cache. -
charValue
- Throws:
IllegalSymbolException
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search
search the Sequence with the patterns already registered with this object. -
search
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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