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java.lang.Objectorg.biojava.utils.regex.Search
public class Search
A utility class to make searching a Sequence with many regex patterns easier.
Nested Class Summary | |
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static interface |
Search.Listener
Interface for a class that will recieve match information from this class. |
Constructor Summary | |
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Search(FiniteAlphabet alfa)
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Method Summary | |
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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)
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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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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 Search(FiniteAlphabet alfa)
Method Detail |
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public void setListener(Search.Listener listener)
public void addPattern(String patternString, boolean overlap) throws RegexException, IllegalAlphabetException
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.
RegexException
- if the requested pattern is not valid
IllegalAlphabetException
- if the requested pattern is not validpublic void addPattern(String label, String patternString, boolean overlap) throws RegexException, IllegalAlphabetException
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.
RegexException
- if the requested pattern is not valid
IllegalAlphabetException
- if the requested pattern is not validpublic void clearPatterns()
public char charValue(Symbol sym) throws IllegalSymbolException
IllegalSymbolException
public void search(SymbolList seq)
public void search(SymbolList seq, int loLimit, int hiLimit)
loLimit
- low limit of search range.hiLimit
- high limit of search range.
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