Search (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.utils.regex.Search

```
public class Search
extends Object
```
A utility class to make searching a Sequence with many regex patterns easier.

Since:

1.4

Author:

David Huen

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.

Nested Classes
Modifier and Type	Class	Description
`static interface`	`Search.Listener`	Interface for a class that will recieve match information from this class.

Constructor Summary

Constructors
Constructor Description

Search(FiniteAlphabet alfa)

Constructors
Constructor	Description
`Search(FiniteAlphabet alfa)`

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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - Search
```
public Search(FiniteAlphabet alfa)
```
- Method Detail
  - setListener
```
public void setListener(Search.Listener listener)
```
  - 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 valid
    
    IllegalAlphabetException - if the requested pattern is not valid
  - 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 valid
    
    IllegalAlphabetException - if the requested pattern is not valid
  - clearPatterns
```
public void clearPatterns()
```
    remove all patterns from the pattern cache.
  - charValue
```
public char charValue(Symbol sym)
               throws IllegalSymbolException
```
    Throws:
    
    IllegalSymbolException
  - search
```
public void search(SymbolList seq)
```
    search the Sequence with the patterns already registered with this object.
  - 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.

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Search

Method Detail

setListener

addPattern

addPattern

clearPatterns

charValue

search

search