org.biopax.paxtools.search

Class SearchEngine

java.lang.Object

org.biopax.paxtools.search.SearchEngine

All Implemented Interfaces:

Indexer, Searcher

public class SearchEngine
extends Object
implements Indexer, Searcher

A full-text searcher/indexer for BioPAX L3 models.

Author:

rodche

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SearchEngine.HitAnnotation A Key for the value in a BioPAX element's annotations map where additional information about corresponding search hit will be stored.

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	DEFAULT_FIELDS
static int	DEFAULT_MAX_HITS_PER_PAGE
static String	FIELD_DATASOURCE
static String	FIELD_KEYWORD
static String	FIELD_NAME
static String	FIELD_ORGANISM
static String	FIELD_PATHWAY
static String	FIELD_SIZE
static String	FIELD_TYPE
static String	FIELD_URI
static String	FIELD_XREFDB
static String	FIELD_XREFID

Constructor Summary

Constructors

Constructor and Description
SearchEngine(Model model, String indexLocation) Main Constructor.

Method Summary

Modifier and Type	Method and Description
int	getMaxHitsPerPage() Gets the maximum no.
void	index()
SearchResult	search(String query, int page, Class<? extends BioPAXElement> filterByType, String[] datasources, String[] organisms) Full-text search for BioPAX elements.
void	setMaxHitsPerPage(int maxHitsPerPage) Sets the maximum no.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FIELD_URI

public static final String FIELD_URI

See Also:

Constant Field Values

FIELD_KEYWORD

public static final String FIELD_KEYWORD

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Constant Field Values

FIELD_NAME

public static final String FIELD_NAME

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Constant Field Values

FIELD_XREFDB

public static final String FIELD_XREFDB

See Also:

Constant Field Values

FIELD_XREFID

public static final String FIELD_XREFID

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Constant Field Values

FIELD_PATHWAY

public static final String FIELD_PATHWAY

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Constant Field Values

FIELD_SIZE

public static final String FIELD_SIZE

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Constant Field Values

FIELD_ORGANISM

public static final String FIELD_ORGANISM

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Constant Field Values

FIELD_DATASOURCE

public static final String FIELD_DATASOURCE

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Constant Field Values

FIELD_TYPE

public static final String FIELD_TYPE

See Also:

Constant Field Values

DEFAULT_FIELDS

public static final String[] DEFAULT_FIELDS

DEFAULT_MAX_HITS_PER_PAGE

public static final int DEFAULT_MAX_HITS_PER_PAGE

See Also:

Constant Field Values

Constructor Detail

SearchEngine

public SearchEngine(Model model,
                    String indexLocation)

Main Constructor.

Parameters:

model - BioPAX object model to be indexed or searched.

indexLocation - full path to the index directory

Method Detail

setMaxHitsPerPage

public void setMaxHitsPerPage(int maxHitsPerPage)

Sets the maximum no. hits per search results page (pagination).

Parameters:

maxHitsPerPage - positive int value; otherwise - unlimited

getMaxHitsPerPage

public int getMaxHitsPerPage()

Gets the maximum no. hits per search results page (pagination parameter).

Returns:

int value

search

public SearchResult search(String query,
                           int page,
                           Class<? extends BioPAXElement> filterByType,
                           String[] datasources,
                           String[] organisms)

Description copied from interface: Searcher

Full-text search for BioPAX elements.

Specified by:

search in interface Searcher

Parameters:

query - String (keywords or Lucene query string)

page - hits page number (when the number of hits exceeds a threshold)

filterByType - - class filter

datasources - - filter by datasource

organisms - - filter by organism

Returns:

a bean that contains the list of BioPAX objects (hits) and annotations.

index

public void index()

Specified by:

index in interface Indexer