Package 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. TODO: upgrade to the latest Lucene API and copy some changes from cPath2 project.

Author:

rodche

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	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	Description
static final String[]	DEFAULT_FIELDS
static final int	DEFAULT_MAX_HITS_PER_PAGE
static final String	FIELD_DATASOURCE
static final String	FIELD_KEYWORD
static final String	FIELD_N
static final String	FIELD_N_PARTICIPANTS
static final String	FIELD_N_PROCESSES
static final String	FIELD_NAME
static final String	FIELD_ORGANISM
static final String	FIELD_PATHWAY
static final String	FIELD_TYPE
static final String	FIELD_URI
static final String	FIELD_XREFID

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	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 Details

FIELD_URI

public static final String FIELD_URI

See Also:

• Constant Field Values

FIELD_KEYWORD

public static final String FIELD_KEYWORD

See Also:

• Constant Field Values

FIELD_NAME

public static final String FIELD_NAME

See Also:

• Constant Field Values

FIELD_XREFID

public static final String FIELD_XREFID

See Also:

• Constant Field Values

FIELD_PATHWAY

public static final String FIELD_PATHWAY

See Also:

• Constant Field Values

FIELD_N_PARTICIPANTS

public static final String FIELD_N_PARTICIPANTS

See Also:

• Constant Field Values

FIELD_N_PROCESSES

public static final String FIELD_N_PROCESSES

See Also:

• Constant Field Values

FIELD_N

public static final String FIELD_N

See Also:

• Constant Field Values

FIELD_ORGANISM

public static final String FIELD_ORGANISM

See Also:

• Constant Field Values

FIELD_DATASOURCE

public static final String FIELD_DATASOURCE

See Also:

• 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 Details

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 Details

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