Package de.julielab.gene.candidateretrieval

Class GeneRecordQueryGenerator

java.lang.Object

de.julielab.geneexpbase.candidateretrieval.QueryGenerator

de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

All Implemented Interfaces:

Serializable

public class GeneRecordQueryGenerator
extends de.julielab.geneexpbase.candidateretrieval.QueryGenerator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static String[]	ALL_FIELDS
static List<String>	ALL_FIELDS_LIST
static String[]	SYNONYM_FIELDS
static String[]	SYNONYM_FIELDS_NOT_CHROMOSOMAL

Constructor Summary

Constructors

Constructor	Description
GeneRecordQueryGenerator()
GeneRecordQueryGenerator(boolean useDisMax)
GeneRecordQueryGenerator(boolean useDisMax, boolean flatDisjunction)
GeneRecordQueryGenerator(boolean useDisMax, boolean flatDisjunction, boolean searchExactMatches, boolean useSynonymMatchesAsRelevanceSignal)
GeneRecordQueryGenerator(boolean useDisMax, boolean flatDisjunction, boolean searchExactMatches, boolean useSynonymMatchesAsRelevanceSignal, boolean useNpContextAsRelevanceSignal)
GeneRecordQueryGenerator(boolean useDisMax, boolean flatDisjunction, boolean searchExactMatches, boolean useSynonymMatchesAsRelevanceSignal, boolean useNpContextAsRelevanceSignal, boolean useAlternativeNamesAsRelevanceSignal, boolean useAppositionsAsRelevanceSignal)
GeneRecordQueryGenerator(boolean useDisMax, boolean flatDisjunction, boolean searchExactMatches, boolean useSynonymMatchesAsRelevanceSignal, boolean useNpContextAsRelevanceSignal, boolean useAlternativeNamesAsRelevanceSignal, boolean useAppositionsAsRelevanceSignal, boolean useContextGenesAsRelevanceSignal)
GeneRecordQueryGenerator(boolean useDisMax, boolean flatDisjunction, boolean searchExactMatches, boolean useSynonymMatchesAsRelevanceSignal, boolean useNpContextAsRelevanceSignal, boolean useAlternativeNamesAsRelevanceSignal, boolean useAppositionsAsRelevanceSignal, boolean useContextGenesAsRelevanceSignal, int relaxation)
GeneRecordQueryGenerator(boolean useDisMax, boolean flatDisjunction, boolean searchExactMatches, boolean useSynonymMatchesAsRelevanceSignal, boolean useNpContextAsRelevanceSignal, boolean useAlternativeNamesAsRelevanceSignal, boolean useAppositionsAsRelevanceSignal, int relaxation)

Method Summary

Modifier and Type	Method	Description
org.apache.lucene.search.Query	generateQuery(de.julielab.geneexpbase.candidateretrieval.CandidateCacheKey key)
String	getName()
boolean	isUseContextGenesAsRelevanceSignal()

Methods inherited from class de.julielab.geneexpbase.candidateretrieval.QueryGenerator

equals, hashCode

Methods inherited from class java.lang.Object

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

Field Detail

ALL_FIELDS

public static final String[] ALL_FIELDS

SYNONYM_FIELDS

public static final String[] SYNONYM_FIELDS

SYNONYM_FIELDS_NOT_CHROMOSOMAL

public static final String[] SYNONYM_FIELDS_NOT_CHROMOSOMAL

ALL_FIELDS_LIST

public static final List<String> ALL_FIELDS_LIST

Constructor Detail

GeneRecordQueryGenerator

public GeneRecordQueryGenerator()

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax)

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax,
                                boolean flatDisjunction)

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax,
                                boolean flatDisjunction,
                                boolean searchExactMatches,
                                boolean useSynonymMatchesAsRelevanceSignal)

Parameters:

useDisMax - Whether to use dis max queries instead of disjunctions in a CNF. Only used when flatDisjunction is false. Defaults to false.

flatDisjunction - If true, create one large disjunction of all tokens on all fields (instead of disjunctions for each token on every field and those in conjunction, CNF). False by default.

searchExactMatches - Whether to match the whole gene name on the fields containing the complete strings, non-tokenized. True by default.

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax,
                                boolean flatDisjunction,
                                boolean searchExactMatches,
                                boolean useSynonymMatchesAsRelevanceSignal,
                                boolean useNpContextAsRelevanceSignal)

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax,
                                boolean flatDisjunction,
                                boolean searchExactMatches,
                                boolean useSynonymMatchesAsRelevanceSignal,
                                boolean useNpContextAsRelevanceSignal,
                                boolean useAlternativeNamesAsRelevanceSignal,
                                boolean useAppositionsAsRelevanceSignal)

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax,
                                boolean flatDisjunction,
                                boolean searchExactMatches,
                                boolean useSynonymMatchesAsRelevanceSignal,
                                boolean useNpContextAsRelevanceSignal,
                                boolean useAlternativeNamesAsRelevanceSignal,
                                boolean useAppositionsAsRelevanceSignal,
                                int relaxation)

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax,
                                boolean flatDisjunction,
                                boolean searchExactMatches,
                                boolean useSynonymMatchesAsRelevanceSignal,
                                boolean useNpContextAsRelevanceSignal,
                                boolean useAlternativeNamesAsRelevanceSignal,
                                boolean useAppositionsAsRelevanceSignal,
                                boolean useContextGenesAsRelevanceSignal)

GeneRecordQueryGenerator

public GeneRecordQueryGenerator(boolean useDisMax,
                                boolean flatDisjunction,
                                boolean searchExactMatches,
                                boolean useSynonymMatchesAsRelevanceSignal,
                                boolean useNpContextAsRelevanceSignal,
                                boolean useAlternativeNamesAsRelevanceSignal,
                                boolean useAppositionsAsRelevanceSignal,
                                boolean useContextGenesAsRelevanceSignal,
                                int relaxation)

Method Detail

generateQuery

public org.apache.lucene.search.Query generateQuery(de.julielab.geneexpbase.candidateretrieval.CandidateCacheKey key)
                                             throws org.apache.lucene.search.BooleanQuery.TooManyClauses

Specified by:

generateQuery in class de.julielab.geneexpbase.candidateretrieval.QueryGenerator

Throws:

org.apache.lucene.search.BooleanQuery.TooManyClauses

getName

public String getName()

Specified by:

getName in class de.julielab.geneexpbase.candidateretrieval.QueryGenerator

isUseContextGenesAsRelevanceSignal

public boolean isUseContextGenesAsRelevanceSignal()