Constant Field Values

Contents

• de.julielab.*

de.julielab.*

de.julielab.jules.ae.genemapping.CandidateFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	SUB_GREEK	"(beta|gamma|delta|epsilon|zeta|eta|theta|iota|kappa|lambda|mu|nu|xi|omicron|pi|rho|sigma|tau|upsilon|phi|chi|psi|omega)"

de.julielab.jules.ae.genemapping.GeneMapping

Modifier and Type	Constant Field	Value
public static final int	JAROWINKLER_SCORER	3
public static final boolean	LEGACY_INDEX_SUPPORT	true
public static final int	LEVENSHTEIN_SCORER	4
public static final int	LUCENE_SCORER	10
public static final java.lang.String	MAPPING_CORE	"mapping_core"
public static final int	MAXENT_SCORER	2
public static final int	SIMPLE_SCORER	0
public static final java.lang.String	SOURCE_DEFINITION	"UniProt ID (any organism)"
public static final int	TFIDF	5
public static final int	TOKEN_JAROWINKLER_SCORER	1

de.julielab.jules.ae.genemapping.GeneMappingAnnotator

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONTEXT_WINDOW_SIZE	"ContextWindowSize"
public static final java.lang.String	ENTITY_MAPPING_TYPES	"EntityMappingTypes"
public static final java.lang.String	MAPPER_CONFIG_FILE	"MapperConfigFile"
public static final java.lang.String	TOKEN_CONTEXT	"TokenContext"

de.julielab.jules.ae.genemapping.GeneMappingConfiguration

Modifier and Type	Constant Field	Value
public static final java.lang.String	APPROX_SCORER_TYPE	"approx_scorer_type"
public static final java.lang.String	CONTEXT_INDEX	"semantic_index"
public static final java.lang.String	CONTEXT_ITEMS_INDEX	"context_items_index"
public static final java.lang.String	DEFAULT_SPECIES	"default_species"
public static final java.lang.String	EXACT_SCORER_TYPE	"exact_scorer_type"
public static final java.lang.String	MAPPING_CORE	"mapping_core"
public static final java.lang.String	MENTION_INDEX	"mention_index"
public static final java.lang.String	SPELLING_INDEX	"spelling_index"
public static final java.lang.String	SYNONYM_INDEX	"mention_index"

de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval

Modifier and Type	Constant Field	Value
public static final int	JAROWINKLER_SCORER	3
public static final int	LEVENSHTEIN_SCORER	4
public static final java.lang.String	LOGGER_NAME_CANDIDATES	"de.julielab.jules.ae.genemapper.candidates"
public static final int	LUCENE_SCORER	10
public static final int	MAXENT_SCORER	2
public static final java.lang.String	MAXENT_SCORER_MODEL	"/genemapper_jules_mallet.mod"
public static final java.lang.String	NAME_PRIO_DELIMITER	"__"
public static final int	SIMPLE_SCORER	0
public static final int	TFIDF	5
public static final int	TOKEN_JAROWINKLER_SCORER	1

de.julielab.jules.ae.genemapping.genemodel.GeneMention

Modifier and Type	Constant Field	Value
public static final java.lang.String	NOID	"NoId"

de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames

Modifier and Type	Constant Field	Value
public static final java.lang.String	FIELD_GENERIF	"generif"
public static final java.lang.String	FIELD_INTERACTION	"interaction"
public static final java.lang.String	FIELD_SUMMARY	"summary"
public static final java.lang.String	LOOKUP_CONTEXT_FIELD	"indexed_context"
public static final java.lang.String	LOOKUP_ID_FIELD	"indexed_id"

de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILTERED	"filtered"
public static final java.lang.String	ID_FIELD	"entry_id"
public static final java.lang.String	ID_FIELD_LEGACY	"uniprot_id"
public static final java.lang.String	LOOKUP_SYN_FIELD	"indexed_syn"
public static final java.lang.String	ORIGINAL_NAME	"original_name"
public static final java.lang.String	PRIORITY	"priority"
public static final java.lang.String	STEMMED_NORMALIZED_NAME	"stemmed_normalized_name"
public static final java.lang.String	TAX_ID_FIELD	"tax_id"
public static final java.lang.String	VARIANT_NAME	"variant_name"

de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore

Modifier and Type	Constant Field	Value
public static final java.lang.String	TAX_IDS	"filter_tax_ids"

de.julielab.jules.ae.genemapping.scoring.Scorer

Modifier and Type	Constant Field	Value
public static final double	PERFECT_SCORE	9999.0