java.lang.Object
- java.util.Dictionary<K,V>
- - java.util.Hashtable<Object,Object>
  - - java.util.Properties
    - - de.julielab.geneexpbase.configuration.Configuration
      - de.julielab.genemapper.Configuration

All Implemented Interfaces:

Serializable, Cloneable, Map<Object,Object>
```
public class Configuration
extends de.julielab.geneexpbase.configuration.Configuration
```
See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`APPROX_MATCH`
`static String`	`APPROX_SCORER_TYPE`
`static String`	`CONTEXT_INDEX`
`static String`	`CONTEXT_ITEMS_INDEX`
`static String`	`EXACT_MATCH`
`static String`	`EXACT_SCORER_TYPE`
`static String`	`FIXED_TAX_ID`	When this parameter is set, the provided value will be used as tax ID for all gene mentions.
`static String`	`GENE_RECORD_INDEX`
`static String`	`GENE_RECORD_ORIGINAL_NAMES_INDEX`
`static String`	`KEY_MAX_FAMILY_MATCH_SCORE`
`static String`	`KEY_MIN_FAMILY_MATCH_SCORE`
`static String`	`MAPPING_CORE`	Deprecated. Not a configurable property any more but bound in the MappingModule
`static String`	`MENTION_INDEX`
`static String`	`PARAM_ADD_CONTEXT_GENES_AS_LUCENE_RELEVANCE_SIGNAL`
`static String`	`PARAM_ADD_SPECIES_PREFIX_STRIPPED_VARIANT_AS_GENENAME_ALTERNATIVE`
`static String`	`PARAM_ALTERNATIVE_NAMES_SEARCH_MODE`	One of `VALUE_CNF_RELEVANCE_SIGNAL`, `VALUE_ADDITIONAL_SEARCH`, `VALUE_ALL` or `VALUE_NONE`.
`static String`	`PARAM_COMPOSITE_FLAIR_MODEL`
`static String`	`PARAM_CONTEXT_GENE_FEATURE_GENERATION`	How to create feature from the context genes.
`static String`	`PARAM_DISAMBIGUATE_BY_MAP_LOCATION`
`static String`	`PARAM_DISAMBIGUATE_EXACT_HITS_BY_ORIGINAL_NAME`
`static String`	`PARAM_DISAMBIGUATION_LINCOMB_MAX_VALUES`
`static String`	`PARAM_DISAMBIGUATION_LINCOMB_MIN_VALUES`
`static String`	`PARAM_DISMAX_TIE_BREAKER`
`static String`	`PARAM_DO_CONTEXTUAL_RANKING`
`static String`	`PARAM_DO_FAMILY_REJECTION`
`static String`	`PARAM_DO_LOW_SCORE_REJECTION`
`static String`	`PARAM_DO_RRF_WITH_CANDIDATE_LISTS`	Whether to merge all candidate lists created in candidate retrieval (gene records CNF, potentially synonym centric retrieval and ML-based re-ranking) via reciprocal rank fusion for the final candidate list.
`static String`	`PARAM_EXCLUDE_GENES_FOR_CONTEXT_ITEM_SCORING`
`static String`	`PARAM_GENE_RECORDS_FIELD_QUERY_TYPE`	Parameter: Which classification/ranking method to use.
`static String`	`PARAM_GPU_COMPOSITE_MENTIONS`	Number of the GPU to use for the flair composite mention resolution
`static String`	`PARAM_GPU_TRANSFORMER_CANDIDATE_RANKING`	Number of the GPU to use for the transformer-based candiate ranking
`static String`	`PARAM_GS_HOMOGENIZATION_ALLOW_CANDIDATE_TRANSFER`	Whether we allow the transfer of candidates from accepted gene mentions to other mentions that have been rejected because they don't have candidates.
`static String`	`PARAM_GS_HOMOGENIZATION_BY_ABBREVIATION`
`static String`	`PARAM_GS_HOMOGENIZATION_BY_LONGFORM`
`static String`	`PARAM_GS_HOMOGENIZATION_METHOD`	The method of GeneSet ID homogenization.
`static String`	`PARAM_GS_MAJORITY_HOMOGENIZATION_TIE_BREAKER_METHOD`	The method to solve majority voting ties.
`static String`	`PARAM_GS_REJECTION_HOMOGENIZATION_METHOD`	What to do when some genes in a gene set have been rejected and others have not? This is checked when doing gene set ID homogenization.
`static String`	`PARAM_INTERSECTION_FILTER`
`static String`	`PARAM_LEX_CONTEXT_FUSE_METHOD`
`static String`	`PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_APPROX`	Must be in [0,1].
`static String`	`PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_EXACT`	Must be in [0,1].
`static String`	`PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING`	Prerequisite test for `PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY`: Only candidates whose Lucene score exceed the given ratio to the Lucene score of the best candidate are included in a re-ranking by original name.
`static String`	`PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_RERANKING`	Similar to `PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING`, this parameter sets a threshold of to be overcome for a candidate to be included in ML-based re-ranking.
`static String`	`PARAM_MAKE_TOKEN_WINDOW_DISTINCT`
`static String`	`PARAM_MAPPING_MODE`	One of `VALUE_GENE_MENTIONS` and `VALUE_GENESETS`
`static String`	`PARAM_MERGE_CONTINUOUS_GENE_ANNOTATIONS`	Whether to invoke `DypsisGeneSelector.mergeContinuousGeneAnnotations(GeneDocument)`.
`static String`	`PARAM_NORMALIZE_JARO_WINKLER_SYNONYM_SCORES`
`static String`	`PARAM_NORMALIZE_LUCENE_SYNONYM_SCORES`
`static String`	`PARAM_RANK_BY_SINGLE_FEATURE_VALUE`	One of `VALUE_SEMANTIC_CONTEXT` or `VALUE_NONE`.
`static String`	`PARAM_REJECT_FAMILY_IN_NP`
`static String`	`PARAM_REJECTION_FAMILY_HIT_RANK_APPROX_MATCH`
`static String`	`PARAM_REJECTION_FAMILY_HIT_RANK_EXACT_MATCH`
`static String`	`PARAM_REMOVE_SPECIES_PREFIXES_FOR_CANDIDATE_RETRIEVAL`
`static String`	`PARAM_REPLACE_ML_MENTIONS_WITH_LONGER_GAZETTEER_MENTIONS`	Whether to invoke `DypsisGeneSelector.selectLongerGazetteerMatchesOverFlair(GeneDocument)`
`static String`	`PARAM_SCALE_FAMILY_NAME_MATCH_SCORE`
`static String`	`PARAM_SCORE_FAMILY_NAMES_WITH_JARO_WINKLER`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_JARO_WINKLER`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_LUCENE`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_GENERIFS_JARO_WINKLER`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_GENERIFS_LUCENE`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_JARO_WINKLER`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_LUCENE`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_JARO_WINKLER`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_LUCENE`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_JARO_WINKLER`
`static String`	`PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_LUCENE`
`static String`	`PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_JARO_WINKLER`
`static String`	`PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_LUCENE`
`static String`	`PARAM_SCORE_SYNONYMS_ON_GENERIFS_JARO_WINKLER`
`static String`	`PARAM_SCORE_SYNONYMS_ON_GENERIFS_LUCENE`
`static String`	`PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_JARO_WINKLER`
`static String`	`PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_LUCENE`
`static String`	`PARAM_SCORE_SYNONYMS_ON_SUMMARIES_JARO_WINKLER`
`static String`	`PARAM_SCORE_SYNONYMS_ON_SUMMARIES_LUCENE`
`static String`	`PARAM_SEARCH_GM_NP_MODE`	One of `VALUE_CNF_RELEVANCE_SIGNAL`, `VALUE_ADDITIONAL_SEARCH` or `VALUE_NONE`.
`static String`	`PARAM_SEARCH_TAX_SPECIFIC_CANDIDATES_FIRST`
`static String`	`PARAM_SORT_CANDIDATES_BY_MATCHED_FIELD`
`static String`	`PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY`	Whether or not to try to disambiguate multiple exact matches with the original names.
`static String`	`PARAM_SORT_ML_BY_EXACT_MATCH_FIRST`
`static String`	`PARAM_SPLIT_AT_SLASH`	Whether to invoke `DypsisGeneSelector.splitDashGenes(GeneDocument, CandidateRetrieval)`.
`static String`	`PARAM_STOP_CANDIDATE_SEARCH_ON_EXACT_MATCH`
`static String`	`PARAM_SYNONYM_SEARCH_MODE`	One of `VALUE_CNF_RELEVANCE_SIGNAL`, `VALUE_ADDITIONAL_SEARCH` or `VALUE_NONE`.
`static String`	`PARAM_THRESHOLD_APPROX_LENGTH_DIFF_PENALTY_FACTOR`	The approx.
`static String`	`PARAM_THRESHOLD_APPROX_MATCHES`
`static String`	`PARAM_THRESHOLD_EXACT_MATCHES`
`static String`	`PARAM_THRESHOLD_GS_REJECTION`	Used to homogenize gene set rejection where some members have been rejected and others haven't.
`static String`	`PARAM_TOKEN_WINDOW_GENE_SETS_SIZE`
`static String`	`PARAM_TOP_N_CANDIDATES_RERANKING`	The top N candidates returned from Lucene to subject to reranking.
`static String`	`PARAM_TRAIN_MODE`
`static String`	`PARAM_TRANSFORMER_RANKING_MODEL`
`static String`	`PARAM_TRY_ORTHOLOGS`	Whether to try ortholog genes when the primary species didn't fit
`static String`	`PARAM_USE_APPOSITIONS_AS_LUCENE_RELEVANCE_SIGNAL`
`static String`	`PARAM_USE_APPOSITIONS_ON_GENE_CONTEXT_FEATURES`
`static String`	`PARAM_USE_FAMILY_MATCH_EXACT_FEATURE`
`static String`	`PARAM_USE_FAMILY_MATCH_FRACTION_FEATURE`
`static String`	`PARAM_USE_FAMILY_MATCH_RANK_FEATURE`
`static String`	`PARAM_USE_FAMILY_MATCH_SCORE_FEATURE`
`static String`	`PARAM_USE_GENE_FAMILY_SCORE_FEATURE`
`static String`	`PARAM_USE_GENERIF`
`static String`	`PARAM_USE_GNORMPLUS_CHEMICAL_SUFFIX_FEATURES`
`static String`	`PARAM_USE_GNORMPLUS_MENTION_TYPE_HINT_FEATURES`
`static String`	`PARAM_USE_GNORMPLUS_PROTEIN_SYMBOLS_FEATURES`
`static String`	`PARAM_USE_GODESC`
`static String`	`PARAM_USE_GOLD_TAX`
`static String`	`PARAM_USE_INTERACTION`
`static String`	`PARAM_USE_JACCARD_FEATURES`
`static String`	`PARAM_USE_JARO_WINKLER_APPROX_SCORES`
`static String`	`PARAM_USE_JARO_WINKLER_EXACT_SCORES`
`static String`	`PARAM_USE_JARO_WINKLER_FEATURES`
`static String`	`PARAM_USE_LASTWORD_FEATURE`
`static String`	`PARAM_USE_LEVENSHTEIN_FEATURES`
`static String`	`PARAM_USE_LUCENE_APPROX_SCORES`
`static String`	`PARAM_USE_LUCENE_EXACT_SCORES`
`static String`	`PARAM_USE_LUCENE_SYNONYM_SET`
`static String`	`PARAM_USE_NEEDLEMANWUNSCH_FEATURES`
`static String`	`PARAM_USE_OTHER_HAS_SPECIFIER_FEATURE`
`static String`	`PARAM_USE_QUERY_FIELD_WEIGHTS`	Whether to use field weights in the Lucene query to the candidate index.
`static String`	`PARAM_USE_SCORER_AVERAGE`
`static String`	`PARAM_USE_SMITHWATERMAN_FEATURES`
`static String`	`PARAM_USE_SUMMARY`
`static String`	`PARAM_USE_TFIDF_FEATURES`
`static String`	`PARAM_USE_TOKEN_FEATURES`
`static String`	`PARAM_USE_TOKEN_JARO_FEATURES`
`static String`	`PREFIX_ANCHORING`
`static String`	`PREFIX_CANDIDATE_FILTER`
`static String`	`PREFIX_CANDIDATE_RETRIEVAL`
`static String`	`PREFIX_DISAMBIGUATION`
`static String`	`PREFIX_ID_HOMOGENIZATION`
`static String`	`PREFIX_RECORD_CONTEXT`
`static String`	`PREFIX_REJECTION`
`static String`	`PREFIX_REJECTION_HOMOGENIZATION`
`static String`	`SPELLING_INDEX`
`static String`	`SYNONYM_INDEX`
`static String`	`USE_LUCENE_CANDIDATES_CACHE`
`static String`	`VALUE_ADDITIONAL_SEARCH`
`static String`	`VALUE_ALL`
`static String`	`VALUE_BALANCED_SCORES`	Boolean toggle.
`static String`	`VALUE_CNF_RELEVANCE_SIGNAL`
`static String`	`VALUE_CONTEXT_SCORES`
`static String`	`VALUE_DISJUNCTION`
`static String`	`VALUE_DISMAX`
`static String`	`VALUE_GENE_MENTIONS`
`static String`	`VALUE_GENE_RECORDS`
`static String`	`VALUE_GENESETS`
`static String`	`VALUE_LINEAR_COMBINATION`
`static String`	`VALUE_MAJORITY_VOTE`
`static String`	`VALUE_MAX`
`static String`	`VALUE_MAX_BALANCED_SCORE`
`static String`	`VALUE_MAX_BALANCED_SCORE_SUM`
`static String`	`VALUE_MEAN_SCORE`	Gene set rejection homogenization method that calculates the mean score of the gene mentions in the set and compares this against the rejection threshold.
`static String`	`VALUE_NAME_CENTRIC`
`static String`	`VALUE_NO_GS_HOMOGENIZATION`
`static String`	`VALUE_NONE`
`static String`	`VALUE_RANK_FUSION`	Method to combine lexical and semantic ranking.
`static String`	`VALUE_SEMANTIC_CONTEXT`	The disambiguation strategy employed by Li, L., Liu, S., Li, L., Fan, W., Huang, D., & Zhou, H.
`static String`	`VALUE_SUM`
`static String`	`WIKIPEDIA_INDEX`

Fields inherited from class de.julielab.geneexpbase.configuration.Configuration
CONCURRENCY_LEVEL, EHCACHE_CONFIG, GENE_ORTHOLOGS_PATH, KEY_CLASSIFIER, KEY_DATA_ALPHABET, KEY_MAX_RESULT_SCORE, KEY_MIN_RESULT_SCORE, KEY_MINMAX_SCALING_VALUES, KEY_RANKER, KEY_STANDARDIZATION_VALUES, KEY_TARGET_ALPHABET, ML, PARAM_ALGORITHM, PARAM_LTR_ALGORITHM, PARAM_LTR_K, PARAM_LTR_METRIC, PARAM_MINMAX_SCALE_FEATURES, PARAM_ML_USE_ALL_CORPUS_TRAINSPLITS, PARAM_MODEL, PARAM_PYTHON_EXECUTABLE, PARAM_SCALE_RESULT_SCORE, PARAM_STANDARDIZE_FEATURES, PARAM_SVM_C, PARAM_SVM_COEF0, PARAM_SVM_DEGREE, PARAM_SVM_GAMMA, PARAM_SVM_KERNEL_TYPE, PARAM_SVM_TYPE, PYTHON_PROCESS_LIMIT, TRAINING_INSTANCES, VALUE_LTR, VALUE_LUCENE, VALUE_MAXENT, VALUE_SVM, VALUE_TRANSFORMER

Fields inherited from class java.util.Properties
defaults

Constructor Summary

Constructors
Constructor	Description
`Configuration()`
`Configuration(de.julielab.geneexpbase.configuration.Configuration baseConfiguration)`
`Configuration(File configurationFile)`
`Configuration(String... parameters)`

Method Summary
- Methods inherited from class de.julielab.geneexpbase.configuration.Configuration
  dot, getBoolean, getDouble, getInteger, getLong
- Methods inherited from class java.util.Properties
  clear, clone, compute, computeIfAbsent, computeIfPresent, contains, containsKey, containsValue, elements, entrySet, equals, forEach, get, getOrDefault, getProperty, getProperty, hashCode, isEmpty, keys, keySet, list, list, load, load, loadFromXML, merge, propertyNames, put, putAll, putIfAbsent, rehash, remove, remove, replace, replace, replaceAll, save, setProperty, size, store, store, storeToXML, storeToXML, storeToXML, stringPropertyNames, toString, values
- Methods inherited from class java.lang.Object
  finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - PREFIX_CANDIDATE_RETRIEVAL
```
public static final String PREFIX_CANDIDATE_RETRIEVAL
```
    See Also:
    
    Constant Field Values
  - PREFIX_CANDIDATE_FILTER
```
public static final String PREFIX_CANDIDATE_FILTER
```
    See Also:
    
    Constant Field Values
  - PREFIX_DISAMBIGUATION
```
public static final String PREFIX_DISAMBIGUATION
```
    See Also:
    
    Constant Field Values
  - PREFIX_REJECTION
```
public static final String PREFIX_REJECTION
```
    See Also:
    
    Constant Field Values
  - PREFIX_ANCHORING
```
public static final String PREFIX_ANCHORING
```
    See Also:
    
    Constant Field Values
  - PREFIX_ID_HOMOGENIZATION
```
public static final String PREFIX_ID_HOMOGENIZATION
```
    See Also:
    
    Constant Field Values
  - PREFIX_REJECTION_HOMOGENIZATION
```
public static final String PREFIX_REJECTION_HOMOGENIZATION
```
    See Also:
    
    Constant Field Values
  - PREFIX_RECORD_CONTEXT
```
public static final String PREFIX_RECORD_CONTEXT
```
    See Also:
    
    Constant Field Values
  - USE_LUCENE_CANDIDATES_CACHE
```
public static final String USE_LUCENE_CANDIDATES_CACHE
```
    See Also:
    
    Constant Field Values
  - EXACT_MATCH
```
public static final String EXACT_MATCH
```
    See Also:
    
    Constant Field Values
  - APPROX_MATCH
```
public static final String APPROX_MATCH
```
    See Also:
    
    Constant Field Values
  - PARAM_GENE_RECORDS_FIELD_QUERY_TYPE
```
public static final String PARAM_GENE_RECORDS_FIELD_QUERY_TYPE
```
    Parameter: Which classification/ranking method to use.
    
    One of:
    
    VALUE_LINEAR_COMBINATION (disambiguation only)
    
    Configuration.VALUE_LTR
    
    Configuration.VALUE_LUCENE (candidate retrieval only)
    
    Configuration.VALUE_MAXENT
    
    Configuration.VALUE_SVM
    
    The values linearCombination and svm require further parameters (the feature weights and the SVM hyper parameters, respectively).
    See Also:
    
    Constant Field Values
  - PARAM_DISMAX_TIE_BREAKER
```
public static final String PARAM_DISMAX_TIE_BREAKER
```
    See Also:
    
    Constant Field Values
  - VALUE_DISMAX
```
public static final String VALUE_DISMAX
```
    See Also:
    
    Constant Field Values
  - VALUE_DISJUNCTION
```
public static final String VALUE_DISJUNCTION
```
    See Also:
    
    Constant Field Values
  - VALUE_LINEAR_COMBINATION
```
public static final String VALUE_LINEAR_COMBINATION
```
    See Also:
    
    Constant Field Values
  - VALUE_NAME_CENTRIC
```
public static final String VALUE_NAME_CENTRIC
```
    See Also:
    
    Constant Field Values
  - VALUE_GENE_RECORDS
```
public static final String VALUE_GENE_RECORDS
```
    See Also:
    
    Constant Field Values
  - CONTEXT_ITEMS_INDEX
```
public static final String CONTEXT_ITEMS_INDEX
```
    See Also:
    
    Constant Field Values
  - SYNONYM_INDEX
```
public static final String SYNONYM_INDEX
```
    See Also:
    
    Constant Field Values
  - CONTEXT_INDEX
```
public static final String CONTEXT_INDEX
```
    See Also:
    
    Constant Field Values
  - WIKIPEDIA_INDEX
```
public static final String WIKIPEDIA_INDEX
```
    See Also:
    
    Constant Field Values
  - FIXED_TAX_ID
```
public static final String FIXED_TAX_ID
```
    When this parameter is set, the provided value will be used as tax ID for all gene mentions. The special value 'gold' will result in the usage of gold annotations.
    
    See Also:
    
    Constant Field Values
  - MAPPING_CORE
```
@Deprecated
public static final String MAPPING_CORE
```
    Deprecated.
    Not a configurable property any more but bound in the MappingModule
    
    See Also:
    
    Constant Field Values
  - EXACT_SCORER_TYPE
```
public static final String EXACT_SCORER_TYPE
```
    See Also:
    
    Constant Field Values
  - APPROX_SCORER_TYPE
```
public static final String APPROX_SCORER_TYPE
```
    See Also:
    
    Constant Field Values
  - SPELLING_INDEX
```
public static final String SPELLING_INDEX
```
    See Also:
    
    Constant Field Values
  - MENTION_INDEX
```
public static final String MENTION_INDEX
```
    See Also:
    
    Constant Field Values
  - GENE_RECORD_INDEX
```
public static final String GENE_RECORD_INDEX
```
    See Also:
    
    Constant Field Values
  - GENE_RECORD_ORIGINAL_NAMES_INDEX
```
public static final String GENE_RECORD_ORIGINAL_NAMES_INDEX
```
    See Also:
    
    Constant Field Values
  - PARAM_GPU_COMPOSITE_MENTIONS
```
public static final String PARAM_GPU_COMPOSITE_MENTIONS
```
    Number of the GPU to use for the flair composite mention resolution
    
    See Also:
    
    Constant Field Values
  - PARAM_GPU_TRANSFORMER_CANDIDATE_RANKING
```
public static final String PARAM_GPU_TRANSFORMER_CANDIDATE_RANKING
```
    Number of the GPU to use for the transformer-based candiate ranking
    
    See Also:
    
    Constant Field Values
  - PARAM_COMPOSITE_FLAIR_MODEL
```
public static final String PARAM_COMPOSITE_FLAIR_MODEL
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_GOLD_TAX
```
public static final String PARAM_USE_GOLD_TAX
```
    See Also:
    
    Constant Field Values
  - PARAM_DISAMBIGUATE_BY_MAP_LOCATION
```
public static final String PARAM_DISAMBIGUATE_BY_MAP_LOCATION
```
    See Also:
    
    Constant Field Values
  - PARAM_TRANSFORMER_RANKING_MODEL
```
public static final String PARAM_TRANSFORMER_RANKING_MODEL
```
    See Also:
    
    Constant Field Values
  - PARAM_TRY_ORTHOLOGS
```
public static final String PARAM_TRY_ORTHOLOGS
```
    Whether to try ortholog genes when the primary species didn't fit
    
    See Also:
    
    Constant Field Values
  - PARAM_SPLIT_AT_SLASH
```
public static final String PARAM_SPLIT_AT_SLASH
```
    Whether to invoke DypsisGeneSelector.splitDashGenes(GeneDocument, CandidateRetrieval).
    
    See Also:
    
    Constant Field Values
  - PARAM_MERGE_CONTINUOUS_GENE_ANNOTATIONS
```
public static final String PARAM_MERGE_CONTINUOUS_GENE_ANNOTATIONS
```
    Whether to invoke DypsisGeneSelector.mergeContinuousGeneAnnotations(GeneDocument).
    
    See Also:
    
    Constant Field Values
  - PARAM_REPLACE_ML_MENTIONS_WITH_LONGER_GAZETTEER_MENTIONS
```
public static final String PARAM_REPLACE_ML_MENTIONS_WITH_LONGER_GAZETTEER_MENTIONS
```
    Whether to invoke DypsisGeneSelector.selectLongerGazetteerMatchesOverFlair(GeneDocument)
    
    See Also:
    
    Constant Field Values
  - PARAM_SYNONYM_SEARCH_MODE
```
public static final String PARAM_SYNONYM_SEARCH_MODE
```
    One of VALUE_CNF_RELEVANCE_SIGNAL, VALUE_ADDITIONAL_SEARCH or VALUE_NONE.
    
    See Also:
    
    Constant Field Values
  - VALUE_CNF_RELEVANCE_SIGNAL
```
public static final String VALUE_CNF_RELEVANCE_SIGNAL
```
    See Also:
    
    Constant Field Values
  - VALUE_ADDITIONAL_SEARCH
```
public static final String VALUE_ADDITIONAL_SEARCH
```
    See Also:
    
    Constant Field Values
  - VALUE_ALL
```
public static final String VALUE_ALL
```
    See Also:
    
    Constant Field Values
  - VALUE_NONE
```
public static final String VALUE_NONE
```
    See Also:
    
    Constant Field Values
  - PARAM_ADD_SPECIES_PREFIX_STRIPPED_VARIANT_AS_GENENAME_ALTERNATIVE
```
public static final String PARAM_ADD_SPECIES_PREFIX_STRIPPED_VARIANT_AS_GENENAME_ALTERNATIVE
```
    See Also:
    
    Constant Field Values
  - PARAM_REMOVE_SPECIES_PREFIXES_FOR_CANDIDATE_RETRIEVAL
```
public static final String PARAM_REMOVE_SPECIES_PREFIXES_FOR_CANDIDATE_RETRIEVAL
```
    See Also:
    
    Constant Field Values
  - PARAM_ADD_CONTEXT_GENES_AS_LUCENE_RELEVANCE_SIGNAL
```
public static final String PARAM_ADD_CONTEXT_GENES_AS_LUCENE_RELEVANCE_SIGNAL
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_APPOSITIONS_AS_LUCENE_RELEVANCE_SIGNAL
```
public static final String PARAM_USE_APPOSITIONS_AS_LUCENE_RELEVANCE_SIGNAL
```
    See Also:
    
    Constant Field Values
  - PARAM_SEARCH_TAX_SPECIFIC_CANDIDATES_FIRST
```
public static final String PARAM_SEARCH_TAX_SPECIFIC_CANDIDATES_FIRST
```
    See Also:
    
    Constant Field Values
  - PARAM_STOP_CANDIDATE_SEARCH_ON_EXACT_MATCH
```
public static final String PARAM_STOP_CANDIDATE_SEARCH_ON_EXACT_MATCH
```
    See Also:
    
    Constant Field Values
  - PARAM_DISAMBIGUATE_EXACT_HITS_BY_ORIGINAL_NAME
```
public static final String PARAM_DISAMBIGUATE_EXACT_HITS_BY_ORIGINAL_NAME
```
    See Also:
    
    Constant Field Values
  - PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY
```
public static final String PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY
```
    Whether or not to try to disambiguate multiple exact matches with the original names.
    
    See Also:
    
    Constant Field Values
  - PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING
```
public static final String PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING
```
    Prerequisite test for PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY: Only candidates whose Lucene score exceed the given ratio to the Lucene score of the best candidate are included in a re-ranking by original name.
    
    See Also:
    
    Constant Field Values
  - PARAM_SEARCH_GM_NP_MODE
```
public static final String PARAM_SEARCH_GM_NP_MODE
```
    One of VALUE_CNF_RELEVANCE_SIGNAL, VALUE_ADDITIONAL_SEARCH or VALUE_NONE.
    
    See Also:
    
    Constant Field Values
  - PARAM_ALTERNATIVE_NAMES_SEARCH_MODE
```
public static final String PARAM_ALTERNATIVE_NAMES_SEARCH_MODE
```
    One of VALUE_CNF_RELEVANCE_SIGNAL, VALUE_ADDITIONAL_SEARCH, VALUE_ALL or VALUE_NONE.
    
    See Also:
    
    Constant Field Values
  - PARAM_DO_RRF_WITH_CANDIDATE_LISTS
```
public static final String PARAM_DO_RRF_WITH_CANDIDATE_LISTS
```
    Whether to merge all candidate lists created in candidate retrieval (gene records CNF, potentially synonym centric retrieval and ML-based re-ranking) via reciprocal rank fusion for the final candidate list.
    
    See Also:
    
    Constant Field Values
  - PARAM_USE_QUERY_FIELD_WEIGHTS
```
public static final String PARAM_USE_QUERY_FIELD_WEIGHTS
```
    Whether to use field weights in the Lucene query to the candidate index.
    
    See Also:
    
    Constant Field Values
  - PARAM_SORT_CANDIDATES_BY_MATCHED_FIELD
```
public static final String PARAM_SORT_CANDIDATES_BY_MATCHED_FIELD
```
    See Also:
    
    Constant Field Values
  - PARAM_TOP_N_CANDIDATES_RERANKING
```
public static final String PARAM_TOP_N_CANDIDATES_RERANKING
```
    The top N candidates returned from Lucene to subject to reranking.
    
    See Also:
    
    Constant Field Values
  - PARAM_USE_JARO_WINKLER_FEATURES
```
public static final String PARAM_USE_JARO_WINKLER_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_TOKEN_JARO_FEATURES
```
public static final String PARAM_USE_TOKEN_JARO_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_LEVENSHTEIN_FEATURES
```
public static final String PARAM_USE_LEVENSHTEIN_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_SMITHWATERMAN_FEATURES
```
public static final String PARAM_USE_SMITHWATERMAN_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_NEEDLEMANWUNSCH_FEATURES
```
public static final String PARAM_USE_NEEDLEMANWUNSCH_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_JACCARD_FEATURES
```
public static final String PARAM_USE_JACCARD_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_TFIDF_FEATURES
```
public static final String PARAM_USE_TFIDF_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_SCORER_AVERAGE
```
public static final String PARAM_USE_SCORER_AVERAGE
```
    See Also:
    
    Constant Field Values
  - PARAM_CONTEXT_GENE_FEATURE_GENERATION
```
public static final String PARAM_CONTEXT_GENE_FEATURE_GENERATION
```
    How to create feature from the context genes. The issue is that there is no fixed number of such genes. So we need to aggregate the scores for multiple context genes into a single number.
    
    One of VALUE_SUM, VALUE_MAX or VALUE_NONE.
    
    See Also:
    
    Constant Field Values
  - PARAM_USE_TOKEN_FEATURES
```
public static final String PARAM_USE_TOKEN_FEATURES
```
    See Also:
    
    Constant Field Values
  - VALUE_SUM
```
public static final String VALUE_SUM
```
    See Also:
    
    Constant Field Values
  - VALUE_MAX
```
public static final String VALUE_MAX
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_GENERIF
```
public static final String PARAM_USE_GENERIF
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_INTERACTION
```
public static final String PARAM_USE_INTERACTION
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_GODESC
```
public static final String PARAM_USE_GODESC
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_SUMMARY
```
public static final String PARAM_USE_SUMMARY
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_APPOSITIONS_ON_GENE_CONTEXT_FEATURES
```
public static final String PARAM_USE_APPOSITIONS_ON_GENE_CONTEXT_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_RERANKING
```
public static final String PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_RERANKING
```
    Similar to PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING, this parameter sets a threshold of to be overcome for a candidate to be included in ML-based re-ranking. The value to compare against the threshold is the percentage of the Lucene score of a candidate to the score of the best candidate. The idea is to use the Lucene score ratios as a confidence measure.
    
    Meant to be used under an Configuration.ML configuration root.
    
    See Also:
    
    Constant Field Values
  - PARAM_MAPPING_MODE
```
public static final String PARAM_MAPPING_MODE
```
    One of VALUE_GENE_MENTIONS and VALUE_GENESETS
    
    See Also:
    
    Constant Field Values
  - VALUE_GENE_MENTIONS
```
public static final String VALUE_GENE_MENTIONS
```
    See Also:
    
    Constant Field Values
  - VALUE_GENESETS
```
public static final String VALUE_GENESETS
```
    See Also:
    
    Constant Field Values
  - PARAM_DO_CONTEXTUAL_RANKING
```
public static final String PARAM_DO_CONTEXTUAL_RANKING
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_LUCENE_SYNONYM_SET
```
public static final String PARAM_USE_LUCENE_SYNONYM_SET
```
    See Also:
    
    Constant Field Values
  - PARAM_MAKE_TOKEN_WINDOW_DISTINCT
```
public static final String PARAM_MAKE_TOKEN_WINDOW_DISTINCT
```
    See Also:
    
    Constant Field Values
  - PARAM_TOKEN_WINDOW_GENE_SETS_SIZE
```
public static final String PARAM_TOKEN_WINDOW_GENE_SETS_SIZE
```
    See Also:
    
    Constant Field Values
  - PARAM_EXCLUDE_GENES_FOR_CONTEXT_ITEM_SCORING
```
public static final String PARAM_EXCLUDE_GENES_FOR_CONTEXT_ITEM_SCORING
```
    See Also:
    
    Constant Field Values
  - PARAM_INTERSECTION_FILTER
```
public static final String PARAM_INTERSECTION_FILTER
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_GENE_FAMILY_SCORE_FEATURE
```
public static final String PARAM_USE_GENE_FAMILY_SCORE_FEATURE
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_GNORMPLUS_CHEMICAL_SUFFIX_FEATURES
```
public static final String PARAM_USE_GNORMPLUS_CHEMICAL_SUFFIX_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_GNORMPLUS_MENTION_TYPE_HINT_FEATURES
```
public static final String PARAM_USE_GNORMPLUS_MENTION_TYPE_HINT_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_GNORMPLUS_PROTEIN_SYMBOLS_FEATURES
```
public static final String PARAM_USE_GNORMPLUS_PROTEIN_SYMBOLS_FEATURES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_LASTWORD_FEATURE
```
public static final String PARAM_USE_LASTWORD_FEATURE
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_OTHER_HAS_SPECIFIER_FEATURE
```
public static final String PARAM_USE_OTHER_HAS_SPECIFIER_FEATURE
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_FAMILY_MATCH_SCORE_FEATURE
```
public static final String PARAM_USE_FAMILY_MATCH_SCORE_FEATURE
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_FAMILY_MATCH_RANK_FEATURE
```
public static final String PARAM_USE_FAMILY_MATCH_RANK_FEATURE
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_FAMILY_MATCH_EXACT_FEATURE
```
public static final String PARAM_USE_FAMILY_MATCH_EXACT_FEATURE
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_FAMILY_MATCH_FRACTION_FEATURE
```
public static final String PARAM_USE_FAMILY_MATCH_FRACTION_FEATURE
```
    See Also:
    
    Constant Field Values
  - PARAM_SORT_ML_BY_EXACT_MATCH_FIRST
```
public static final String PARAM_SORT_ML_BY_EXACT_MATCH_FIRST
```
    See Also:
    
    Constant Field Values
  - PARAM_RANK_BY_SINGLE_FEATURE_VALUE
```
public static final String PARAM_RANK_BY_SINGLE_FEATURE_VALUE
```
    One of VALUE_SEMANTIC_CONTEXT or VALUE_NONE.
    
    See Also:
    
    Constant Field Values
  - VALUE_SEMANTIC_CONTEXT
```
public static final String VALUE_SEMANTIC_CONTEXT
```
    The disambiguation strategy employed by Li, L., Liu, S., Li, L., Fan, W., Huang, D., & Zhou, H. (2013). A Multistage Gene Normalization System Integrating Multiple Effective Methods. PLoS ONE, 8(12). https://doi.org/10.1371/journal.pone.0081956
    
    See Also:
    
    Constant Field Values
  - PARAM_LEX_CONTEXT_FUSE_METHOD
```
public static final String PARAM_LEX_CONTEXT_FUSE_METHOD
```
    See Also:
    
    Constant Field Values
  - VALUE_RANK_FUSION
```
public static final String VALUE_RANK_FUSION
```
    Method to combine lexical and semantic ranking. Uses reciprocal rank fusion. Excludes VALUE_BALANCED_SCORES.
    
    See Also:
    
    Constant Field Values
  - VALUE_BALANCED_SCORES
```
public static final String VALUE_BALANCED_SCORES
```
    Boolean toggle. Method to combine lexical and semantic ranking. Excludes VALUE_RANK_FUSION. Builds the balanced sum of both in the form balancingFactor*lexicalScore + (1-balancingFactor)*semanticScore where balancing factor is PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_EXACT for exact matches and PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_APPROX for approximate matches.
    
    See Also:
    
    Constant Field Values
  - VALUE_CONTEXT_SCORES
```
public static final String VALUE_CONTEXT_SCORES
```
    See Also:
    
    Constant Field Values
  - PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_EXACT
```
public static final String PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_EXACT
```
    Must be in [0,1]. Used to obtain a final score for a gene candidate that was an exact match as:
    factor*lexicalScore + (1-factor)*semanticScore
    
    See Also:
    
    Constant Field Values
  - PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_APPROX
```
public static final String PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_APPROX
```
    Must be in [0,1]. Used to obtain a final score for a gene candidate that was an approximate match as:
    factor*lexicalScore + (1-factor)*semanticScore
    
    See Also:
    
    Constant Field Values
  - PARAM_NORMALIZE_LUCENE_SYNONYM_SCORES
```
public static final String PARAM_NORMALIZE_LUCENE_SYNONYM_SCORES
```
    See Also:
    
    Constant Field Values
  - PARAM_NORMALIZE_JARO_WINKLER_SYNONYM_SCORES
```
public static final String PARAM_NORMALIZE_JARO_WINKLER_SYNONYM_SCORES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_LUCENE_EXACT_SCORES
```
public static final String PARAM_USE_LUCENE_EXACT_SCORES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_JARO_WINKLER_EXACT_SCORES
```
public static final String PARAM_USE_JARO_WINKLER_EXACT_SCORES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_LUCENE_APPROX_SCORES
```
public static final String PARAM_USE_LUCENE_APPROX_SCORES
```
    See Also:
    
    Constant Field Values
  - PARAM_USE_JARO_WINKLER_APPROX_SCORES
```
public static final String PARAM_USE_JARO_WINKLER_APPROX_SCORES
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_GENERIFS_LUCENE
```
public static final String PARAM_SCORE_GSCONTEXT_ON_GENERIFS_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_GENERIFS_JARO_WINKLER
```
public static final String PARAM_SCORE_GSCONTEXT_ON_GENERIFS_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_LUCENE
```
public static final String PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_JARO_WINKLER
```
public static final String PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_LUCENE
```
public static final String PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_JARO_WINKLER
```
public static final String PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_LUCENE
```
public static final String PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_JARO_WINKLER
```
public static final String PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_GENERIFS_LUCENE
```
public static final String PARAM_SCORE_SYNONYMS_ON_GENERIFS_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_GENERIFS_JARO_WINKLER
```
public static final String PARAM_SCORE_SYNONYMS_ON_GENERIFS_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_LUCENE
```
public static final String PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_JARO_WINKLER
```
public static final String PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_SUMMARIES_LUCENE
```
public static final String PARAM_SCORE_SYNONYMS_ON_SUMMARIES_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_SUMMARIES_JARO_WINKLER
```
public static final String PARAM_SCORE_SYNONYMS_ON_SUMMARIES_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_LUCENE
```
public static final String PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_JARO_WINKLER
```
public static final String PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_LUCENE
```
public static final String PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_LUCENE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_JARO_WINKLER
```
public static final String PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - PARAM_SCALE_FAMILY_NAME_MATCH_SCORE
```
public static final String PARAM_SCALE_FAMILY_NAME_MATCH_SCORE
```
    See Also:
    
    Constant Field Values
  - PARAM_SCORE_FAMILY_NAMES_WITH_JARO_WINKLER
```
public static final String PARAM_SCORE_FAMILY_NAMES_WITH_JARO_WINKLER
```
    See Also:
    
    Constant Field Values
  - KEY_MAX_FAMILY_MATCH_SCORE
```
public static final String KEY_MAX_FAMILY_MATCH_SCORE
```
    See Also:
    
    Constant Field Values
  - KEY_MIN_FAMILY_MATCH_SCORE
```
public static final String KEY_MIN_FAMILY_MATCH_SCORE
```
    See Also:
    
    Constant Field Values
  - PARAM_DO_LOW_SCORE_REJECTION
```
public static final String PARAM_DO_LOW_SCORE_REJECTION
```
    See Also:
    
    Constant Field Values
  - PARAM_DO_FAMILY_REJECTION
```
public static final String PARAM_DO_FAMILY_REJECTION
```
    See Also:
    
    Constant Field Values
  - PARAM_THRESHOLD_EXACT_MATCHES
```
public static final String PARAM_THRESHOLD_EXACT_MATCHES
```
    See Also:
    
    Constant Field Values
  - PARAM_THRESHOLD_APPROX_MATCHES
```
public static final String PARAM_THRESHOLD_APPROX_MATCHES
```
    See Also:
    
    Constant Field Values
  - PARAM_THRESHOLD_GS_REJECTION
```
public static final String PARAM_THRESHOLD_GS_REJECTION
```
    Used to homogenize gene set rejection where some members have been rejected and others haven't. One homogenization method is to calculate the mean overall score of all members and compare this against this threshold.
  - PARAM_THRESHOLD_APPROX_LENGTH_DIFF_PENALTY_FACTOR
```
public static final String PARAM_THRESHOLD_APPROX_LENGTH_DIFF_PENALTY_FACTOR
```
    The approx. penalty is subtracted from the overall score value following the formula:
    effective_score = overallscore - log(|symmetricDifferenceGeneTokens&SynhitTokens|) * penalty
    Thus, if this parameter is set to 0, the number of tokens is ignored.
    
    See Also:
    
    Constant Field Values
  - PARAM_DISAMBIGUATION_LINCOMB_MAX_VALUES
```
public static final String PARAM_DISAMBIGUATION_LINCOMB_MAX_VALUES
```
  - PARAM_DISAMBIGUATION_LINCOMB_MIN_VALUES
```
public static final String PARAM_DISAMBIGUATION_LINCOMB_MIN_VALUES
```
  - PARAM_TRAIN_MODE
```
public static final String PARAM_TRAIN_MODE
```
    See Also:
    
    Constant Field Values
  - PARAM_GS_HOMOGENIZATION_METHOD
```
public static final String PARAM_GS_HOMOGENIZATION_METHOD
```
    The method of GeneSet ID homogenization. Of one VALUE_MAJORITY_VOTE, VALUE_MAX_BALANCED_SCORE and VALUE_MAX_BALANCED_SCORE_SUM.
  - VALUE_MAJORITY_VOTE
```
public static final String VALUE_MAJORITY_VOTE
```
    See Also:
    
    Constant Field Values
  - PARAM_GS_MAJORITY_HOMOGENIZATION_TIE_BREAKER_METHOD
```
public static final String PARAM_GS_MAJORITY_HOMOGENIZATION_TIE_BREAKER_METHOD
```
    The method to solve majority voting ties. Of one VALUE_MAX_BALANCED_SCORE and VALUE_MAX_BALANCED_SCORE_SUM.
  - VALUE_MAX_BALANCED_SCORE
```
public static final String VALUE_MAX_BALANCED_SCORE
```
    See Also:
    
    Constant Field Values
  - VALUE_MAX_BALANCED_SCORE_SUM
```
public static final String VALUE_MAX_BALANCED_SCORE_SUM
```
    See Also:
    
    Constant Field Values
  - VALUE_NO_GS_HOMOGENIZATION
```
public static final String VALUE_NO_GS_HOMOGENIZATION
```
    See Also:
    
    Constant Field Values
  - PARAM_GS_HOMOGENIZATION_BY_ABBREVIATION
```
public static final String PARAM_GS_HOMOGENIZATION_BY_ABBREVIATION
```
  - PARAM_GS_HOMOGENIZATION_BY_LONGFORM
```
public static final String PARAM_GS_HOMOGENIZATION_BY_LONGFORM
```
  - PARAM_GS_HOMOGENIZATION_ALLOW_CANDIDATE_TRANSFER
```
public static final String PARAM_GS_HOMOGENIZATION_ALLOW_CANDIDATE_TRANSFER
```
    Whether we allow the transfer of candidates from accepted gene mentions to other mentions that have been rejected because they don't have candidates.
  - PARAM_GS_REJECTION_HOMOGENIZATION_METHOD
```
public static final String PARAM_GS_REJECTION_HOMOGENIZATION_METHOD
```
    What to do when some genes in a gene set have been rejected and others have not? This is checked when doing gene set ID homogenization. One of VALUE_MAJORITY_VOTE and VALUE_MEAN_SCORE.
  - VALUE_MEAN_SCORE
```
public static final String VALUE_MEAN_SCORE
```
    Gene set rejection homogenization method that calculates the mean score of the gene mentions in the set and compares this against the rejection threshold.
    
    See Also:
    
    Constant Field Values
  - PARAM_REJECTION_FAMILY_HIT_RANK_EXACT_MATCH
```
public static final String PARAM_REJECTION_FAMILY_HIT_RANK_EXACT_MATCH
```
  - PARAM_REJECTION_FAMILY_HIT_RANK_APPROX_MATCH
```
public static final String PARAM_REJECTION_FAMILY_HIT_RANK_APPROX_MATCH
```
  - PARAM_REJECT_FAMILY_IN_NP
```
public static final String PARAM_REJECT_FAMILY_IN_NP
```
- Constructor Detail
  - Configuration
```
public Configuration(de.julielab.geneexpbase.configuration.Configuration baseConfiguration)
```
  - Configuration
```
public Configuration()
```
  - Configuration
```
public Configuration(String... parameters)
```
  - Configuration
```
public Configuration(File configurationFile)
              throws IOException
```
    Throws:
    
    IOException

Class Configuration

Field Summary

Fields inherited from class de.julielab.geneexpbase.configuration.Configuration

Fields inherited from class java.util.Properties

Constructor Summary

Method Summary

Methods inherited from class de.julielab.geneexpbase.configuration.Configuration

Methods inherited from class java.util.Properties

Methods inherited from class java.lang.Object

Field Detail

PREFIX_CANDIDATE_RETRIEVAL

PREFIX_CANDIDATE_FILTER

PREFIX_DISAMBIGUATION

PREFIX_REJECTION

PREFIX_ANCHORING

PREFIX_ID_HOMOGENIZATION

PREFIX_REJECTION_HOMOGENIZATION

PREFIX_RECORD_CONTEXT

USE_LUCENE_CANDIDATES_CACHE

EXACT_MATCH

APPROX_MATCH

PARAM_GENE_RECORDS_FIELD_QUERY_TYPE

PARAM_DISMAX_TIE_BREAKER

VALUE_DISMAX

VALUE_DISJUNCTION

VALUE_LINEAR_COMBINATION

VALUE_NAME_CENTRIC

VALUE_GENE_RECORDS

CONTEXT_ITEMS_INDEX

SYNONYM_INDEX

CONTEXT_INDEX

WIKIPEDIA_INDEX

FIXED_TAX_ID

MAPPING_CORE

EXACT_SCORER_TYPE

APPROX_SCORER_TYPE

SPELLING_INDEX

MENTION_INDEX

GENE_RECORD_INDEX

GENE_RECORD_ORIGINAL_NAMES_INDEX

PARAM_GPU_COMPOSITE_MENTIONS

PARAM_GPU_TRANSFORMER_CANDIDATE_RANKING

PARAM_COMPOSITE_FLAIR_MODEL

PARAM_USE_GOLD_TAX

PARAM_DISAMBIGUATE_BY_MAP_LOCATION

PARAM_TRANSFORMER_RANKING_MODEL

PARAM_TRY_ORTHOLOGS

PARAM_SPLIT_AT_SLASH

PARAM_MERGE_CONTINUOUS_GENE_ANNOTATIONS

PARAM_REPLACE_ML_MENTIONS_WITH_LONGER_GAZETTEER_MENTIONS

PARAM_SYNONYM_SEARCH_MODE

VALUE_CNF_RELEVANCE_SIGNAL

VALUE_ADDITIONAL_SEARCH

VALUE_ALL

VALUE_NONE

PARAM_ADD_SPECIES_PREFIX_STRIPPED_VARIANT_AS_GENENAME_ALTERNATIVE

PARAM_REMOVE_SPECIES_PREFIXES_FOR_CANDIDATE_RETRIEVAL

PARAM_ADD_CONTEXT_GENES_AS_LUCENE_RELEVANCE_SIGNAL

PARAM_USE_APPOSITIONS_AS_LUCENE_RELEVANCE_SIGNAL

PARAM_SEARCH_TAX_SPECIFIC_CANDIDATES_FIRST

PARAM_STOP_CANDIDATE_SEARCH_ON_EXACT_MATCH

PARAM_DISAMBIGUATE_EXACT_HITS_BY_ORIGINAL_NAME

PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY

PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING

PARAM_SEARCH_GM_NP_MODE

PARAM_ALTERNATIVE_NAMES_SEARCH_MODE

PARAM_DO_RRF_WITH_CANDIDATE_LISTS

PARAM_USE_QUERY_FIELD_WEIGHTS

PARAM_SORT_CANDIDATES_BY_MATCHED_FIELD

PARAM_TOP_N_CANDIDATES_RERANKING

PARAM_USE_JARO_WINKLER_FEATURES

PARAM_USE_TOKEN_JARO_FEATURES

PARAM_USE_LEVENSHTEIN_FEATURES

PARAM_USE_SMITHWATERMAN_FEATURES

PARAM_USE_NEEDLEMANWUNSCH_FEATURES

PARAM_USE_JACCARD_FEATURES

PARAM_USE_TFIDF_FEATURES

PARAM_USE_SCORER_AVERAGE

PARAM_CONTEXT_GENE_FEATURE_GENERATION

PARAM_USE_TOKEN_FEATURES