Twease Evaluation
A B C D E F G H I J L M N O P Q R S T U V W

A

AbstractPassageConsensus - Class in evaluation.passage
Abstract class that implements a simple conversion of EvaluationLineItem objects into Range objects so that classes implementing PassageConsensus don't need to worry about conversion details.
AbstractPassageConsensus() - Constructor for class evaluation.passage.AbstractPassageConsensus
 
addConcept(String) - Method in class trec.xml.topics.Concepts
 
addConcept(int, String) - Method in class trec.xml.topics.Concepts
 
addDocument(Document) - Method in class evaluation.xml.relevancejudgements.Topic
 
addDocument(int, Document) - Method in class evaluation.xml.relevancejudgements.Topic
 
addInputFilename(String) - Method in class evaluation.LegalSpanValidator
 
addInputFilename(String) - Method in class evaluation.passage.PassageConsensusEvaluation
 
addInteraction(Interaction) - Method in class evaluation.Evaluate
 
addItem(Item) - Method in class evaluation.xml.searchresults.TopicResult
 
addItem(int, Item) - Method in class evaluation.xml.searchresults.TopicResult
 
addMolecule(NamedMolecule) - Method in class sigpath.Interaction
 
addOptionalParameterToUrl(MutableString, String, String) - Method in class pubmed.EUtility
Add an optional variable to the exiting url.
addOverlapFile(List<OverlapFile>, File) - Method in class edu.cornell.med.icb.omim.OmimUtil
Add the candidate OverlapFile to the collection if it meets the specified criteria.
addPubMedResultForRank(int, RankResult) - Method in class evaluation.PrecisionResult
 
addRelevantPMID(String) - Method in class sigpath.Interaction
 
addTopic(Topic) - Method in class evaluation.Judgements
 
addTopic(Topic) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
addTopic(int, Topic) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
addTopic(Topic) - Method in class trec.xml.topics.Topics
 
addTopic(int, Topic) - Method in class trec.xml.topics.Topics
 
addTopicResult(TopicResult) - Method in class evaluation.xml.searchresults.SearchResults
 
addTopicResult(int, TopicResult) - Method in class evaluation.xml.searchresults.SearchResults
 
addTweaseItem(Collection<Item>, int, String, int, double, double, SelectedInterval[]) - Method in class evaluation.Evaluator
 
addTweaseResultForRank(int, RankResult) - Method in class evaluation.PrecisionResult
 
appendEvaluationLineForFile(String, String) - Method in class evaluation.passage.PassageConsensusEvaluation
 
appendEvaluationLineForFile(String, EvaluationLineItem) - Method in class evaluation.passage.PassageConsensusEvaluation
 
articleParsed(Article, MutableString) - Method in class edu.cornell.med.icb.omim.OmimUtil
The callback from parsing the XML.

B

baseQuery - Variable in class evaluation.Evaluate
 

C

calculateMAP(Judgements, SearchResults) - Method in class evaluation.PrecisionRecallAtRank
 
calculatePassageConsensus() - Method in class evaluation.passage.PassageConsensusEvaluation
 
CalculatePassagesForRun - Class in evaluation
Calculate passages for a combination of runs with or without passage information.
CalculatePassagesForRun() - Constructor for class evaluation.CalculatePassagesForRun
 
calculateSequenceStats - Variable in class evaluation.Evaluate
 
characters(char[], int, int) - Method in class pubmed.xml.EInfoHandler
 
characters(char[], int, int) - Method in class pubmed.xml.ESearchHandler
 
characters(char[], int, int) - Method in class sigpath.SigpathXMLHandler
 
characters(char[], int, int) - Method in class synonyms.SynonymHandler
 
combineScores(float, float, Item) - Method in class fusion.InnerWeightRankFusion
 
combineScores(float, float, Item) - Method in class fusion.RankFusion
 
combineScores(float, float, Item) - Method in class fusion.SumOfScoresRankFusion
 
compare(Item, Item) - Method in class fusion.DocumentScoreComparator
Perform a comparison of to Items.
compare(Item, Item) - Method in class fusion.PassageScoreComparator
Perform a comparison of to Items.
compare(Item, Item) - Method in class fusion.ScoreSubscoreComparator
Perform a comparison of to Items.
COMPOSITION_RESIDUES_TYPES - Static variable in class evaluation.Evaluate
 
Concepts - Class in trec.xml.topics
Class Concepts.
Concepts() - Constructor for class trec.xml.topics.Concepts
 
ConceptsDescriptor - Class in trec.xml.topics
Class ConceptsDescriptor.
ConceptsDescriptor() - Constructor for class trec.xml.topics.ConceptsDescriptor
 
conditionFilename - Variable in class evaluation.Evaluate
 
conditions - Variable in class evaluation.Evaluate
 
configure(String[]) - Method in class fusion.ItemRanking
Perform actual configuration.
configure(String) - Method in class fusion.ItemRanking
Configure via parameter string, will convert to array for actual configuration.
configure(String[]) - Method in class fusion.ItemRankingByDocumentScore
Configuration method.
configure(String[]) - Method in class fusion.ItemRankingByGradientInterleave
Configuration method.
configure(String[]) - Method in class fusion.ItemRankingByGradientInterleaveByRank
Configuration method.
configure(String[]) - Method in class fusion.ItemRankingByInterleave
Configuration method.
configure(String[]) - Method in class fusion.ItemRankingByPassageScore
Configuration method.
configure(String[]) - Method in class fusion.ItemRankingByScoreThenSubscore
Configuration method.
consensus(EvaluationLineItem...) - Method in class evaluation.passage.AbstractPassageConsensus
Determines a range that is based on the given lines from a trec evaluation file.
consensus(Collection<EvaluationLineItem>) - Method in class evaluation.passage.AbstractPassageConsensus
Determines a range that is based on the given lines from a trec evaluation file.
consensus(Range...) - Method in class evaluation.passage.MeanConsensus
Returns a range that is the mean overlap of the given ranges.
consensus(Range...) - Method in class evaluation.passage.MedianConsensus
Returns a range that is the median overlap of the given ranges.
consensus(Range...) - Method in interface evaluation.passage.PassageConsensus
Determines a range that is based on the given ranges.
consensus(EvaluationLineItem...) - Method in interface evaluation.passage.PassageConsensus
Determines a range that is based on the given lines from a trec evaluation file.
consensus(Collection<EvaluationLineItem>) - Method in interface evaluation.passage.PassageConsensus
Determines a range that is based on the given lines from a trec evaluation file.
consensus(Range...) - Method in class evaluation.passage.UnionConsensus
Returns a range that is the maximal overlap (union) of the given ranges.
convertMedPostStringToConceptList(String) - Static method in class evaluation.EvalTopicUtils
The incoming string needs to be in MedPost format.
convertMedPostStringToConceptList(String, boolean) - Static method in class evaluation.EvalTopicUtils
This version exists so TestEvalTopicUtils can have a simplified (non-fancy) output that isn't decorated with quotes, parens, etc.
convertResultsToItems(ArrayList<ResultItem>) - Method in class evaluation.Evaluator
 
convertSigPathToTopics() - Method in class evaluation.Evaluate
Convert a SigPath XML file to a trec topics.
copy() - Method in class evaluation.TweaseRunExperimentalCondition
Return a copy of this condition.
CornellMedDepartments - Enum in edu.cornell.med
Enum to track the WMC departments and keywords to help search text to determine the department.
createRange(EvaluationLineItem) - Static method in class evaluation.EvaluationUtils
Create a Range from an EvaluationLineItem.
createRange(int, int) - Static method in class evaluation.EvaluationUtils
Create a Range int start with int length.

D

debug - Static variable in class evaluation.Evaluate
 
DEFAULT_MAX - Static variable in class fusion.ItemRankingByGradientInterleave
 
DEFAULT_MAX - Static variable in class fusion.ItemRankingByGradientInterleaveByRank
 
DEFAULT_MAX_PASSAGES_PER_DOCUMENT - Static variable in class fusion.ItemRankingByInterleave
 
DEFAULT_PAGE_SIZE - Static variable in class evaluation.TweaseRunExperimentalCondition
Default number of results per query.
DEFAULT_QUERY_DISTRIBUTOR_CLASSNAME - Static variable in class evaluation.Evaluate
 
DEFAULT_QUERY_EXPANDER_CLASSNAME - Static variable in class evaluation.Evaluate
 
DEFAULT_TERM_SELECTION - Static variable in class evaluation.Evaluate
 
delay - Variable in class evaluation.Evaluate
 
deleteLength() - Method in class evaluation.xml.searchresults.Item
 
deleteRank() - Method in class evaluation.xml.searchresults.Item
 
deleteScore() - Method in class evaluation.xml.searchresults.Item
 
deleteStartPos() - Method in class evaluation.xml.searchresults.Item
 
deleteSubScore() - Method in class evaluation.xml.searchresults.Item
 
describeParams() - Method in class fusion.ItemRanking
Describe JUST the paramters of the ItemRanking.
describeParams() - Method in class fusion.ItemRankingByDocumentScore
Desciption of parameters.
describeParams() - Method in class fusion.ItemRankingByGradientInterleave
Desciption of parameters.
describeParams() - Method in class fusion.ItemRankingByGradientInterleaveByRank
Desciption of parameters.
describeParams() - Method in class fusion.ItemRankingByInterleave
Desciption of parameters.
describeParams() - Method in class fusion.ItemRankingByPassageScore
Desciption of parameters.
describeParams() - Method in class fusion.ItemRankingByScoreThenSubscore
Desciption of parameters.
doBlindQueryExpansion - Variable in class evaluation.Evaluate
 
Document - Class in evaluation.xml.relevancejudgements
Class Document.
Document() - Constructor for class evaluation.xml.relevancejudgements.Document
 
document - Variable in class fusion.DocumentRank
 
DocumentDescriptor - Class in evaluation.xml.relevancejudgements
Class DocumentDescriptor.
DocumentDescriptor() - Constructor for class evaluation.xml.relevancejudgements.DocumentDescriptor
 
documentIds(Topic) - Method in class evaluation.Judgements
 
DocumentRank - Class in fusion
 
DocumentRank() - Constructor for class fusion.DocumentRank
 
documentRankingMap - Variable in class fusion.RankFusion2
Used for combining runs based on document scores.
DocumentScoreComparator - Class in fusion
This comparator does the re-ranking of the Item elements by document score.
DocumentScoreComparator() - Constructor for class fusion.DocumentScoreComparator
 

E

edu.cornell.med - package edu.cornell.med
 
edu.cornell.med.icb.omim - package edu.cornell.med.icb.omim
OMIM utility package (disease/protein overlaps, etc).
edu.cornell.med.icb.wmcpubs - package edu.cornell.med.icb.wmcpubs
 
EInfo - Class in pubmed
 
EInfo(String) - Constructor for class pubmed.EInfo
 
EInfoHandler - Class in pubmed.xml
 
EInfoHandler() - Constructor for class pubmed.xml.EInfoHandler
 
elementContents - Variable in class pubmed.xml.ESearchHandler
 
end() - Method in class evaluation.Timer
 
endElement(String, String, String) - Method in class pubmed.xml.EInfoHandler
 
endElement(String, String, String) - Method in class pubmed.xml.ESearchHandler
 
endElement(String, String, String) - Method in class sigpath.SigpathXMLHandler
 
endElement(String, String, String) - Method in class synonyms.SynonymHandler
 
enrichQuery(QueryExpander, QueryExecutionState, TweaseRunExperimentalCondition, Set<TermWeight>, String, QueryDistributor) - Method in class evaluation.Evaluator
 
enumerateConcept() - Method in class trec.xml.topics.Concepts
Method enumerateConcept
enumerateDocument() - Method in class evaluation.xml.relevancejudgements.Topic
Method enumerateDocument
enumerateItem() - Method in class evaluation.xml.searchresults.TopicResult
Method enumerateItem
enumerateTopic() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method enumerateTopic
enumerateTopic() - Method in class trec.xml.topics.Topics
Method enumerateTopic
enumerateTopicResult() - Method in class evaluation.xml.searchresults.SearchResults
Method enumerateTopicResult
equals(Object) - Method in class evaluation.TopicIdDocItem
 
ESearch - Class in pubmed
 
ESearch(String) - Constructor for class pubmed.ESearch
 
ESearchHandler - Class in pubmed.xml
 
ESearchHandler() - Constructor for class pubmed.xml.ESearchHandler
 
EUtility - Class in pubmed
Abstract class for fetching data from PubMed.
EUtility() - Constructor for class pubmed.EUtility
 
EvalTopicUtils - Class in evaluation
Utility class to handle MedPost related functions.
EvalTopicUtils() - Constructor for class evaluation.EvalTopicUtils
 
Evaluate - Class in evaluation
 
Evaluate() - Constructor for class evaluation.Evaluate
 
evaluation - package evaluation
 
evaluation.passage - package evaluation.passage
 
evaluation.xml.relevancejudgements - package evaluation.xml.relevancejudgements
 
evaluation.xml.searchresults - package evaluation.xml.searchresults
 
EvaluationLineItem - Class in evaluation
Represents a single line of a trec evaluation file.
EvaluationLineItem(String) - Constructor for class evaluation.EvaluationLineItem
Create an object based on a line of text from an evaluation file.
EvaluationLineItem(String, String) - Constructor for class evaluation.EvaluationLineItem
Create an object based on a line of text from an evaluation file.
EvaluationLineItem(String, String[]) - Constructor for class evaluation.EvaluationLineItem
Create an object based on tokens extracted from line of text of an evaluation file.
EvaluationResults - Class in evaluation
TODO: document this class.
EvaluationResults(boolean, boolean) - Constructor for class evaluation.EvaluationResults
 
EvaluationResults() - Constructor for class evaluation.EvaluationResults
 
EvaluationUtils - Class in evaluation
Utility methods that deal with passage calculation during the Evaluate stage.
Evaluator - Class in evaluation
Comparator class for topics by topic id, ascending.
Evaluator() - Constructor for class evaluation.Evaluator
 
extractConceptFromTopic(String) - Static method in class evaluation.EvalTopicUtils
Trec 2007 topics come in the format of What [TOXICITIES] are associated with zoledronic acid? this method will return the string "toxicities" or null if the [WORD] isn't found.

F

fancify(String) - Static method in class evaluation.EvalTopicUtils
Fancify a concept, decorate it with parens and quotes.
filenameSafe(String) - Static method in class edu.cornell.med.icb.omim.ProteinToPmidsEvaluate
 
filenameString() - Method in class evaluation.TweaseRunExperimentalCondition
Generate a filename for this condition.
filenameWithoutSuffix(String, String) - Static method in class edu.cornell.med.icb.omim.OmimUtil
Remove a suffix off a filename.
filterTerms() - Method in class evaluation.CalculatePassagesForRun
Take termSet and make an MutableString[] with the terms to use.
find() - Method in class edu.cornell.med.icb.wmcpubs.FindWmcPubs
 
findProteinDiseaseOverlaps() - Method in class edu.cornell.med.icb.omim.OmimUtil
Read the proteins and diseases, write the overlaps of the PMIDs.
FindWmcPubs - Class in edu.cornell.med.icb.wmcpubs
Find WMC publications
FindWmcPubs() - Constructor for class edu.cornell.med.icb.wmcpubs.FindWmcPubs
 
formattedOutput(MutableString) - Method in class sirt.search.SearchHit
 
fusedResults - Variable in class fusion.RankFusion
 
fusedResults - Variable in class fusion.RankFusion2
 
fuseRuns() - Method in class fusion.RankFusion
 
fuseRuns() - Method in class fusion.RankFusion2
 
fusion - package fusion
 

G

generateDocMapId(Item) - Method in class fusion.RankFusion
 
generateDocMapId(Item) - Method in class fusion.RankFusion2
 
generateOrsFromOverlaps() - Method in class edu.cornell.med.icb.omim.OmimUtil
This algorithm is based on the Javascript from the page http://www.hutchon.net/ConfidOR.htm This will calculate the OR (Odds Ratio) for each of the overlaps found from running findProteinDiseaseOverlaps() but filtering out entries who don't have at least MIN_OVERLAPS_TO_GEN_OR overlaps.
generateSingleDiseaseReport() - Method in class edu.cornell.med.icb.omim.OmimUtil
When an overlap can be done from a single eval (no intersection need be performed) this method can be used to output the results as HTML.
genResultFormat(TopicResult, Item) - Method in class fusion.RankFusion
 
genResultFormat(TopicResult, Item) - Method in class fusion.RankFusion2
 
getAccessionCode() - Method in class sirt.search.SearchHit
 
getAccessMode() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getAccessMode
getAccessMode() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getAccessMode
getAccessMode() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getAccessMode
getAccessMode() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getAccessMode
getAccessMode() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getAccessMode
getAccessMode() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getAccessMode
getAccessMode() - Method in class trec.xml.topics.ConceptsDescriptor
Method getAccessMode
getAccessMode() - Method in class trec.xml.topics.TopicDescriptor
Method getAccessMode
getAccessMode() - Method in class trec.xml.topics.TopicsDescriptor
Method getAccessMode
getAliasCount() - Method in class synonyms.SynonymQuery
 
getAllInteractionTypes() - Method in class evaluation.Evaluate
 
getBackgroundTermWeightAdjustmentFactor() - Method in class evaluation.TweaseRunExperimentalCondition
 
getBlindFeedbackQueryComponent() - Method in class evaluation.TrecTopic
 
getBm25ecb() - Method in class evaluation.TweaseRunExperimentalCondition
Get the BM25EC b variable value to use.
getBm25ecFreqType() - Method in class evaluation.TweaseRunExperimentalCondition
Get the BM25EC frequency type to use.
getBm25ecFreqTypeAsString() - Method in class evaluation.TweaseRunExperimentalCondition
Get the BM25EC frequency type to use as a string.
getBm25eck1() - Method in class evaluation.TweaseRunExperimentalCondition
Get the BM25EC k1 variable value to use.
getCharsToFilterRegex() - Method in class evaluation.Evaluate
 
getConcept(int) - Method in class trec.xml.topics.Concepts
Method getConcept
getConcept() - Method in class trec.xml.topics.Concepts
Method getConcept
getConceptCount() - Method in class trec.xml.topics.Concepts
Method getConceptCount
getConcepts() - Method in class trec.xml.topics.Topic
Returns the value of field 'concepts'.
getConceptSubQueries() - Method in class evaluation.TrecTopic
 
getContentForURL(MutableString) - Method in class pubmed.ESearch
 
getContentForURL(MutableString) - Method in class pubmed.EUtility
Base implementation to read the specified URL the parse the content.
getDebugText() - Method in class evaluation.xml.searchresults.Item
Returns the value of field 'debugText'.
getDepartmaneName() - Method in enum edu.cornell.med.CornellMedDepartments
 
getDistributeParameter() - Method in class evaluation.TweaseRunExperimentalCondition
The number of terms that will be in a conjunctive clause.
getDocManager() - Method in class evaluation.Evaluator
 
getDocStoreReader() - Method in class evaluation.Evaluator
 
getDocument(int) - Method in class evaluation.xml.relevancejudgements.Topic
Method getDocument
getDocument() - Method in class evaluation.xml.relevancejudgements.Topic
Method getDocument
getDocumentCount() - Method in class evaluation.xml.relevancejudgements.Topic
Method getDocumentCount
getDocumentCount() - Method in class pubmed.EInfo
 
getDocumentCount() - Method in class pubmed.xml.EInfoHandler
 
getDocumentId() - Method in class evaluation.TopicIdDocItem
 
getDocumentIdsByRank(String, int, Map<String, Item[]>) - Method in class evaluation.EvaluationResults
 
getDocumentIdsByRankAbstractLevel(String, int) - Method in class evaluation.EvaluationResults
 
getDocumentIdsByRankHitLevel(String, int) - Method in class evaluation.EvaluationResults
 
getDocumentIdsByZScore(String, float, Map<String, Item[]>) - Method in class evaluation.EvaluationResults
 
getDocumentIdsByZScoreAbstractLevel(String, int) - Method in class evaluation.EvaluationResults
 
getDocumentIdsByZScoreHitLevel(String, int) - Method in class evaluation.EvaluationResults
 
getElapsedHours() - Method in class evaluation.Timer
 
getElapsedMilliseconds() - Method in class evaluation.Timer
 
getElapsedMinutes() - Method in class evaluation.Timer
 
getElapsedSeconds() - Method in class evaluation.Timer
 
getEmailAddress() - Method in class pubmed.ESearch
Get the email address that will be supplied during the pubmed query.
getEvalLinesForFile(String) - Method in class evaluation.passage.PassageConsensusEvaluation
 
getExponent() - Method in class evaluation.TweaseRunExperimentalCondition
Get the BM25 exponent parameter value.
getExtends() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getExtends
getExtends() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getExtends
getExtends() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getExtends
getExtends() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getExtends
getExtends() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getExtends
getExtends() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getExtends
getExtends() - Method in class trec.xml.topics.ConceptsDescriptor
Method getExtends
getExtends() - Method in class trec.xml.topics.TopicDescriptor
Method getExtends
getExtends() - Method in class trec.xml.topics.TopicsDescriptor
Method getExtends
getFilename() - Method in class evaluation.EvaluationLineItem
 
getFinalQuery() - Method in class evaluation.TrecTopic
 
getFormattedUrl() - Method in class pubmed.ESearch
 
getHitCount() - Method in class evaluation.RankResult
 
getId() - Method in class evaluation.EvaluationLineItem
 
getId() - Method in class evaluation.xml.relevancejudgements.Document
Returns the value of field 'id'.
getId() - Method in class evaluation.xml.relevancejudgements.Topic
Returns the value of field 'id'.
getId() - Method in class evaluation.xml.searchresults.Item
Returns the value of field 'id'.
getId() - Method in class evaluation.xml.searchresults.TopicResult
Returns the value of field 'id'.
getId() - Method in class sigpath.Interaction
 
getId() - Method in class sigpath.NamedMolecule
 
getId() - Method in class trec.xml.topics.Topic
Returns the value of field 'id'.
getIdentity() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getIdentity
getIdentity() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getIdentity
getIdentity() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getIdentity
getIdentity() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getIdentity
getIdentity() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getIdentity
getIdentity() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getIdentity
getIdentity() - Method in class trec.xml.topics.ConceptsDescriptor
Method getIdentity
getIdentity() - Method in class trec.xml.topics.TopicDescriptor
Method getIdentity
getIdentity() - Method in class trec.xml.topics.TopicsDescriptor
Method getIdentity
getIdIntList(String) - Method in class pubmed.ESearch
 
getIdList(String) - Method in class pubmed.ESearch
Perform the actualy pubmed query, return the list of results.
getInputFilenames() - Method in class evaluation.LegalSpanValidator
 
getInputFilenames() - Method in class evaluation.passage.PassageConsensusEvaluation
 
getInteractingNamedMolecules() - Method in class sigpath.Interaction
 
getInteractions() - Method in class evaluation.Evaluate
 
getInteractions() - Method in class sigpath.SigpathCommunicator
 
getInteractions() - Method in class synonyms.SynonymCommunicator
 
getInteractions() - Method in class synonyms.SynonymHandler
 
getInvalidOutputFileExtension() - Method in class evaluation.LegalSpanValidator
 
getItem(int) - Method in class evaluation.xml.searchresults.TopicResult
Method getItem
getItem() - Method in class evaluation.xml.searchresults.TopicResult
Method getItem
getItemCount() - Method in class evaluation.xml.searchresults.TopicResult
Method getItemCount
getItems() - Method in class pubmed.xml.ESearchHandler
 
getJavaClass() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getJavaClass
getJavaClass() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getJavaClass
getJavaClass() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getJavaClass
getJavaClass() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getJavaClass
getJavaClass() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getJavaClass
getJavaClass() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getJavaClass
getJavaClass() - Method in class trec.xml.topics.ConceptsDescriptor
Method getJavaClass
getJavaClass() - Method in class trec.xml.topics.TopicDescriptor
Method getJavaClass
getJavaClass() - Method in class trec.xml.topics.TopicsDescriptor
Method getJavaClass
getKeywords() - Method in enum edu.cornell.med.CornellMedDepartments
 
getLastUpdate() - Method in class pubmed.EInfo
 
getLastUpdate() - Method in class pubmed.xml.EInfoHandler
 
getLength() - Method in class evaluation.EvaluationLineItem
 
getLength() - Method in class evaluation.xml.searchresults.Item
Returns the value of field 'length'.
getManuallyConstructedQuery() - Method in class evaluation.TrecTopic
Obtain the query that was manually tuned.
getMaxDate() - Method in class pubmed.ESearch
Get the ending date.
getMaxResults() - Method in class pubmed.ESearch
Get the number of maximum results to return.
getMedpostTagged() - Method in class trec.xml.topics.Topic
Returns the value of field 'medpostTagged'.
getMinDate() - Method in class pubmed.ESearch
Get the starting date.
getName() - Method in class sigpath.NamedMolecule
 
getNameCount() - Method in class synonyms.SynonymQuery
 
getNamedInteractions() - Method in class sigpath.SigpathXMLHandler
 
getNamedMolecules() - Method in class evaluation.Evaluate
 
getNamedMolecules() - Method in class sigpath.SigpathCommunicator
 
getNamedMolecules() - Method in class sigpath.SigpathXMLHandler
 
getNameSpacePrefix() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class trec.xml.topics.ConceptsDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class trec.xml.topics.TopicDescriptor
Method getNameSpacePrefix
getNameSpacePrefix() - Method in class trec.xml.topics.TopicsDescriptor
Method getNameSpacePrefix
getNameSpaceURI() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class trec.xml.topics.ConceptsDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class trec.xml.topics.TopicDescriptor
Method getNameSpaceURI
getNameSpaceURI() - Method in class trec.xml.topics.TopicsDescriptor
Method getNameSpaceURI
getNarrative() - Method in class evaluation.TrecTopic
Obtain the narrative for this topic.
getNarrative() - Method in class trec.xml.topics.Topic
Returns the value of field 'narrative'.
getOriginalLength() - Method in class evaluation.EvaluationLineItem
 
getOriginalScore() - Method in class evaluation.EvaluationLineItem
 
getOriginalStart() - Method in class evaluation.EvaluationLineItem
 
getOriginalSubscore() - Method in class evaluation.EvaluationLineItem
 
getOutputFileExtension() - Method in class evaluation.passage.PassageConsensusEvaluation
 
getOutputFilename() - Method in class fusion.RankFusion
 
getOutputFilename() - Method in class fusion.RankFusion2
 
getOverlappingItems() - Method in class evaluation.EvaluationLineItem
 
getOverlappingRange(Range, Range) - Static method in class evaluation.EvaluationUtils
Returns the range that represents the overlap (intersection) of two ranges.
getPageSize() - Method in class evaluation.TweaseRunExperimentalCondition
Get the max number of results to be gathered per query.
getParseParameters() - Method in class evaluation.TweaseRunExperimentalCondition
 
getPassageBoundary() - Method in class evaluation.TweaseRunExperimentalCondition
Get the passage boundry for this condition.
getPassageConsensus() - Method in class evaluation.passage.PassageConsensusEvaluation
 
getPassageScorer() - Method in class evaluation.TweaseRunExperimentalCondition
Get the passage scorer object (will create it if it hasn't already been created for this condition).
getPassageScorerClassName() - Method in class evaluation.TweaseRunExperimentalCondition
Get the passage scorer class name.
getPassagesPerDocument() - Method in class evaluation.TweaseRunExperimentalCondition
The max number of passages returned for a single document when doing passage scoring.
getPassageTokenizer() - Method in class evaluation.TweaseRunExperimentalCondition
Get the passage scorer object (will create it if it hasn't already been created for this condition).
getPassageTokenizerClassName() - Method in class evaluation.TweaseRunExperimentalCondition
Get the passage tokenizer class name.
getPmid() - Method in class synonyms.Synonym
 
getPrecision() - Method in class evaluation.RankResult
 
getPubmedRankResults() - Method in class evaluation.PrecisionResult
 
getPubMedResultForRank(int) - Method in class evaluation.PrecisionResult
 
getPubmedUniquePMIDCount() - Method in class evaluation.PrecisionResult
 
getQuery() - Method in class synonyms.SynonymQuery
 
getQuery() - Method in class trec.xml.topics.Topic
Returns the value of field 'query'.
getQueryDistributor() - Method in class evaluation.TweaseRunExperimentalCondition
Get the query distributor object (will create it if it hasn't already been created for this condition).
getQueryDistributorClassName() - Method in class evaluation.TweaseRunExperimentalCondition
Get the query distributor class name.
getQueryExpander() - Method in class evaluation.TweaseRunExperimentalCondition
 
getQueryExpanderClassName() - Method in class evaluation.TweaseRunExperimentalCondition
Get the query expander class name.
getQueryTerms() - Method in class evaluation.TweaseRunExperimentalCondition
Get the query terms.
getRank() - Method in class evaluation.EvaluationLineItem
 
getRank() - Method in class evaluation.RankResult
 
getRank() - Method in class evaluation.TopicIdDocItem
 
getRank() - Method in class evaluation.xml.searchresults.Item
Returns the value of field 'rank'.
getRelevantPubmedIDs() - Method in class sigpath.Interaction
 
getResultCount() - Method in class pubmed.xml.ESearchHandler
 
getRunId() - Method in class evaluation.EvaluationLineItem
 
getRunId() - Method in class evaluation.Evaluator
 
getRunId() - Method in class evaluation.TopicIdDocItem
 
getRunId() - Method in class evaluation.xml.searchresults.SearchResults
Returns the value of field 'runId'.
getRunType() - Method in class evaluation.TweaseRunExperimentalCondition
Get the run type that will be used.
getScore() - Method in class evaluation.EvaluationLineItem
 
getScore() - Method in class evaluation.xml.searchresults.Item
Returns the value of field 'score'.
getScore() - Method in class sirt.search.SearchHit
 
getScoreComponent(float, Item) - Method in class fusion.InnerWeightRankFusion
 
getScoreComponent(float, Item) - Method in class fusion.RankFusion
 
getScoreComponent(float, Item) - Method in class fusion.SumOfScoresRankFusion
 
getScorerName() - Method in class evaluation.TweaseRunExperimentalCondition
Get the scorer name to use.
getScorerOpts(TweaseRunExperimentalCondition) - Method in class evaluation.Evaluator
 
getSign() - Method in class evaluation.TweaseRunExperimentalCondition
Get the BM25 sign parameter value.
getSliderValue() - Method in class evaluation.TweaseRunExperimentalCondition
Get the slider value to use.
getSpid() - Method in class sigpath.Interaction
 
getSpid() - Method in class sigpath.NamedMolecule
 
getSpid() - Method in class synonyms.Synonym
 
getStart() - Method in class evaluation.EvaluationLineItem
 
getStartPos() - Method in class evaluation.xml.searchresults.Item
Returns the value of field 'startPos'.
getSubscore() - Method in class evaluation.EvaluationLineItem
 
getSubScore() - Method in class evaluation.xml.searchresults.Item
Returns the value of field 'subScore'.
getSuggestedExpandedQuery() - Method in class evaluation.TrecTopic
 
getSynonymMap() - Method in class synonyms.Synonym
 
getSynonyms() - Method in class synonyms.Synonym
 
getTag() - Method in class evaluation.TweaseRunExperimentalCondition
Get the tag for this condition (helpful to differientiage different runs).
getTerms() - Method in class trec.xml.topics.Topic
Returns the value of field 'terms'.
getTool() - Method in class pubmed.EUtility
 
getTopic() - Method in class evaluation.EvaluationLineItem
 
getTopic() - Method in class evaluation.Judgements
 
getTopic(String) - Method in class evaluation.Judgements
 
getTopic(int) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method getTopic
getTopic() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method getTopic
getTopic(int) - Method in class trec.xml.topics.Topics
Method getTopic
getTopic() - Method in class trec.xml.topics.Topics
Method getTopic
getTopicCount() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method getTopicCount
getTopicCount() - Method in class trec.xml.topics.Topics
Method getTopicCount
getTopicIdentifier() - Method in class evaluation.TrecTopic
 
getTopicIdNumber() - Method in class evaluation.TopicIdDocItem
 
getTopicIds() - Method in class evaluation.EvaluationResults
 
getTopicIdToAbstractLevelSearchResult() - Method in class evaluation.EvaluationResults
 
getTopicIdToSentenceLevelSearchResult() - Method in class evaluation.EvaluationResults
 
getTopicNumber(String) - Method in class evaluation.Judgements
 
getTopicResult(int) - Method in class evaluation.xml.searchresults.SearchResults
Method getTopicResult
getTopicResult() - Method in class evaluation.xml.searchresults.SearchResults
Method getTopicResult
getTopicResultCount() - Method in class evaluation.xml.searchresults.SearchResults
Method getTopicResultCount
getTotalCount() - Method in class evaluation.RankResult
 
getTotalTermCount() - Method in class synonyms.SynonymQuery
 
getTrecEvalString2006(TrecTopic, Collection<Item>, int, DocumentStoreReader, DocumentIndexManager, String) - Static method in class evaluation.Evaluate
Format of each line is as follows:
getTrecEvalString2006(TrecTopic, Collection<Item>, int, DocumentStoreReader, DocumentIndexManager) - Static method in class evaluation.Evaluator
 
getTrecEvalStringLegacy(TrecTopic, Collection<Item>, int, String, boolean) - Static method in class evaluation.Evaluate
 
getTweaseOccurence() - Method in class sigpath.Interaction
 
getTweaseRankResults() - Method in class evaluation.PrecisionResult
 
getTweaseResultForRank(int) - Method in class evaluation.PrecisionResult
 
getTweaseResultItems() - Method in class sigpath.Interaction
 
getTweaseUniquePMIDCount() - Method in class evaluation.PrecisionResult
 
getTweaseUniquePMIDsAtRank(int) - Method in class sigpath.Interaction
 
getType() - Method in class sigpath.Interaction
 
getUrl() - Method in enum edu.cornell.med.CornellMedDepartments
 
getValidator() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getValidator
getValidator() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getValidator
getValidator() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getValidator
getValidator() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getValidator
getValidator() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getValidator
getValidator() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getValidator
getValidator() - Method in class trec.xml.topics.ConceptsDescriptor
Method getValidator
getValidator() - Method in class trec.xml.topics.TopicDescriptor
Method getValidator
getValidator() - Method in class trec.xml.topics.TopicsDescriptor
Method getValidator
getValidOutputFileExtension() - Method in class evaluation.LegalSpanValidator
 
getXMLName() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method getXMLName
getXMLName() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method getXMLName
getXMLName() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method getXMLName
getXMLName() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method getXMLName
getXMLName() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method getXMLName
getXMLName() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method getXMLName
getXMLName() - Method in class trec.xml.topics.ConceptsDescriptor
Method getXMLName
getXMLName() - Method in class trec.xml.topics.TopicDescriptor
Method getXMLName
getXMLName() - Method in class trec.xml.topics.TopicsDescriptor
Method getXMLName

H

handshakeWithEntrez() - Method in class evaluation.Evaluator
 
hashCode() - Method in class evaluation.TopicIdDocItem
 
hasLength() - Method in class evaluation.xml.searchresults.Item
Method hasLength
hasRank() - Method in class evaluation.xml.searchresults.Item
Method hasRank
hasScore() - Method in class evaluation.xml.searchresults.Item
Method hasScore
hasStartPos() - Method in class evaluation.xml.searchresults.Item
Method hasStartPos
hasSubScore() - Method in class evaluation.xml.searchresults.Item
Method hasSubScore

I

initialCombinedScore() - Method in class fusion.RankFusion
 
initialCombinedScore() - Method in class fusion.RankFusion2
 
initializeQueryEngine() - Method in class evaluation.Evaluator
 
initStatWriter() - Method in class evaluation.Evaluate
 
InnerWeightRankFusion - Class in fusion
 
InnerWeightRankFusion() - Constructor for class fusion.InnerWeightRankFusion
 
inResultSet - Variable in class pubmed.xml.ESearchHandler
 
Interaction - Class in sigpath
 
Interaction() - Constructor for class sigpath.Interaction
 
interactions - Variable in class evaluation.Evaluate
 
InteractionWriter - Class in evaluation
 
InteractionWriter() - Constructor for class evaluation.InteractionWriter
 
isAddBackgroundTerms() - Method in class evaluation.TweaseRunExperimentalCondition
 
isConsensusRangeUpdated() - Method in class evaluation.EvaluationLineItem
 
isDoBlindQueryExpansion() - Method in class evaluation.TweaseRunExperimentalCondition
True if blind query expansion will be performed.
isDocumentRelevant(Topic, String) - Method in class evaluation.Judgements
Return True if a document is relevant to a topic.
isDoPassageRetrieval() - Method in class evaluation.TweaseRunExperimentalCondition
True if passage retrieval should be performed.
isElementDefinition() - Method in class evaluation.xml.relevancejudgements.DocumentDescriptor
Method isElementDefinition
isElementDefinition() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
Method isElementDefinition
isElementDefinition() - Method in class evaluation.xml.relevancejudgements.TopicDescriptor
Method isElementDefinition
isElementDefinition() - Method in class evaluation.xml.searchresults.ItemDescriptor
Method isElementDefinition
isElementDefinition() - Method in class evaluation.xml.searchresults.SearchResultsDescriptor
Method isElementDefinition
isElementDefinition() - Method in class evaluation.xml.searchresults.TopicResultDescriptor
Method isElementDefinition
isElementDefinition() - Method in class trec.xml.topics.ConceptsDescriptor
Method isElementDefinition
isElementDefinition() - Method in class trec.xml.topics.TopicDescriptor
Method isElementDefinition
isElementDefinition() - Method in class trec.xml.topics.TopicsDescriptor
Method isElementDefinition
isExtend() - Method in class evaluation.LegalSpanValidator
 
isKeepReferences() - Method in enum edu.cornell.med.CornellMedDepartments
 
isQueryExpanded() - Method in class evaluation.TrecTopic
Returns true if the expanded query component has already been calculated.
isRerank() - Method in class evaluation.LegalSpanValidator
 
isShortFilenames() - Method in class evaluation.TweaseRunExperimentalCondition
True if short filenames should be written.
isTextContainsKeyword(String) - Method in enum edu.cornell.med.CornellMedDepartments
 
isValid() - Method in class evaluation.xml.relevancejudgements.Document
Method isValid
isValid() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method isValid
isValid() - Method in class evaluation.xml.relevancejudgements.Topic
Method isValid
isValid() - Method in class evaluation.xml.searchresults.Item
Method isValid
isValid() - Method in class evaluation.xml.searchresults.SearchResults
Method isValid
isValid() - Method in class evaluation.xml.searchresults.TopicResult
Method isValid
isValid() - Method in class trec.xml.topics.Concepts
Method isValid
isValid() - Method in class trec.xml.topics.Topic
Method isValid
isValid() - Method in class trec.xml.topics.Topics
Method isValid
isVerbose() - Method in class evaluation.LegalSpanValidator
 
Item - Class in evaluation.xml.searchresults
Class Item.
Item() - Constructor for class evaluation.xml.searchresults.Item
 
ItemDescriptor - Class in evaluation.xml.searchresults
Class ItemDescriptor.
ItemDescriptor() - Constructor for class evaluation.xml.searchresults.ItemDescriptor
 
ItemRanking - Class in fusion
Abstract class for reranking items.
ItemRanking() - Constructor for class fusion.ItemRanking
 
ItemRankingByDocumentScore - Class in fusion
Class for reranking items by document score (item score).
ItemRankingByDocumentScore() - Constructor for class fusion.ItemRankingByDocumentScore
 
ItemRankingByGradientInterleave - Class in fusion
Class for reranking items by interleaving the document score-subScore values.
ItemRankingByGradientInterleave() - Constructor for class fusion.ItemRankingByGradientInterleave
 
ItemRankingByGradientInterleaveByRank - Class in fusion
Class for reranking items by interleaving the document score-subScore values.
ItemRankingByGradientInterleaveByRank() - Constructor for class fusion.ItemRankingByGradientInterleaveByRank
 
ItemRankingByInterleave - Class in fusion
Class for reranking items by interleaving the document score-subScore values.
ItemRankingByInterleave() - Constructor for class fusion.ItemRankingByInterleave
 
ItemRankingByPassageScore - Class in fusion
Class for reranking items by passage score (item subScore).
ItemRankingByPassageScore() - Constructor for class fusion.ItemRankingByPassageScore
 
ItemRankingByScoreThenSubscore - Class in fusion
Class for reranking items by score then subscore.
ItemRankingByScoreThenSubscore() - Constructor for class fusion.ItemRankingByScoreThenSubscore
 
iterateConcept() - Method in class trec.xml.topics.Concepts
Method iterateConcept
iterateDocument() - Method in class evaluation.xml.relevancejudgements.Topic
Method iterateDocument
iterateItem() - Method in class evaluation.xml.searchresults.TopicResult
Method iterateItem
iterateTopic() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method iterateTopic
iterateTopic() - Method in class trec.xml.topics.Topics
Method iterateTopic
iterateTopicResult() - Method in class evaluation.xml.searchresults.SearchResults
Method iterateTopicResult

J

judgementFilename - Variable in class evaluation.Evaluate
 
Judgements - Class in evaluation
TODO: document this class
Judgements() - Constructor for class evaluation.Judgements
 

L

legacyAsGenScorable - Variable in class evaluation.Evaluate
 
LegalSpanValidator - Class in evaluation
Tool used to process trec legal span file and remove passages that are not within an "official" legal span.
LegalSpanValidator() - Constructor for class evaluation.LegalSpanValidator
Create a new legal span object.
LegalSpanValidator.ValidationResult - Enum in evaluation
Possible return values from ValidateEntry..
listToString(List<String>) - Method in class edu.cornell.med.icb.wmcpubs.FindWmcPubs
 
loadJudgements(String) - Method in class evaluation.Judgements
 
loadPubmedFileDisc(File) - Static method in class edu.cornell.med.icb.wmcpubs.FindWmcPubs
Load a serialized PubMedInfo file from the specified File.
loadSearchResults(String) - Method in class evaluation.EvaluationResults
 

M

main(String[]) - Static method in class edu.cornell.med.icb.omim.OmimUtil
Read the command line arguments, start the program.
main(String[]) - Static method in class edu.cornell.med.icb.omim.ProteinToPmidsEvaluate
 
main(String[]) - Static method in class edu.cornell.med.icb.wmcpubs.FindWmcPubs
 
main(String[]) - Static method in class evaluation.CalculatePassagesForRun
 
main(String[]) - Static method in class evaluation.Evaluate
 
main(String[]) - Static method in class evaluation.InteractionWriter
 
main(String[]) - Static method in class evaluation.LegalSpanValidator
 
main(String[]) - Static method in class evaluation.passage.PassageConsensusEvaluation
 
main(String[]) - Static method in class evaluation.PrecisionRecallAtRank
 
main(String[]) - Static method in class evaluation.ProduceFakeJudgements
 
main(String[]) - Static method in class evaluation.ResultsToJudgements
 
main(String[]) - Static method in class evaluation.SigPathEvaluator
 
main(String[]) - Static method in class fusion.RankFusion
 
main(String[]) - Static method in class fusion.RankFusion2
 
main(String[]) - Static method in class trec.TrecEvaluate
Deprecated. Perform a Trec evaluation.
makePmidLink(String) - Method in class edu.cornell.med.icb.wmcpubs.FindWmcPubs
 
map - Variable in class fusion.RankFusion
{topic -> {(doc -> combinedScore)}}.
marshal(Writer) - Method in class evaluation.xml.relevancejudgements.Document
 
marshal(ContentHandler) - Method in class evaluation.xml.relevancejudgements.Document
 
marshal(Writer) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
marshal(ContentHandler) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
marshal(Writer) - Method in class evaluation.xml.relevancejudgements.Topic
 
marshal(ContentHandler) - Method in class evaluation.xml.relevancejudgements.Topic
 
marshal(Writer) - Method in class evaluation.xml.searchresults.Item
 
marshal(ContentHandler) - Method in class evaluation.xml.searchresults.Item
 
marshal(Writer) - Method in class evaluation.xml.searchresults.SearchResults
 
marshal(ContentHandler) - Method in class evaluation.xml.searchresults.SearchResults
 
marshal(Writer) - Method in class evaluation.xml.searchresults.TopicResult
 
marshal(ContentHandler) - Method in class evaluation.xml.searchresults.TopicResult
 
marshal(Writer) - Method in class trec.xml.topics.Concepts
 
marshal(ContentHandler) - Method in class trec.xml.topics.Concepts
 
marshal(Writer) - Method in class trec.xml.topics.Topic
 
marshal(ContentHandler) - Method in class trec.xml.topics.Topic
 
marshal(Writer) - Method in class trec.xml.topics.Topics
 
marshal(ContentHandler) - Method in class trec.xml.topics.Topics
 
MAX_PASSAGES_PER_DOCUMENT - Static variable in class evaluation.Evaluate
 
maxTimesDocFused - Variable in class fusion.RankFusion
 
MeanConsensus - Class in evaluation.passage
Determine passage consensus based on the mean of all the ranges.
MeanConsensus() - Constructor for class evaluation.passage.MeanConsensus
Creates a new PassageConsensus object.
MedianConsensus - Class in evaluation.passage
Determine passage consensus based on the median of all the ranges.
MedianConsensus() - Constructor for class evaluation.passage.MedianConsensus
Creates a new PassageConsensus object.
moleculeWithID(String) - Method in class sigpath.SigpathXMLHandler
 

N

NamedMolecule - Class in sigpath
 
NamedMolecule() - Constructor for class sigpath.NamedMolecule
 
namedMolecules - Variable in class evaluation.Evaluate
 
noTrecGen - Variable in class evaluation.Evaluate
 

O

obtainItemRanker(String) - Static method in class fusion.ItemRanking
Create an ItemRanking object by description.
obtainQueryResults(TrecTopic, TweaseRunExperimentalCondition) - Method in class evaluation.Evaluator
 
obtainQueryResults(TrecTopic, TweaseRunExperimentalCondition, QueryExecutionPlan) - Method in class evaluation.Evaluator
 
obtainRunType(String) - Static method in class evaluation.TweaseRunExperimentalCondition
Obtain a RunType from the run type's string value.
obtainTermSelection(String) - Static method in class evaluation.Evaluate
 
OmimUtil - Class in edu.cornell.med.icb.omim
Work with OMIM files that have already been processed to either Disease->PMIDs or Protein->PMIds.
OmimUtil() - Constructor for class edu.cornell.med.icb.omim.OmimUtil
Configure the class.
orderData(List<OverlapFile>, OverlapFileField) - Method in class edu.cornell.med.icb.omim.OmimUtil
Take the data in src and order it according to the specified primaryField.
outputDir - Variable in class evaluation.Evaluator
 
outputEvalDir - Variable in class evaluation.Evaluate
 
outputRun(int) - Method in class fusion.RankFusion
 
outputRun(int) - Method in class fusion.RankFusion2
 
overlaps(EvaluationLineItem, EvaluationLineItem) - Static method in class evaluation.EvaluationUtils
Determines whether or not two passages within an evaluation item overlap.
overlaps(EvaluationLineItem, EvaluationLineItem, int) - Static method in class evaluation.EvaluationUtils
Determines whether or not two passages within an evaluation item overlap.

P

parseArgs(String[], boolean) - Method in class evaluation.Evaluate
 
parseDataAsXML(String) - Method in class sigpath.SigpathCommunicator
 
parseDataAsXML(String) - Method in class synonyms.SynonymCommunicator
 
parser - Variable in class pubmed.EUtility
 
PassageConsensus - Interface in evaluation.passage
Interface for classes that are used to calculate a Range using a list of ranges.
PassageConsensusEvaluation - Class in evaluation.passage
Class used to read evaluation files containing passage information for Trec written by Evaluate and create new evaluation based on the consensus of multiple runs.
PassageConsensusEvaluation() - Constructor for class evaluation.passage.PassageConsensusEvaluation
 
PassageScoreComparator - Class in fusion
This comparator does the re-ranking of the Item elements by document score.
PassageScoreComparator() - Constructor for class fusion.PassageScoreComparator
 
performTweaseQuery(TrecTopic, TweaseRunExperimentalCondition) - Method in class evaluation.Evaluator
 
positionOfPMID(String, ArrayList<String>) - Method in class sigpath.Interaction
 
postFusionNormalize() - Method in class fusion.InnerWeightRankFusion
 
postFusionNormalize() - Method in class fusion.RankFusion
 
postFusionNormalize() - Method in class fusion.SumOfScoresRankFusion
 
postFusionNormalizeScore(String, int, float) - Method in class fusion.InnerWeightRankFusion
 
PrecisionRecallAtRank - Class in evaluation
 
PrecisionRecallAtRank() - Constructor for class evaluation.PrecisionRecallAtRank
 
PrecisionResult - Class in evaluation
 
PrecisionResult() - Constructor for class evaluation.PrecisionResult
 
prepareFinalQueryForCondition(TweaseRunExperimentalCondition, TrecTopic) - Method in class evaluation.Evaluate
 
process() - Method in class edu.cornell.med.icb.omim.OmimUtil
Run whichever utility was sepecified by the command line options.
process(Collection<TrecTopic>, Evaluate) - Method in class edu.cornell.med.icb.omim.ProteinToPmidsEvaluate
Process a set of topics, querying PubMed and Twease, as appropriate, and generating trec_eval and TweaseEvaluation format results file.
process(Collection<TrecTopic>, Evaluate) - Method in class evaluation.Evaluate
Process a set of topics, querying PubMed and Twease, as appropriate, and generating trec_eval and TweaseEvaluation format results file.
process(Judgements, SearchResults, String) - Method in class evaluation.PrecisionRecallAtRank
 
process(String, String[], String) - Method in class evaluation.PrecisionRecallAtRank
 
process(List<String>, List<Float>) - Method in class fusion.RankFusion
 
process(List<String>, List<Float>, ItemRanking, Object2ObjectOpenHashMap<String, Object2ObjectOpenHashMap<String, Item>>) - Method in class fusion.RankFusion2
 
ProduceFakeJudgements - Class in evaluation
Load a set of evaluation results and produce fake judgements.
ProduceFakeJudgements() - Constructor for class evaluation.ProduceFakeJudgements
 
ProteinToPmidsEvaluate - Class in edu.cornell.med.icb.omim
Based on evaluation.Evaluate but specifically for looking up protein -> pmid and writing in a specific format, notably for use with OMIM protein - disease corelation work.
ProteinToPmidsEvaluate() - Constructor for class edu.cornell.med.icb.omim.ProteinToPmidsEvaluate
 
pubmed - package pubmed
 
pubmed.xml - package pubmed.xml
 
PubMedQuery - Interface in pubmed
 

Q

QUERY_DELAY - Static variable in class evaluation.Evaluate
 
queryPubmed - Variable in class evaluation.Evaluate
 
queryTwease - Variable in class evaluation.Evaluate
 

R

rank - Variable in class fusion.DocumentRank
 
RankFusion - Class in fusion
Fuse search results by the RankFusion approach.
RankFusion() - Constructor for class fusion.RankFusion
 
RankFusion2 - Class in fusion
Fuse search results by the RankFusion approach.
RankFusion2() - Constructor for class fusion.RankFusion2
 
RankResult - Class in evaluation
 
RankResult() - Constructor for class evaluation.RankResult
 
readBackgroundTerms(boolean) - Static method in class evaluation.Evaluator
 
readCount(String) - Method in class edu.cornell.med.icb.omim.OmimUtil
Given a root, read the # of pmids in the associated -pmids file (it is read from the -count file).
readCountCached(String) - Method in class edu.cornell.med.icb.omim.OmimUtil
Given a root, read the # of pmids in the associated -pmids file, but cache them in the countsMap map.
readExperimentalConditions(String) - Method in class evaluation.Evaluate
Read experimental conditions from a tab delimited file.
readLegalSpans(String) - Method in class evaluation.LegalSpanValidator
 
readOverlapsFile(String) - Method in class edu.cornell.med.icb.omim.OmimUtil
Read the pmids file.
readPmidsFile(String) - Method in class edu.cornell.med.icb.omim.OmimUtil
Read the pmids file.
readPmidsFile(String, int) - Method in class edu.cornell.med.icb.omim.OmimUtil
Read the pmids file assuming the count is already known.
readPmidsFileCache(String) - Method in class edu.cornell.med.icb.omim.OmimUtil
Read pmids from an overlap file but try to first get the pmids from a local cache to speed things up.
readProteinFile(String, boolean, boolean) - Static method in class edu.cornell.med.icb.omim.ProteinToPmidsEvaluate
 
readProteinFile(String, boolean, boolean, String) - Static method in class edu.cornell.med.icb.omim.ProteinToPmidsEvaluate
 
readQueryFile(String) - Method in class edu.cornell.med.icb.omim.OmimUtil
Read the query file asociated with the root.
readTopics() - Method in class evaluation.Evaluate
 
readZScoresFile(String, int) - Method in class edu.cornell.med.icb.omim.OmimUtil
Read the zscores file assuming the count is already known.
recordDocument(String, float, Item) - Method in class fusion.RankFusion
 
recordDocument(String, float, Item, Object2ObjectOpenHashMap<String, Object2ObjectOpenHashMap<String, Item>>) - Method in class fusion.RankFusion2
 
registerFile(String) - Method in class evaluation.passage.PassageConsensusEvaluation
 
RelevanceJudgements - Class in evaluation.xml.relevancejudgements
Comment describing your root element
RelevanceJudgements() - Constructor for class evaluation.xml.relevancejudgements.RelevanceJudgements
 
RelevanceJudgementsDescriptor - Class in evaluation.xml.relevancejudgements
Class RelevanceJudgementsDescriptor.
RelevanceJudgementsDescriptor() - Constructor for class evaluation.xml.relevancejudgements.RelevanceJudgementsDescriptor
 
removeAllConcept() - Method in class trec.xml.topics.Concepts
 
removeAllDocument() - Method in class evaluation.xml.relevancejudgements.Topic
 
removeAllItem() - Method in class evaluation.xml.searchresults.TopicResult
 
removeAllTopic() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
removeAllTopic() - Method in class trec.xml.topics.Topics
 
removeAllTopicResult() - Method in class evaluation.xml.searchresults.SearchResults
 
removeConcept(String) - Method in class trec.xml.topics.Concepts
Method removeConcept
removeConceptAt(int) - Method in class trec.xml.topics.Concepts
Method removeConceptAt
removeDocument(Document) - Method in class evaluation.xml.relevancejudgements.Topic
Method removeDocument
removeDocumentAt(int) - Method in class evaluation.xml.relevancejudgements.Topic
Method removeDocumentAt
removeItem(Item) - Method in class evaluation.xml.searchresults.TopicResult
Method removeItem
removeItemAt(int) - Method in class evaluation.xml.searchresults.TopicResult
Method removeItemAt
removePMID(String) - Method in class sigpath.Interaction
 
removePMID(String) - Method in class sigpath.SigpathCommunicator
 
removeRepeatingPubMedIDs() - Method in class sigpath.SigpathCommunicator
 
removeTopic(Topic) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method removeTopic
removeTopic(Topic) - Method in class trec.xml.topics.Topics
Method removeTopic
removeTopicAt(int) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method removeTopicAt
removeTopicAt(int) - Method in class trec.xml.topics.Topics
Method removeTopicAt
removeTopicResult(TopicResult) - Method in class evaluation.xml.searchresults.SearchResults
Method removeTopicResult
removeTopicResultAt(int) - Method in class evaluation.xml.searchresults.SearchResults
Method removeTopicResultAt
reRankItems(Item[]) - Method in class fusion.ItemRanking
Helper method, takes an Item array, makes an Item List out of it so the ItemRanking* method only has to handle re-ranking List to List.
reRankItems(List<Item>) - Method in class fusion.ItemRanking
The method that is implemented by ItemRanking* classes.
reRankItems(List<Item>) - Method in class fusion.ItemRankingByDocumentScore
Rerank the Item elements to a more desirable order.
reRankItems(List<Item>) - Method in class fusion.ItemRankingByGradientInterleave
Rerank the Item elements to a more desirable order.
reRankItems(List<Item>) - Method in class fusion.ItemRankingByGradientInterleaveByRank
Rerank the Item elements to a more desirable order.
reRankItems(List<Item>) - Method in class fusion.ItemRankingByInterleave
Rerank the Item elements to a more desirable order.
reRankItems(List<Item>) - Method in class fusion.ItemRankingByPassageScore
Rerank the Item elements to a more desirable order.
reRankItems(List<Item>) - Method in class fusion.ItemRankingByScoreThenSubscore
Rerank the Item elements to a more desirable order.
resetOverlappingItems() - Method in class evaluation.EvaluationLineItem
Reset the list of overlapping items.
resetRankByScore(List<Item>) - Static method in class fusion.ItemRankingByDocumentScore
 
resetRanks(List<Item>) - Static method in class fusion.ItemRanking
Method to take a ranked Item List and set all the ranks in increasing order.
responseForQuery(MutableString) - Method in class pubmed.EUtility
Retrieve the content of the URL into a String.
resultsFilename - Variable in class evaluation.Evaluate
 
ResultsToJudgements - Class in evaluation
Load evaluation results and produce a judgements file with results that score above a threshold.
ResultsToJudgements() - Constructor for class evaluation.ResultsToJudgements
 
runId - Variable in class evaluation.Evaluate
 
runType - Variable in class evaluation.Evaluate
 

S

saveConceptsToList(List<String>, List<String>) - Static method in class evaluation.EvalTopicUtils
A version of saveConceptToList that can be used externally to save a list of concepts to the existing concept list.
savePubmedToDisc(int, String) - Method in class edu.cornell.med.icb.wmcpubs.FindWmcPubs
Use PubMedInfo to load the pubmed XML into an object.
score - Variable in class fusion.DocumentRank
 
scorerName - Variable in class evaluation.Evaluate
 
ScoreSubscoreComparator - Class in fusion
This comparator does the re-ranking of the Item elements by score then sub-score.
ScoreSubscoreComparator() - Constructor for class fusion.ScoreSubscoreComparator
 
Search - Class in sirt.search
 
Search() - Constructor for class sirt.search.Search
 
SearchHit - Class in sirt.search
Represents a sequence search hit.
SearchHit() - Constructor for class sirt.search.SearchHit
 
SearchResults - Class in evaluation.xml.searchresults
Comment describing your root element
SearchResults() - Constructor for class evaluation.xml.searchresults.SearchResults
 
SearchResultsDescriptor - Class in evaluation.xml.searchresults
Class SearchResultsDescriptor.
SearchResultsDescriptor() - Constructor for class evaluation.xml.searchresults.SearchResultsDescriptor
 
setAccessionCode(String) - Method in class sirt.search.SearchHit
 
setAddBackgroundTerms(boolean) - Method in class evaluation.TweaseRunExperimentalCondition
 
setAliasCount(int) - Method in class synonyms.SynonymQuery
 
setBackgroundTermWeightAdjustmentFactor(float) - Method in class evaluation.TweaseRunExperimentalCondition
 
setBlindFeedbackQueryComponent(String) - Method in class evaluation.TrecTopic
 
setCharsToFilterRegex(String) - Method in class evaluation.Evaluate
 
setConcept(int, String) - Method in class trec.xml.topics.Concepts
 
setConcept(String[]) - Method in class trec.xml.topics.Concepts
 
setConcepts(Concepts) - Method in class trec.xml.topics.Topic
Sets the value of field 'concepts'.
setConceptSubQueries(List<String>) - Method in class evaluation.TrecTopic
 
setConsensusRangeUpdated(boolean) - Method in class evaluation.EvaluationLineItem
 
setDebugText(String) - Method in class evaluation.xml.searchresults.Item
Sets the value of field 'debugText'.
setDistributeParameter(int) - Method in class evaluation.TweaseRunExperimentalCondition
Set the number of terms that will be in a conjunctive clause.
setDoBlindQueryExpansion(boolean) - Method in class evaluation.TweaseRunExperimentalCondition
 
setDocManager(DocumentIndexManager) - Method in class evaluation.Evaluator
 
setDocManager(DocumentIndexManager) - Method in class evaluation.TweaseRunExperimentalCondition
Set the DocumentIndexManager to use.
setDocStoreReader(DocumentStoreReader) - Method in class evaluation.Evaluator
 
setDocument(int, Document) - Method in class evaluation.xml.relevancejudgements.Topic
 
setDocument(Document[]) - Method in class evaluation.xml.relevancejudgements.Topic
 
setDocumentCount(String) - Method in class pubmed.EInfo
 
setDocumentCount(String) - Method in class pubmed.xml.EInfoHandler
 
setDocumentId(String) - Method in class evaluation.TopicIdDocItem
 
setDoPassageRetrieval(boolean) - Method in class evaluation.TweaseRunExperimentalCondition
Set to true if passage retrieval should be performed.
setEmailAddress(String) - Method in class pubmed.ESearch
Set the email address that will be supplied during the pubmed query.
setExtend(boolean) - Method in class evaluation.LegalSpanValidator
 
setFinalQuery(String) - Method in class evaluation.TrecTopic
The query that has been transformed in various ways and is now ready to be run by Twease.
setFusePassages(boolean) - Method in class fusion.RankFusion
 
setFusePassages(boolean) - Method in class fusion.RankFusion2
 
setHitCount(int) - Method in class evaluation.RankResult
 
setId(String) - Method in class evaluation.xml.relevancejudgements.Document
Sets the value of field 'id'.
setId(String) - Method in class evaluation.xml.relevancejudgements.Topic
Sets the value of field 'id'.
setId(String) - Method in class evaluation.xml.searchresults.Item
Sets the value of field 'id'.
setId(String) - Method in class evaluation.xml.searchresults.TopicResult
Sets the value of field 'id'.
setId(String) - Method in class sigpath.Interaction
 
setId(String) - Method in class sigpath.NamedMolecule
 
setId(String) - Method in class trec.xml.topics.Topic
Sets the value of field 'id'.
setInputFilenames(List<String>) - Method in class evaluation.LegalSpanValidator
 
setInputFilenames(String[]) - Method in class evaluation.LegalSpanValidator
 
setInputFilenames(List<String>) - Method in class evaluation.passage.PassageConsensusEvaluation
 
setInputFilenames(String[]) - Method in class evaluation.passage.PassageConsensusEvaluation
 
setInputRunFilename(String) - Method in class evaluation.CalculatePassagesForRun
 
setInteractingNamedMolecules(ArrayList<NamedMolecule>) - Method in class sigpath.Interaction
 
setInteraction(Interaction) - Method in class pubmed.xml.ESearchHandler
 
setInteractions(List<Interaction>) - Method in class evaluation.Evaluate
 
setInteractions(ArrayList<Interaction>) - Method in class sigpath.SigpathCommunicator
 
setInvalidOutputFileExtension(String) - Method in class evaluation.LegalSpanValidator
 
setItem(int, Item) - Method in class evaluation.xml.searchresults.TopicResult
 
setItem(Item[]) - Method in class evaluation.xml.searchresults.TopicResult
 
setItemRanker(String) - Method in class fusion.RankFusion
 
setLastUpdate(String) - Method in class pubmed.EInfo
 
setLastUpdate(String) - Method in class pubmed.xml.EInfoHandler
 
setLegalSpanFilename(String) - Method in class evaluation.CalculatePassagesForRun
 
setLength(int) - Method in class evaluation.EvaluationLineItem
 
setLength(int) - Method in class evaluation.xml.searchresults.Item
Sets the value of field 'length'.
setManuallyConstructedQuery(String) - Method in class evaluation.TrecTopic
 
setMaxDate(String) - Method in class pubmed.ESearch
Set the ending date.
setMaxPassagesPerDocument(int) - Method in class fusion.RankFusion2
 
setMaxResults(int) - Method in class pubmed.ESearch
Set the number of maximum results to return.
setMedpostTagged(String) - Method in class trec.xml.topics.Topic
Sets the value of field 'medpostTagged'.
setMinDate(String) - Method in class pubmed.ESearch
Set the starting date.
setName(String) - Method in class sigpath.NamedMolecule
 
setNameCount(int) - Method in class synonyms.SynonymQuery
 
setNamedMolecules(List<NamedMolecule>) - Method in class evaluation.Evaluate
 
setNamedMolecules(ArrayList<NamedMolecule>) - Method in class sigpath.SigpathCommunicator
 
setNarrative(String) - Method in class evaluation.TrecTopic
 
setNarrative(String) - Method in class trec.xml.topics.Topic
Sets the value of field 'narrative'.
setNewTag(String) - Method in class evaluation.CalculatePassagesForRun
 
setNewTag(String) - Method in class fusion.RankFusion
 
setOutputDir(String) - Method in class edu.cornell.med.icb.omim.OmimUtil
Set the output dir.
setOutputDirs(String, String) - Method in class evaluation.Evaluate
 
setOutputFileExtension(String) - Method in class evaluation.passage.PassageConsensusEvaluation
 
setOutputFilename(String) - Method in class evaluation.CalculatePassagesForRun
 
setOutputFilename(String) - Method in class fusion.RankFusion
 
setOutputFilename(String) - Method in class fusion.RankFusion2
 
setOutputTrecEvalFormat(boolean) - Method in class evaluation.PrecisionRecallAtRank
 
setPageSize(int) - Method in class evaluation.TweaseRunExperimentalCondition
Set the max number of results to be gathered per query.
setParseParameters(String) - Method in class evaluation.TweaseRunExperimentalCondition
Calls the String[] version of parse paramters when a single string is provided.
setParseParameters(String[]) - Method in class evaluation.TweaseRunExperimentalCondition
Parse the paramters for this condition.
setPassageBoundary(String) - Method in class evaluation.TweaseRunExperimentalCondition
Set the passage boundry for this condition.
setPassageConsensus(PassageConsensus) - Method in class evaluation.passage.PassageConsensusEvaluation
 
setPassageScorerClassName(String) - Method in class evaluation.TweaseRunExperimentalCondition
Set the passage scorer class name.
setPassagesPerDocument(int) - Method in class evaluation.CalculatePassagesForRun
 
setPassageTokenizerClassName(String) - Method in class evaluation.TweaseRunExperimentalCondition
Set the passage tokenizer class name.
setPmid(String) - Method in class synonyms.Synonym
 
setPrecision(float) - Method in class evaluation.RankResult
 
setPubmedRankResults(HashMap<Integer, RankResult>) - Method in class evaluation.PrecisionResult
 
setPubmedUniquePMIDCount(int) - Method in class evaluation.PrecisionResult
 
setQuery(String) - Method in class synonyms.SynonymQuery
 
setQuery(String) - Method in class trec.xml.topics.Topic
Sets the value of field 'query'.
setQueryDistributorClassName(String) - Method in class evaluation.TweaseRunExperimentalCondition
Set the query distributor class name.
setQueryExpanderClassName(String) - Method in class evaluation.TweaseRunExperimentalCondition
Set the query expander class name.
setQueryTerms(String[]) - Method in class evaluation.TweaseRunExperimentalCondition
Set the query terms.
setRank(int) - Method in class evaluation.EvaluationLineItem
 
setRank(int) - Method in class evaluation.RankResult
 
setRank(int) - Method in class evaluation.TopicIdDocItem
 
setRank(int) - Method in class evaluation.xml.searchresults.Item
Sets the value of field 'rank'.
setRankFusionRunListFilename(String) - Method in class evaluation.CalculatePassagesForRun
 
setRerank(boolean) - Method in class evaluation.LegalSpanValidator
 
setResultCount(String) - Method in class pubmed.xml.ESearchHandler
 
setResultItems(ArrayList<Item>) - Method in class sigpath.Interaction
 
setRunId(String) - Method in class evaluation.EvaluationLineItem
 
setRunId(String) - Method in class evaluation.Evaluator
 
setRunId(String) - Method in class evaluation.TopicIdDocItem
 
setRunId(String) - Method in class evaluation.xml.searchresults.SearchResults
Sets the value of field 'runId'.
setRunType(TweaseRunExperimentalCondition.RunType) - Method in class evaluation.TweaseRunExperimentalCondition
Set the run type for this condition.
setScore(double) - Method in class evaluation.EvaluationLineItem
 
setScore(float) - Method in class evaluation.xml.searchresults.Item
Sets the value of field 'score'.
setScore(double) - Method in class sirt.search.SearchHit
 
setScorerName(String) - Method in class evaluation.TweaseRunExperimentalCondition
Set the scorer name to use.
setSlider(int) - Method in class evaluation.TweaseRunExperimentalCondition
Set the slider value to use.
setSpid(String) - Method in class sigpath.Interaction
 
setSpid(String) - Method in class sigpath.NamedMolecule
 
setSpid(String) - Method in class synonyms.Synonym
 
setStart(int) - Method in class evaluation.EvaluationLineItem
 
setStartPos(int) - Method in class evaluation.xml.searchresults.Item
Sets the value of field 'startPos'.
setSubscore(double) - Method in class evaluation.EvaluationLineItem
 
setSubScore(float) - Method in class evaluation.xml.searchresults.Item
Sets the value of field 'subScore'.
setSuggestedExpandedQuery(String) - Method in class evaluation.TrecTopic
 
setSynonymMap(HashMap<String, ArrayList<String>>) - Method in class synonyms.Synonym
 
setTag(String) - Method in class evaluation.TweaseRunExperimentalCondition
Set the tag for this condition (helpful to differientiage different runs).
setTermInMinNumberOfRuns(int) - Method in class evaluation.CalculatePassagesForRun
 
setTerms(String) - Method in class trec.xml.topics.Topic
Sets the value of field 'terms'.
setTool(String) - Method in class pubmed.EUtility
 
setTopic(int, Topic) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
setTopic(Topic[]) - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
setTopic(int, Topic) - Method in class trec.xml.topics.Topics
 
setTopic(Topic[]) - Method in class trec.xml.topics.Topics
 
setTopicIdentifier(String) - Method in class evaluation.TrecTopic
 
setTopicIdNumber(String) - Method in class evaluation.TopicIdDocItem
 
setTopicResult(int, TopicResult) - Method in class evaluation.xml.searchresults.SearchResults
 
setTopicResult(TopicResult[]) - Method in class evaluation.xml.searchresults.SearchResults
 
setTotalCount(int) - Method in class evaluation.RankResult
 
setTotalTermCount(int) - Method in class synonyms.SynonymQuery
 
setTweaseOccurence(String) - Method in class sigpath.Interaction
 
setTweaseRankResults(HashMap<Integer, RankResult>) - Method in class evaluation.PrecisionResult
 
setTweaseUniquePMIDCount(int) - Method in class evaluation.PrecisionResult
 
setType(String) - Method in class sigpath.Interaction
 
setUseBackgroundAndFilter(boolean) - Method in class evaluation.CalculatePassagesForRun
 
setValidOutputFileExtension(String) - Method in class evaluation.LegalSpanValidator
 
setVerbose(boolean) - Method in class evaluation.LegalSpanValidator
 
showPmidsFile() - Method in class edu.cornell.med.icb.omim.OmimUtil
Display the PMIDs specified by a file, no scores.
showScoredPmidsFile() - Method in class edu.cornell.med.icb.omim.OmimUtil
Display the PMIDs specified by a file showing the associated zscores.
sigpath - package sigpath
 
SigpathCommunicator - Class in sigpath
 
SigpathCommunicator() - Constructor for class sigpath.SigpathCommunicator
 
SigPathEvaluator - Class in evaluation
 
SigPathEvaluator() - Constructor for class evaluation.SigPathEvaluator
 
SigpathXMLHandler - Class in sigpath
 
SigpathXMLHandler() - Constructor for class sigpath.SigpathXMLHandler
 
simplifyTopic(String, Map<String, String>) - Static method in class evaluation.EvalTopicUtils
Trec 2007 topics come in the format of "What [TOXICITIES] are associated with zoledronic acid?" this method will return the string "What toxicities are associated with zoledronic acid?" It is fine if there are multiple [CONCEPT] phrases.
sirt.search - package sirt.search
 
sliderValue - Variable in class evaluation.Evaluate
 
spidIsAlreadyPresent(String) - Method in class evaluation.Evaluate
 
start() - Method in class evaluation.Timer
 
startElement(String, String, String, Attributes) - Method in class pubmed.xml.EInfoHandler
 
startElement(String, String, String, Attributes) - Method in class pubmed.xml.ESearchHandler
 
startElement(String, String, String, Attributes) - Method in class sigpath.SigpathXMLHandler
 
startElement(String, String, String, Attributes) - Method in class synonyms.SynonymHandler
 
SumOfScoresRankFusion - Class in fusion
 
SumOfScoresRankFusion() - Constructor for class fusion.SumOfScoresRankFusion
 
Synonym - Class in synonyms
 
SynonymCommunicator - Class in synonyms
 
SynonymCommunicator() - Constructor for class synonyms.SynonymCommunicator
 
SynonymHandler - Class in synonyms
 
SynonymHandler() - Constructor for class synonyms.SynonymHandler
 
SynonymQuery - Class in synonyms
 
SynonymQuery(String, int, int) - Constructor for class synonyms.SynonymQuery
 
synonyms - package synonyms
 

T

termSelection - Variable in class evaluation.Evaluate
 
termSelectionToString(Evaluate.TermSelection) - Static method in class evaluation.Evaluate
 
Timer - Class in evaluation
 
Timer() - Constructor for class evaluation.Timer
 
timesFused - Variable in class fusion.RankFusion
 
Topic - Class in evaluation.xml.relevancejudgements
Class Topic.
Topic() - Constructor for class evaluation.xml.relevancejudgements.Topic
 
Topic - Class in trec.xml.topics
Class Topic.
Topic() - Constructor for class trec.xml.topics.Topic
 
TopicDescriptor - Class in evaluation.xml.relevancejudgements
Class TopicDescriptor.
TopicDescriptor() - Constructor for class evaluation.xml.relevancejudgements.TopicDescriptor
 
TopicDescriptor - Class in trec.xml.topics
Class TopicDescriptor.
TopicDescriptor() - Constructor for class trec.xml.topics.TopicDescriptor
 
TopicIdDocItem - Class in evaluation
TODO: document this class
TopicIdDocItem(String, String) - Constructor for class evaluation.TopicIdDocItem
 
topicInputFasta - Variable in class evaluation.Evaluate
 
topicInputMedline - Variable in class evaluation.Evaluate
 
topicInputSigPath - Variable in class evaluation.Evaluate
 
topicInputTrecTopics - Variable in class evaluation.Evaluate
 
TopicResult - Class in evaluation.xml.searchresults
Class TopicResult.
TopicResult() - Constructor for class evaluation.xml.searchresults.TopicResult
 
TopicResultDescriptor - Class in evaluation.xml.searchresults
Class TopicResultDescriptor.
TopicResultDescriptor() - Constructor for class evaluation.xml.searchresults.TopicResultDescriptor
 
Topics - Class in trec.xml.topics
Trec topics file
Topics() - Constructor for class trec.xml.topics.Topics
 
TopicsDescriptor - Class in trec.xml.topics
Class TopicsDescriptor.
TopicsDescriptor() - Constructor for class trec.xml.topics.TopicsDescriptor
 
toString() - Method in class evaluation.EvaluationLineItem
Returns a string representation of the object.
toString() - Method in class evaluation.Timer
 
toString() - Method in class evaluation.TweaseRunExperimentalCondition
 
toString() - Method in class fusion.ItemRanking
String that is equivalent to that which was used to perform the creation of the ItemRanking object (with paramters information, if there are any paramters).
trec - package trec
 
trec.xml.topics - package trec.xml.topics
 
TrecEvaluate - Class in trec
Deprecated. Use evaluation.Evaluate instead.
TrecEvaluate() - Constructor for class trec.TrecEvaluate
Deprecated.  
TrecTopic - Class in evaluation
 
TrecTopic(String, String) - Constructor for class evaluation.TrecTopic
 
TweaseRunExperimentalCondition - Class in evaluation
 
TweaseRunExperimentalCondition() - Constructor for class evaluation.TweaseRunExperimentalCondition
Constructor.
TweaseRunExperimentalCondition.RunType - Enum in evaluation
The supported run types.

U

UnionConsensus - Class in evaluation.passage
Determine passage consensus based on the union of all the ranges.
UnionConsensus() - Constructor for class evaluation.passage.UnionConsensus
Creates a new PassageConsensus object.
unmarshal(Reader) - Static method in class evaluation.xml.relevancejudgements.Document
Method unmarshal
unmarshal(Reader) - Static method in class evaluation.xml.relevancejudgements.RelevanceJudgements
Method unmarshal
unmarshal(Reader) - Static method in class evaluation.xml.relevancejudgements.Topic
Method unmarshal
unmarshal(Reader) - Static method in class evaluation.xml.searchresults.Item
Method unmarshal
unmarshal(Reader) - Static method in class evaluation.xml.searchresults.SearchResults
Method unmarshal
unmarshal(Reader) - Static method in class evaluation.xml.searchresults.TopicResult
Method unmarshal
unmarshal(Reader) - Static method in class trec.xml.topics.Concepts
Method unmarshal
unmarshal(Reader) - Static method in class trec.xml.topics.Topic
Method unmarshal
unmarshal(Reader) - Static method in class trec.xml.topics.Topics
Method unmarshal
updateOverlappingItems(Collection<EvaluationLineItem>) - Method in class evaluation.EvaluationLineItem
If the given items overlap with this item they are added to the list of overlapping items.
updateOverlappingItems(EvaluationLineItem...) - Method in class evaluation.EvaluationLineItem
If the given items overlap with this item they are added to the list of overlapping items.
updateOverlappingItems(int, EvaluationLineItem...) - Method in class evaluation.EvaluationLineItem
If the given items overlap with this item they are added to the list of overlapping items.
useAbnerConversion - Variable in class evaluation.Evaluate
 

V

validate(String) - Method in class evaluation.LegalSpanValidator
 
validate() - Method in class evaluation.xml.relevancejudgements.Document
 
validate() - Method in class evaluation.xml.relevancejudgements.RelevanceJudgements
 
validate() - Method in class evaluation.xml.relevancejudgements.Topic
 
validate() - Method in class evaluation.xml.searchresults.Item
 
validate() - Method in class evaluation.xml.searchresults.SearchResults
 
validate() - Method in class evaluation.xml.searchresults.TopicResult
 
validate() - Method in class trec.xml.topics.Concepts
 
validate() - Method in class trec.xml.topics.Topic
 
validate() - Method in class trec.xml.topics.Topics
 
validateEntry(String, Range) - Method in class evaluation.LegalSpanValidator
Validate a single entry
validDir(String, String) - Static method in class edu.cornell.med.icb.omim.OmimUtil
Checks that a directory is valid.
validFile(String, String) - Static method in class edu.cornell.med.icb.omim.OmimUtil
Checks that a file is valid.
validRoot(String) - Static method in class edu.cornell.med.icb.omim.OmimUtil
Verifies if a root appears to be valid, not blank or null, not equal to "-".
valueOf(String) - Static method in enum edu.cornell.med.CornellMedDepartments
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum evaluation.LegalSpanValidator.ValidationResult
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum evaluation.TweaseRunExperimentalCondition.RunType
Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.cornell.med.CornellMedDepartments
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum evaluation.LegalSpanValidator.ValidationResult
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum evaluation.TweaseRunExperimentalCondition.RunType
Returns an array containing the constants of this enum type, in the order they are declared.

W

write(String) - Method in class evaluation.Judgements
 
writeHtmlCloseList(PrintWriter) - Method in class edu.cornell.med.icb.omim.OmimUtil
Close the list (all secondary entries written).
writeOutputFiles() - Method in class evaluation.passage.PassageConsensusEvaluation
 
writeTrecEvalFormat(String) - Method in class evaluation.Judgements
 

A B C D E F G H I J L M N O P Q R S T U V W
Twease Evaluation

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