A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

AAMC - Static variable in class textractor.xml.pubmed.xml.types.OtherAbstractTypeType

The instance of the AAMC type

AAMC - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherAbstractTypeType

The instance of the AAMC type

AAMC_TYPE - Static variable in class textractor.xml.pubmed.xml.types.OtherAbstractTypeType

The AAMC type

AAMC_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherAbstractTypeType

The AAMC type

Abbreviation - Class in textractor.abbreviation

Finds possible abbreviations when given a long form search term, and returns a result ranked by relevance.

Abbreviation(DocumentIndexManager) - Constructor for class textractor.abbreviation.Abbreviation

Constructor for Abbreviation searcher.

Abbreviation(DocumentIndexManager, DocumentStoreReader) - Constructor for class textractor.abbreviation.Abbreviation

Constructore for Abbreviation searcher.

ABBREVIATION - Static variable in class textractor.xml.uniprot.xml.types.OrganismNameTypeTypeType

The instance of the abbreviation type

ABBREVIATION_TYPE - Static variable in class textractor.xml.uniprot.xml.types.OrganismNameTypeTypeType

The abbreviation type

AbnerSentenceTransformer - Class in textractor.chain.transformer

A SentenceTransformer which will replace sentence named entities text and positions with their more generic type names (i.e., protein, dna, etc.)

AbnerSentenceTransformer() - Constructor for class textractor.chain.transformer.AbnerSentenceTransformer

Create a new SentenceTransformer that that replaces named entities in a sentence.

abortTxn() - Method in class textractor.database.DbManager

Abort a transaction.

abortTxn() - Method in interface textractor.database.TransactionManager

Abort a transaction.

Absorption - Class in textractor.xml.uniprot.xml

Class Absorption.

Absorption() - Constructor for class textractor.xml.uniprot.xml.Absorption

AbsorptionDescriptor - Class in textractor.xml.uniprot.xml

Class AbsorptionDescriptor.

AbsorptionDescriptor() - Constructor for class textractor.xml.uniprot.xml.AbsorptionDescriptor

Abstract - Class in textractor.xml.pubmed.xml

Class Abstract.

Abstract() - Constructor for class textractor.xml.pubmed.xml.Abstract

Abstract - Class in textractor.xml.pubmedabstracts.xml

Class Abstract.

Abstract() - Constructor for class textractor.xml.pubmedabstracts.xml.Abstract

Abstract - Class in textractor.xml.yapex.xml

Class Abstract.

Abstract() - Constructor for class textractor.xml.yapex.xml.Abstract

ABSTRACT_SECTION - Static variable in class textractor.datamodel.TextractorDocument

AbstractDescriptor - Class in textractor.xml.pubmed.xml

Class AbstractDescriptor.

AbstractDescriptor() - Constructor for class textractor.xml.pubmed.xml.AbstractDescriptor

AbstractDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AbstractDescriptor.

AbstractDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AbstractDescriptor

AbstractDescriptor - Class in textractor.xml.yapex.xml

Class AbstractDescriptor.

AbstractDescriptor() - Constructor for class textractor.xml.yapex.xml.AbstractDescriptor

AbstractFileLoader - Class in textractor.chain.loader

Abstract base class that can be used to load articles from files and process them into sentences that can be then further processed, indexed or stored into a database via an appropriate SentenceConsumer or SentenceProcessor.

AbstractFileLoader() - Constructor for class textractor.chain.loader.AbstractFileLoader

Create a new SentenceProducer that loads sentences from files.

AbstractHtml2Text - Class in textractor.html

Converts HTML to Text.

AbstractHtml2Text(String[]) - Constructor for class textractor.html.AbstractHtml2Text

AbstractLookupProteinname - Class in textractor.tools.lookup

Provides basic functionality for looking up protein names.

AbstractLookupProteinname() - Constructor for class textractor.tools.lookup.AbstractLookupProteinname

AbstractLookupProteinname(String[]) - Constructor for class textractor.tools.lookup.AbstractLookupProteinname

Abstracts - Class in textractor.xml.yapex.xml

Class Abstracts.

Abstracts() - Constructor for class textractor.xml.yapex.xml.Abstracts

AbstractsDescriptor - Class in textractor.xml.yapex.xml

Class AbstractsDescriptor.

AbstractsDescriptor() - Constructor for class textractor.xml.yapex.xml.AbstractsDescriptor

AbstractSentenceConsumer - Class in textractor.chain

Command implementation that executes a SentenceConsumer.

AbstractSentenceConsumer() - Constructor for class textractor.chain.AbstractSentenceConsumer

Create a new Command to consume sentences.

AbstractSentenceProcessor - Class in textractor.sentence

Convenience base class for SentenceProcessor implementations.

AbstractSentenceProcessor() - Constructor for class textractor.sentence.AbstractSentenceProcessor

Create a new SentenceProcessor.

AbstractSentenceProducer - Class in textractor.chain

Base class for Chain implementations that contain one or more SentenceProcessor commands.

AbstractSentenceProducer() - Constructor for class textractor.chain.AbstractSentenceProducer

Create a new Chain.

AbstractSentenceProducer(Command) - Constructor for class textractor.chain.AbstractSentenceProducer

Construct a Chain configured with the specified Command.

AbstractSentenceProducer(Command[]) - Constructor for class textractor.chain.AbstractSentenceProducer

Construct a Chain configured with the specified Commands.

AbstractSentenceProducer(Collection<Command>) - Constructor for class textractor.chain.AbstractSentenceProducer

Construct a Chain configured with the specified Commands.

AbstractSentenceTransformer - Class in textractor.chain

Base class for Chain implementations that contain one or more SentenceProcessor commands.

AbstractSentenceTransformer() - Constructor for class textractor.chain.AbstractSentenceTransformer

Create a new Chain.

AbstractSentenceTransformer(Command) - Constructor for class textractor.chain.AbstractSentenceTransformer

Construct a Chain configured with the specified Command.

AbstractSentenceTransformer(Command[]) - Constructor for class textractor.chain.AbstractSentenceTransformer

Construct a Chain configured with the specified Commands.

AbstractSentenceTransformer(Collection<Command>) - Constructor for class textractor.chain.AbstractSentenceTransformer

Construct a Chain configured with the specified Commands.

AbstractText - Class in textractor.xml.pubmed.xml

Class AbstractText.

AbstractText() - Constructor for class textractor.xml.pubmed.xml.AbstractText

AbstractText - Class in textractor.xml.pubmedabstracts.xml

Class AbstractText.

AbstractText() - Constructor for class textractor.xml.pubmedabstracts.xml.AbstractText

AbstractTextDescriptor - Class in textractor.xml.pubmed.xml

Class AbstractTextDescriptor.

AbstractTextDescriptor() - Constructor for class textractor.xml.pubmed.xml.AbstractTextDescriptor

AbstractTextDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AbstractTextDescriptor.

AbstractTextDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AbstractTextDescriptor

AbstractTextItem - Class in textractor.xml.pubmed.xml

Class AbstractTextItem.

AbstractTextItem() - Constructor for class textractor.xml.pubmed.xml.AbstractTextItem

AbstractTextItem - Class in textractor.xml.pubmedabstracts.xml

Class AbstractTextItem.

AbstractTextItem() - Constructor for class textractor.xml.pubmedabstracts.xml.AbstractTextItem

AbstractTextItemDescriptor - Class in textractor.xml.pubmed.xml

Class AbstractTextItemDescriptor.

AbstractTextItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.AbstractTextItemDescriptor

AbstractTextItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AbstractTextItemDescriptor.

AbstractTextItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AbstractTextItemDescriptor

AbstractTextractorDocumentFactory - Class in textractor.mg4j.document

A factory that can produce MG4J documents from Textractor sentences.

AbstractTextractorDocumentFactory() - Constructor for class textractor.mg4j.document.AbstractTextractorDocumentFactory

Construct a new DocumentFactory.

AbstractTextractorDocumentFactory(Reference2ObjectMap<Enum<?>, Object>) - Constructor for class textractor.mg4j.document.AbstractTextractorDocumentFactory

Construct a new DocumentFactory.

AbstractTextractorDocumentFactory(Properties) - Constructor for class textractor.mg4j.document.AbstractTextractorDocumentFactory

Construct a new DocumentFactory.

AbstractTextractorDocumentFactory(String[]) - Constructor for class textractor.mg4j.document.AbstractTextractorDocumentFactory

Construct a new DocumentFactory.

AbstractTextractorDocumentFactory.MetadataKeys - Enum in textractor.mg4j.document

Case-insensitive keys for metadata passed to DocumentFactory.getDocument(java.io.InputStream, it.unimi.dsi.fastutil.objects.Reference2ObjectMap).

AbstractTextractorDocumentIterator - Class in textractor.mg4j.document

An iterator over textractor documents.

AbstractTextractorDocumentIterator(DocumentFactory, SentenceFilter) - Constructor for class textractor.mg4j.document.AbstractTextractorDocumentIterator

accept(DocumentIteratorVisitor) - Method in class textractor.tools.QueryResultDocumentIterator

accept(String) - Method in class textractor.util.ProcessDirectory

ACCEPTED - Static variable in class textractor.xml.pubmedabstracts.xml.types.PubMedPubDatePubStatusType

The instance of the accepted type

ACCEPTED_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.PubMedPubDatePubStatusType

The accepted type

acceptOnTruePaths(DocumentIteratorVisitor) - Method in class textractor.tools.QueryResultDocumentIterator

AccessionNumber - Class in textractor.xml.pubmed.xml

Class AccessionNumber.

AccessionNumber() - Constructor for class textractor.xml.pubmed.xml.AccessionNumber

AccessionNumber - Class in textractor.xml.pubmedabstracts.xml

Class AccessionNumber.

AccessionNumber() - Constructor for class textractor.xml.pubmedabstracts.xml.AccessionNumber

AccessionNumberDescriptor - Class in textractor.xml.pubmed.xml

Class AccessionNumberDescriptor.

AccessionNumberDescriptor() - Constructor for class textractor.xml.pubmed.xml.AccessionNumberDescriptor

AccessionNumberDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AccessionNumberDescriptor.

AccessionNumberDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AccessionNumberDescriptor

AccessionNumberItem - Class in textractor.xml.pubmed.xml

Class AccessionNumberItem.

AccessionNumberItem() - Constructor for class textractor.xml.pubmed.xml.AccessionNumberItem

AccessionNumberItem - Class in textractor.xml.pubmedabstracts.xml

Class AccessionNumberItem.

AccessionNumberItem() - Constructor for class textractor.xml.pubmedabstracts.xml.AccessionNumberItem

AccessionNumberItemDescriptor - Class in textractor.xml.pubmed.xml

Class AccessionNumberItemDescriptor.

AccessionNumberItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.AccessionNumberItemDescriptor

AccessionNumberItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AccessionNumberItemDescriptor.

AccessionNumberItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AccessionNumberItemDescriptor

AccessionNumberList - Class in textractor.xml.pubmed.xml

Class AccessionNumberList.

AccessionNumberList() - Constructor for class textractor.xml.pubmed.xml.AccessionNumberList

AccessionNumberList - Class in textractor.xml.pubmedabstracts.xml

Class AccessionNumberList.

AccessionNumberList() - Constructor for class textractor.xml.pubmedabstracts.xml.AccessionNumberList

AccessionNumberListDescriptor - Class in textractor.xml.pubmed.xml

Class AccessionNumberListDescriptor.

AccessionNumberListDescriptor() - Constructor for class textractor.xml.pubmed.xml.AccessionNumberListDescriptor

AccessionNumberListDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AccessionNumberListDescriptor.

AccessionNumberListDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AccessionNumberListDescriptor

accumulate(String) - Static method in class textractor.util.ParseOutput

Acronym - Class in textractor.acronyms.xml

Class Acronym.

Acronym() - Constructor for class textractor.acronyms.xml.Acronym

Acronym - Class in textractor.xml.pubmed.xml

Class Acronym.

Acronym() - Constructor for class textractor.xml.pubmed.xml.Acronym

Acronym - Class in textractor.xml.pubmedabstracts.xml

Class Acronym.

Acronym() - Constructor for class textractor.xml.pubmedabstracts.xml.Acronym

AcronymDescriptor - Class in textractor.acronyms.xml

Class AcronymDescriptor.

AcronymDescriptor() - Constructor for class textractor.acronyms.xml.AcronymDescriptor

AcronymDescriptor - Class in textractor.xml.pubmed.xml

Class AcronymDescriptor.

AcronymDescriptor() - Constructor for class textractor.xml.pubmed.xml.AcronymDescriptor

AcronymDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AcronymDescriptor.

AcronymDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AcronymDescriptor

AcronymItem - Class in textractor.xml.pubmed.xml

Class AcronymItem.

AcronymItem() - Constructor for class textractor.xml.pubmed.xml.AcronymItem

AcronymItem - Class in textractor.xml.pubmedabstracts.xml

Class AcronymItem.

AcronymItem() - Constructor for class textractor.xml.pubmedabstracts.xml.AcronymItem

AcronymItemDescriptor - Class in textractor.xml.pubmed.xml

Class AcronymItemDescriptor.

AcronymItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.AcronymItemDescriptor

AcronymItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AcronymItemDescriptor.

AcronymItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AcronymItemDescriptor

Acronyms - Class in textractor.acronyms.xml

List of acronym/expansion pairs

Acronyms() - Constructor for class textractor.acronyms.xml.Acronyms

AcronymsDescriptor - Class in textractor.acronyms.xml

Class AcronymsDescriptor.

AcronymsDescriptor() - Constructor for class textractor.acronyms.xml.AcronymsDescriptor

AcronymsItem - Class in textractor.acronyms.xml

Class AcronymsItem.

AcronymsItem() - Constructor for class textractor.acronyms.xml.AcronymsItem

AcronymsItemDescriptor - Class in textractor.acronyms.xml

Class AcronymsItemDescriptor.

AcronymsItemDescriptor() - Constructor for class textractor.acronyms.xml.AcronymsItemDescriptor

ACTIVE_SITE - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The instance of the active site type

ACTIVE_SITE_TYPE - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The active site type

add(String) - Method in class textractor.tools.expansion.CandidateExpansion

add_abstract(Abstract) - Method in class textractor.xml.yapex.xml.Abstracts

Method add_abstract

add_abstract(int, Abstract) - Method in class textractor.xml.yapex.xml.Abstracts

Method add_abstract

add_escapes(String) - Method in exception textractor.parsers.extractor.ParseException

Used to convert raw characters to their escaped version when these raw version cannot be used as part of an ASCII string literal.

addAbstractTextItem(AbstractTextItem) - Method in class textractor.xml.pubmed.xml.AbstractText

addAbstractTextItem(int, AbstractTextItem) - Method in class textractor.xml.pubmed.xml.AbstractText

addAbstractTextItem(AbstractTextItem) - Method in class textractor.xml.pubmedabstracts.xml.AbstractText

addAbstractTextItem(int, AbstractTextItem) - Method in class textractor.xml.pubmedabstracts.xml.AbstractText

addAccession(String) - Method in class textractor.xml.uniprot.xml.EntryType

addAccession(int, String) - Method in class textractor.xml.uniprot.xml.EntryType

addAccessionNumber(AccessionNumber) - Method in class textractor.xml.pubmed.xml.AccessionNumberList

addAccessionNumber(int, AccessionNumber) - Method in class textractor.xml.pubmed.xml.AccessionNumberList

addAccessionNumber(AccessionNumber) - Method in class textractor.xml.pubmedabstracts.xml.AccessionNumberList

addAccessionNumber(int, AccessionNumber) - Method in class textractor.xml.pubmedabstracts.xml.AccessionNumberList

addAccessionNumberItem(AccessionNumberItem) - Method in class textractor.xml.pubmed.xml.AccessionNumber

addAccessionNumberItem(int, AccessionNumberItem) - Method in class textractor.xml.pubmed.xml.AccessionNumber

addAccessionNumberItem(AccessionNumberItem) - Method in class textractor.xml.pubmedabstracts.xml.AccessionNumber

addAccessionNumberItem(int, AccessionNumberItem) - Method in class textractor.xml.pubmedabstracts.xml.AccessionNumber

addAcronymItem(AcronymItem) - Method in class textractor.xml.pubmed.xml.Acronym

addAcronymItem(int, AcronymItem) - Method in class textractor.xml.pubmed.xml.Acronym

addAcronymItem(AcronymItem) - Method in class textractor.xml.pubmedabstracts.xml.Acronym

addAcronymItem(int, AcronymItem) - Method in class textractor.xml.pubmedabstracts.xml.Acronym

addAcronymsItem(AcronymsItem) - Method in class textractor.acronyms.xml.Acronyms

addAcronymsItem(int, AcronymsItem) - Method in class textractor.acronyms.xml.Acronyms

addAffiliationItem(AffiliationItem) - Method in class textractor.xml.pubmed.xml.Affiliation

addAffiliationItem(int, AffiliationItem) - Method in class textractor.xml.pubmed.xml.Affiliation

addAffiliationItem(AffiliationItem) - Method in class textractor.xml.pubmedabstracts.xml.Affiliation

addAffiliationItem(int, AffiliationItem) - Method in class textractor.xml.pubmedabstracts.xml.Affiliation

addAgencyItem(AgencyItem) - Method in class textractor.xml.pubmed.xml.Agency

addAgencyItem(int, AgencyItem) - Method in class textractor.xml.pubmed.xml.Agency

addAgencyItem(AgencyItem) - Method in class textractor.xml.pubmedabstracts.xml.Agency

addAgencyItem(int, AgencyItem) - Method in class textractor.xml.pubmedabstracts.xml.Agency

addAll(CandidateExpansion) - Method in class textractor.tools.expansion.CandidateExpansion

addArticleDate(ArticleDate) - Method in class textractor.xml.pubmed.xml.Article

addArticleDate(int, ArticleDate) - Method in class textractor.xml.pubmed.xml.Article

addArticleDate(ArticleDate) - Method in class textractor.xml.pubmedabstracts.xml.Article

addArticleDate(int, ArticleDate) - Method in class textractor.xml.pubmedabstracts.xml.Article

addArticleId(ArticleId) - Method in class textractor.xml.pubmedabstracts.xml.ArticleIdList

addArticleId(int, ArticleId) - Method in class textractor.xml.pubmedabstracts.xml.ArticleIdList

addArticleIdItem(ArticleIdItem) - Method in class textractor.xml.pubmedabstracts.xml.ArticleId

addArticleIdItem(int, ArticleIdItem) - Method in class textractor.xml.pubmedabstracts.xml.ArticleId

addArticleTitleItem(ArticleTitleItem) - Method in class textractor.xml.pubmed.xml.ArticleTitle

addArticleTitleItem(int, ArticleTitleItem) - Method in class textractor.xml.pubmed.xml.ArticleTitle

addArticleTitleItem(ArticleTitleItem) - Method in class textractor.xml.pubmedabstracts.xml.ArticleTitle

addArticleTitleItem(int, ArticleTitleItem) - Method in class textractor.xml.pubmedabstracts.xml.ArticleTitle

addAuthor(Author) - Method in class textractor.xml.pubmed.xml.AuthorList

addAuthor(int, Author) - Method in class textractor.xml.pubmed.xml.AuthorList

addAuthor(Author) - Method in class textractor.xml.pubmedabstracts.xml.AuthorList

addAuthor(int, Author) - Method in class textractor.xml.pubmedabstracts.xml.AuthorList

addBroadJournalHeading(BroadJournalHeading) - Method in class textractor.xml.pubmed.xml.BroadJournalHeadingList

addBroadJournalHeading(int, BroadJournalHeading) - Method in class textractor.xml.pubmed.xml.BroadJournalHeadingList

addBroadJournalHeading(BroadJournalHeading) - Method in class textractor.xml.pubmedabstracts.xml.BroadJournalHeadingList

addBroadJournalHeading(int, BroadJournalHeading) - Method in class textractor.xml.pubmedabstracts.xml.BroadJournalHeadingList

addBroadJournalHeadingItem(BroadJournalHeadingItem) - Method in class textractor.xml.pubmed.xml.BroadJournalHeading

addBroadJournalHeadingItem(int, BroadJournalHeadingItem) - Method in class textractor.xml.pubmed.xml.BroadJournalHeading

addBroadJournalHeadingItem(BroadJournalHeadingItem) - Method in class textractor.xml.pubmedabstracts.xml.BroadJournalHeading

addBroadJournalHeadingItem(int, BroadJournalHeadingItem) - Method in class textractor.xml.pubmedabstracts.xml.BroadJournalHeading

addChemical(Chemical) - Method in class textractor.xml.pubmed.xml.ChemicalList

addChemical(int, Chemical) - Method in class textractor.xml.pubmed.xml.ChemicalList

addChemical(Chemical) - Method in class textractor.xml.pubmedabstracts.xml.ChemicalList

addChemical(int, Chemical) - Method in class textractor.xml.pubmedabstracts.xml.ChemicalList

addCitationSubset(CitationSubset) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addCitationSubset(int, CitationSubset) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addCitationSubset(CitationSubset) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addCitationSubset(int, CitationSubset) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addCitationSubsetItem(CitationSubsetItem) - Method in class textractor.xml.pubmed.xml.CitationSubset

addCitationSubsetItem(int, CitationSubsetItem) - Method in class textractor.xml.pubmed.xml.CitationSubset

addCitationSubsetItem(CitationSubsetItem) - Method in class textractor.xml.pubmedabstracts.xml.CitationSubset

addCitationSubsetItem(int, CitationSubsetItem) - Method in class textractor.xml.pubmedabstracts.xml.CitationSubset

addCodenItem(CodenItem) - Method in class textractor.xml.pubmed.xml.Coden

addCodenItem(int, CodenItem) - Method in class textractor.xml.pubmed.xml.Coden

addCodenItem(CodenItem) - Method in class textractor.xml.pubmedabstracts.xml.Coden

addCodenItem(int, CodenItem) - Method in class textractor.xml.pubmedabstracts.xml.Coden

addCollectionTitleItem(CollectionTitleItem) - Method in class textractor.xml.pubmed.xml.CollectionTitle

addCollectionTitleItem(int, CollectionTitleItem) - Method in class textractor.xml.pubmed.xml.CollectionTitle

addCollectionTitleItem(CollectionTitleItem) - Method in class textractor.xml.pubmedabstracts.xml.CollectionTitle

addCollectionTitleItem(int, CollectionTitleItem) - Method in class textractor.xml.pubmedabstracts.xml.CollectionTitle

addCollectiveNameItem(CollectiveNameItem) - Method in class textractor.xml.pubmed.xml.CollectiveName

addCollectiveNameItem(int, CollectiveNameItem) - Method in class textractor.xml.pubmed.xml.CollectiveName

addCollectiveNameItem(CollectiveNameItem) - Method in class textractor.xml.pubmedabstracts.xml.CollectiveName

addCollectiveNameItem(int, CollectiveNameItem) - Method in class textractor.xml.pubmedabstracts.xml.CollectiveName

addCommand(Command) - Method in class textractor.chain.AbstractSentenceProducer

See the Chain JavaDoc.

addCommand(Command) - Method in class textractor.chain.AbstractSentenceTransformer

See the Chain JavaDoc.

addComment(Comment) - Method in class textractor.xml.uniprot.xml.EntryType

addComment(int, Comment) - Method in class textractor.xml.uniprot.xml.EntryType

addCommentIn(CommentIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addCommentIn(int, CommentIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addCommentIn(CommentIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addCommentIn(int, CommentIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addCommentOn(CommentOn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addCommentOn(int, CommentOn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addCommentOn(CommentOn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addCommentOn(int, CommentOn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addComponent(Component) - Method in class textractor.xml.uniprot.xml.ProteinType

addComponent(int, Component) - Method in class textractor.xml.uniprot.xml.ProteinType

addCopyrightInformationItem(CopyrightInformationItem) - Method in class textractor.xml.pubmed.xml.CopyrightInformation

addCopyrightInformationItem(int, CopyrightInformationItem) - Method in class textractor.xml.pubmed.xml.CopyrightInformation

addCopyrightInformationItem(CopyrightInformationItem) - Method in class textractor.xml.pubmedabstracts.xml.CopyrightInformation

addCopyrightInformationItem(int, CopyrightInformationItem) - Method in class textractor.xml.pubmedabstracts.xml.CopyrightInformation

addCountryItem(CountryItem) - Method in class textractor.xml.pubmed.xml.Country

addCountryItem(int, CountryItem) - Method in class textractor.xml.pubmed.xml.Country

addCountryItem(CountryItem) - Method in class textractor.xml.pubmedabstracts.xml.Country

addCountryItem(int, CountryItem) - Method in class textractor.xml.pubmedabstracts.xml.Country

addCoverageItem(CoverageItem) - Method in class textractor.xml.pubmed.xml.Coverage

addCoverageItem(int, CoverageItem) - Method in class textractor.xml.pubmed.xml.Coverage

addCoverageItem(CoverageItem) - Method in class textractor.xml.pubmedabstracts.xml.Coverage

addCoverageItem(int, CoverageItem) - Method in class textractor.xml.pubmedabstracts.xml.Coverage

addDataBank(DataBank) - Method in class textractor.xml.pubmed.xml.DataBankList

addDataBank(int, DataBank) - Method in class textractor.xml.pubmed.xml.DataBankList

addDataBank(DataBank) - Method in class textractor.xml.pubmedabstracts.xml.DataBankList

addDataBank(int, DataBank) - Method in class textractor.xml.pubmedabstracts.xml.DataBankList

addDataBankNameItem(DataBankNameItem) - Method in class textractor.xml.pubmed.xml.DataBankName

addDataBankNameItem(int, DataBankNameItem) - Method in class textractor.xml.pubmed.xml.DataBankName

addDataBankNameItem(DataBankNameItem) - Method in class textractor.xml.pubmedabstracts.xml.DataBankName

addDataBankNameItem(int, DataBankNameItem) - Method in class textractor.xml.pubmedabstracts.xml.DataBankName

addDateIssued(DateIssued) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addDateIssued(int, DateIssued) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addDateIssued(DateIssued) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addDateIssued(int, DateIssued) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addDateIssuedItem(DateIssuedItem) - Method in class textractor.xml.pubmed.xml.DateIssued

addDateIssuedItem(int, DateIssuedItem) - Method in class textractor.xml.pubmed.xml.DateIssued

addDateIssuedItem(DateIssuedItem) - Method in class textractor.xml.pubmedabstracts.xml.DateIssued

addDateIssuedItem(int, DateIssuedItem) - Method in class textractor.xml.pubmedabstracts.xml.DateIssued

addDatesAssociatedWithNameItem(DatesAssociatedWithNameItem) - Method in class textractor.xml.pubmed.xml.DatesAssociatedWithName

addDatesAssociatedWithNameItem(int, DatesAssociatedWithNameItem) - Method in class textractor.xml.pubmed.xml.DatesAssociatedWithName

addDatesAssociatedWithNameItem(DatesAssociatedWithNameItem) - Method in class textractor.xml.pubmedabstracts.xml.DatesAssociatedWithName

addDatesAssociatedWithNameItem(int, DatesAssociatedWithNameItem) - Method in class textractor.xml.pubmedabstracts.xml.DatesAssociatedWithName

addDatesOfSerialPublication(DatesOfSerialPublication) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addDatesOfSerialPublication(int, DatesOfSerialPublication) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addDatesOfSerialPublication(DatesOfSerialPublication) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addDatesOfSerialPublication(int, DatesOfSerialPublication) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addDatesOfSerialPublicationItem(DatesOfSerialPublicationItem) - Method in class textractor.xml.pubmed.xml.DatesOfSerialPublication

addDatesOfSerialPublicationItem(int, DatesOfSerialPublicationItem) - Method in class textractor.xml.pubmed.xml.DatesOfSerialPublication

addDatesOfSerialPublicationItem(DatesOfSerialPublicationItem) - Method in class textractor.xml.pubmedabstracts.xml.DatesOfSerialPublication

addDatesOfSerialPublicationItem(int, DatesOfSerialPublicationItem) - Method in class textractor.xml.pubmedabstracts.xml.DatesOfSerialPublication

addDayItem(DayItem) - Method in class textractor.xml.pubmed.xml.Day

addDayItem(int, DayItem) - Method in class textractor.xml.pubmed.xml.Day

addDayItem(DayItem) - Method in class textractor.xml.pubmedabstracts.xml.Day

addDayItem(int, DayItem) - Method in class textractor.xml.pubmedabstracts.xml.Day

addDbReference(DbReference) - Method in class textractor.xml.uniprot.xml.CitationType

addDbReference(int, DbReference) - Method in class textractor.xml.uniprot.xml.CitationType

addDbReference(DbReference) - Method in class textractor.xml.uniprot.xml.EntryType

addDbReference(int, DbReference) - Method in class textractor.xml.uniprot.xml.EntryType

addDbReference(DbReference) - Method in class textractor.xml.uniprot.xml.Organism

addDbReference(int, DbReference) - Method in class textractor.xml.uniprot.xml.Organism

addDescriptorNameItem(DescriptorNameItem) - Method in class textractor.xml.pubmed.xml.DescriptorName

addDescriptorNameItem(int, DescriptorNameItem) - Method in class textractor.xml.pubmed.xml.DescriptorName

addDescriptorNameItem(DescriptorNameItem) - Method in class textractor.xml.pubmedabstracts.xml.DescriptorName

addDescriptorNameItem(int, DescriptorNameItem) - Method in class textractor.xml.pubmedabstracts.xml.DescriptorName

addDistance(double) - Method in class textractor.datamodel.TermPredictionStatistics

addDocumentPMID(long, long) - Method in class textractor.mg4j.docstore.DocumentStoreWriter

Add a pmid for a document number.

addDomain(Domain) - Method in class textractor.xml.uniprot.xml.ProteinType

addDomain(int, Domain) - Method in class textractor.xml.uniprot.xml.ProteinType

addEditionItem(EditionItem) - Method in class textractor.xml.pubmed.xml.Edition

addEditionItem(int, EditionItem) - Method in class textractor.xml.pubmed.xml.Edition

addEditionItem(EditionItem) - Method in class textractor.xml.pubmedabstracts.xml.Edition

addEditionItem(int, EditionItem) - Method in class textractor.xml.pubmedabstracts.xml.Edition

addEndPageItem(EndPageItem) - Method in class textractor.xml.pubmed.xml.EndPage

addEndPageItem(int, EndPageItem) - Method in class textractor.xml.pubmed.xml.EndPage

addEndPageItem(EndPageItem) - Method in class textractor.xml.pubmedabstracts.xml.EndPage

addEndPageItem(int, EndPageItem) - Method in class textractor.xml.pubmedabstracts.xml.EndPage

addEntry(Entry) - Method in class textractor.xml.uniprot.xml.Uniprot

addEntry(int, Entry) - Method in class textractor.xml.uniprot.xml.Uniprot

addErratumFor(ErratumFor) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addErratumFor(int, ErratumFor) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addErratumFor(ErratumFor) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addErratumFor(int, ErratumFor) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addErratumIn(ErratumIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addErratumIn(int, ErratumIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addErratumIn(ErratumIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addErratumIn(int, ErratumIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addEscapes(String) - Static method in error textractor.parsers.extractor.TokenMgrError

Replaces unprintable characters by their espaced (or unicode escaped) equivalents in the given string

addEvent(Event) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence3

addEvent(int, Event) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence3

addEvidence(Evidence) - Method in class textractor.xml.uniprot.xml.EntryType

addEvidence(int, Evidence) - Method in class textractor.xml.uniprot.xml.EntryType

addExpansionsItem(ExpansionsItem) - Method in class textractor.acronyms.xml.Expansions

addExpansionsItem(int, ExpansionsItem) - Method in class textractor.acronyms.xml.Expansions

addFeature(Feature) - Method in class textractor.xml.uniprot.xml.EntryType

addFeature(int, Feature) - Method in class textractor.xml.uniprot.xml.EntryType

addFirstNameItem(FirstNameItem) - Method in class textractor.xml.pubmed.xml.FirstName

addFirstNameItem(int, FirstNameItem) - Method in class textractor.xml.pubmed.xml.FirstName

addFirstNameItem(FirstNameItem) - Method in class textractor.xml.pubmedabstracts.xml.FirstName

addFirstNameItem(int, FirstNameItem) - Method in class textractor.xml.pubmedabstracts.xml.FirstName

addForeNameItem(ForeNameItem) - Method in class textractor.xml.pubmed.xml.ForeName

addForeNameItem(int, ForeNameItem) - Method in class textractor.xml.pubmed.xml.ForeName

addForeNameItem(ForeNameItem) - Method in class textractor.xml.pubmedabstracts.xml.ForeName

addForeNameItem(int, ForeNameItem) - Method in class textractor.xml.pubmedabstracts.xml.ForeName

addFrequency(Frequency) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addFrequency(int, Frequency) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addFrequency(Frequency) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addFrequency(int, Frequency) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addFrequencyItem(FrequencyItem) - Method in class textractor.xml.pubmed.xml.Frequency

addFrequencyItem(int, FrequencyItem) - Method in class textractor.xml.pubmed.xml.Frequency

addFrequencyItem(FrequencyItem) - Method in class textractor.xml.pubmedabstracts.xml.Frequency

addFrequencyItem(int, FrequencyItem) - Method in class textractor.xml.pubmedabstracts.xml.Frequency

addGene(Gene) - Method in class textractor.xml.uniprot.xml.EntryType

addGene(int, Gene) - Method in class textractor.xml.uniprot.xml.EntryType

addGeneLocation(GeneLocation) - Method in class textractor.xml.uniprot.xml.EntryType

addGeneLocation(int, GeneLocation) - Method in class textractor.xml.uniprot.xml.EntryType

addGeneralNote(GeneralNote) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addGeneralNote(int, GeneralNote) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addGeneralNote(GeneralNote) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addGeneralNote(int, GeneralNote) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addGeneralNoteItem(GeneralNoteItem) - Method in class textractor.xml.pubmed.xml.GeneralNote

addGeneralNoteItem(int, GeneralNoteItem) - Method in class textractor.xml.pubmed.xml.GeneralNote

addGeneralNoteItem(GeneralNoteItem) - Method in class textractor.xml.pubmedabstracts.xml.GeneralNote

addGeneralNoteItem(int, GeneralNoteItem) - Method in class textractor.xml.pubmedabstracts.xml.GeneralNote

addGeneSymbol(GeneSymbol) - Method in class textractor.xml.pubmed.xml.GeneSymbolList

addGeneSymbol(int, GeneSymbol) - Method in class textractor.xml.pubmed.xml.GeneSymbolList

addGeneSymbol(GeneSymbol) - Method in class textractor.xml.pubmedabstracts.xml.GeneSymbolList

addGeneSymbol(int, GeneSymbol) - Method in class textractor.xml.pubmedabstracts.xml.GeneSymbolList

addGeneSymbolItem(GeneSymbolItem) - Method in class textractor.xml.pubmed.xml.GeneSymbol

addGeneSymbolItem(int, GeneSymbolItem) - Method in class textractor.xml.pubmed.xml.GeneSymbol

addGeneSymbolItem(GeneSymbolItem) - Method in class textractor.xml.pubmedabstracts.xml.GeneSymbol

addGeneSymbolItem(int, GeneSymbolItem) - Method in class textractor.xml.pubmedabstracts.xml.GeneSymbol

addGrant(Grant) - Method in class textractor.xml.pubmed.xml.GrantList

addGrant(int, Grant) - Method in class textractor.xml.pubmed.xml.GrantList

addGrant(Grant) - Method in class textractor.xml.pubmedabstracts.xml.GrantList

addGrant(int, Grant) - Method in class textractor.xml.pubmedabstracts.xml.GrantList

addGrantIDItem(GrantIDItem) - Method in class textractor.xml.pubmed.xml.GrantID

addGrantIDItem(int, GrantIDItem) - Method in class textractor.xml.pubmed.xml.GrantID

addGrantIDItem(GrantIDItem) - Method in class textractor.xml.pubmedabstracts.xml.GrantID

addGrantIDItem(int, GrantIDItem) - Method in class textractor.xml.pubmedabstracts.xml.GrantID

addHistory(History) - Method in class textractor.xml.pubmedabstracts.xml.PubmedData

addHistory(int, History) - Method in class textractor.xml.pubmedabstracts.xml.PubmedData

addHourItem(HourItem) - Method in class textractor.xml.pubmed.xml.Hour

addHourItem(int, HourItem) - Method in class textractor.xml.pubmed.xml.Hour

addHourItem(HourItem) - Method in class textractor.xml.pubmedabstracts.xml.Hour

addHourItem(int, HourItem) - Method in class textractor.xml.pubmedabstracts.xml.Hour

addId(String) - Method in class textractor.xml.uniprot.xml.IsoformType

addId(int, String) - Method in class textractor.xml.uniprot.xml.IsoformType

addImprint(Imprint) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addImprint(int, Imprint) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addImprint(Imprint) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addImprint(int, Imprint) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addImprintItem(ImprintItem) - Method in class textractor.xml.pubmed.xml.Imprint

addImprintItem(int, ImprintItem) - Method in class textractor.xml.pubmed.xml.Imprint

addImprintItem(ImprintItem) - Method in class textractor.xml.pubmedabstracts.xml.Imprint

addImprintItem(int, ImprintItem) - Method in class textractor.xml.pubmedabstracts.xml.Imprint

addInitialsItem(InitialsItem) - Method in class textractor.xml.pubmed.xml.Initials

addInitialsItem(int, InitialsItem) - Method in class textractor.xml.pubmed.xml.Initials

addInitialsItem(InitialsItem) - Method in class textractor.xml.pubmedabstracts.xml.Initials

addInitialsItem(int, InitialsItem) - Method in class textractor.xml.pubmedabstracts.xml.Initials

addInteractant(Interactant) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence4

addInteractant(int, Interactant) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence4

addInterval(int, Interval) - Method in class textractor.tools.DocumentQueryResult

addInvestigator(Investigator) - Method in class textractor.xml.pubmed.xml.InvestigatorList

addInvestigator(int, Investigator) - Method in class textractor.xml.pubmed.xml.InvestigatorList

addInvestigator(Investigator) - Method in class textractor.xml.pubmedabstracts.xml.InvestigatorList

addInvestigator(int, Investigator) - Method in class textractor.xml.pubmedabstracts.xml.InvestigatorList

addISOAbbreviationItem(ISOAbbreviationItem) - Method in class textractor.xml.pubmed.xml.ISOAbbreviation

addISOAbbreviationItem(int, ISOAbbreviationItem) - Method in class textractor.xml.pubmed.xml.ISOAbbreviation

addISOAbbreviationItem(ISOAbbreviationItem) - Method in class textractor.xml.pubmedabstracts.xml.ISOAbbreviation

addISOAbbreviationItem(int, ISOAbbreviationItem) - Method in class textractor.xml.pubmedabstracts.xml.ISOAbbreviation

addIsoform(Isoform) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence3

addIsoform(int, Isoform) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence3

addISSNItem(ISSNItem) - Method in class textractor.xml.pubmed.xml.ISSN

addISSNItem(int, ISSNItem) - Method in class textractor.xml.pubmed.xml.ISSN

addISSNItem(ISSNItem) - Method in class textractor.xml.pubmedabstracts.xml.ISSN

addISSNItem(int, ISSNItem) - Method in class textractor.xml.pubmedabstracts.xml.ISSN

addIssueItem(IssueItem) - Method in class textractor.xml.pubmed.xml.Issue

addIssueItem(int, IssueItem) - Method in class textractor.xml.pubmed.xml.Issue

addIssueItem(IssueItem) - Method in class textractor.xml.pubmedabstracts.xml.Issue

addIssueItem(int, IssueItem) - Method in class textractor.xml.pubmedabstracts.xml.Issue

addKeyword(Keyword) - Method in class textractor.xml.pubmed.xml.KeywordList

addKeyword(int, Keyword) - Method in class textractor.xml.pubmed.xml.KeywordList

addKeyword(Keyword) - Method in class textractor.xml.pubmedabstracts.xml.KeywordList

addKeyword(int, Keyword) - Method in class textractor.xml.pubmedabstracts.xml.KeywordList

addKeyword(Keyword) - Method in class textractor.xml.uniprot.xml.EntryType

addKeyword(int, Keyword) - Method in class textractor.xml.uniprot.xml.EntryType

addKeywordItem(KeywordItem) - Method in class textractor.xml.pubmed.xml.Keyword

addKeywordItem(int, KeywordItem) - Method in class textractor.xml.pubmed.xml.Keyword

addKeywordItem(KeywordItem) - Method in class textractor.xml.pubmedabstracts.xml.Keyword

addKeywordItem(int, KeywordItem) - Method in class textractor.xml.pubmedabstracts.xml.Keyword

addKeywordList(KeywordList) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addKeywordList(int, KeywordList) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addKeywordList(KeywordList) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addKeywordList(int, KeywordList) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addKM(String) - Method in class textractor.xml.uniprot.xml.Kinetics

addKM(int, String) - Method in class textractor.xml.uniprot.xml.Kinetics

addLanguage(Language) - Method in class textractor.xml.pubmed.xml.Article

addLanguage(int, Language) - Method in class textractor.xml.pubmed.xml.Article

addLanguage(Language) - Method in class textractor.xml.pubmedabstracts.xml.Article

addLanguage(int, Language) - Method in class textractor.xml.pubmedabstracts.xml.Article

addLanguageItem(LanguageItem) - Method in class textractor.xml.pubmed.xml.Language

addLanguageItem(int, LanguageItem) - Method in class textractor.xml.pubmed.xml.Language

addLanguageItem(LanguageItem) - Method in class textractor.xml.pubmedabstracts.xml.Language

addLanguageItem(int, LanguageItem) - Method in class textractor.xml.pubmedabstracts.xml.Language

addLastNameItem(LastNameItem) - Method in class textractor.xml.pubmed.xml.LastName

addLastNameItem(int, LastNameItem) - Method in class textractor.xml.pubmed.xml.LastName

addLastNameItem(LastNameItem) - Method in class textractor.xml.pubmedabstracts.xml.LastName

addLastNameItem(int, LastNameItem) - Method in class textractor.xml.pubmedabstracts.xml.LastName

addLink(Link) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence

addLink(int, Link) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence

addLocation(Location) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence2

addLocation(int, Location) - Method in class textractor.xml.uniprot.xml.CommentTypeChoiceSequence2

addMatch(int) - Method in class textractor.tools.DocumentQueryResult

Add a match for this expansion.

addMedlineCitation(MedlineCitation) - Method in class textractor.xml.pubmed.xml.MedlineCitationSet

addMedlineCitation(int, MedlineCitation) - Method in class textractor.xml.pubmed.xml.MedlineCitationSet

addMedlineCitation(MedlineCitation) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitationSet

addMedlineCitation(int, MedlineCitation) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitationSet

addMedlineDateItem(MedlineDateItem) - Method in class textractor.xml.pubmed.xml.MedlineDate

addMedlineDateItem(int, MedlineDateItem) - Method in class textractor.xml.pubmed.xml.MedlineDate

addMedlineDateItem(MedlineDateItem) - Method in class textractor.xml.pubmedabstracts.xml.MedlineDate

addMedlineDateItem(int, MedlineDateItem) - Method in class textractor.xml.pubmedabstracts.xml.MedlineDate

addMedlinePgnItem(MedlinePgnItem) - Method in class textractor.xml.pubmed.xml.MedlinePgn

addMedlinePgnItem(int, MedlinePgnItem) - Method in class textractor.xml.pubmed.xml.MedlinePgn

addMedlinePgnItem(MedlinePgnItem) - Method in class textractor.xml.pubmedabstracts.xml.MedlinePgn

addMedlinePgnItem(int, MedlinePgnItem) - Method in class textractor.xml.pubmedabstracts.xml.MedlinePgn

addMedlineTAItem(MedlineTAItem) - Method in class textractor.xml.pubmed.xml.MedlineTA

addMedlineTAItem(int, MedlineTAItem) - Method in class textractor.xml.pubmed.xml.MedlineTA

addMedlineTAItem(MedlineTAItem) - Method in class textractor.xml.pubmedabstracts.xml.MedlineTA

addMedlineTAItem(int, MedlineTAItem) - Method in class textractor.xml.pubmedabstracts.xml.MedlineTA

addMeshHeading(MeshHeading) - Method in class textractor.xml.pubmed.xml.MeshHeadingList

addMeshHeading(int, MeshHeading) - Method in class textractor.xml.pubmed.xml.MeshHeadingList

addMeshHeading(MeshHeading) - Method in class textractor.xml.pubmedabstracts.xml.MeshHeadingList

addMeshHeading(int, MeshHeading) - Method in class textractor.xml.pubmedabstracts.xml.MeshHeadingList

addMiddleNameItem(MiddleNameItem) - Method in class textractor.xml.pubmed.xml.MiddleName

addMiddleNameItem(int, MiddleNameItem) - Method in class textractor.xml.pubmed.xml.MiddleName

addMiddleNameItem(MiddleNameItem) - Method in class textractor.xml.pubmedabstracts.xml.MiddleName

addMiddleNameItem(int, MiddleNameItem) - Method in class textractor.xml.pubmedabstracts.xml.MiddleName

addMinuteItem(MinuteItem) - Method in class textractor.xml.pubmed.xml.Minute

addMinuteItem(int, MinuteItem) - Method in class textractor.xml.pubmed.xml.Minute

addMinuteItem(MinuteItem) - Method in class textractor.xml.pubmedabstracts.xml.Minute

addMinuteItem(int, MinuteItem) - Method in class textractor.xml.pubmedabstracts.xml.Minute

addMonthItem(MonthItem) - Method in class textractor.xml.pubmed.xml.Month

addMonthItem(int, MonthItem) - Method in class textractor.xml.pubmed.xml.Month

addMonthItem(MonthItem) - Method in class textractor.xml.pubmedabstracts.xml.Month

addMonthItem(int, MonthItem) - Method in class textractor.xml.pubmedabstracts.xml.Month

addName(Name) - Method in class textractor.xml.uniprot.xml.Component

addName(int, Name) - Method in class textractor.xml.uniprot.xml.Component

addName(Name) - Method in class textractor.xml.uniprot.xml.Domain

addName(int, Name) - Method in class textractor.xml.uniprot.xml.Domain

addName(String) - Method in class textractor.xml.uniprot.xml.EntryType

addName(int, String) - Method in class textractor.xml.uniprot.xml.EntryType

addName(Name) - Method in class textractor.xml.uniprot.xml.Gene

addName(int, Name) - Method in class textractor.xml.uniprot.xml.Gene

addName(Name) - Method in class textractor.xml.uniprot.xml.IsoformType

addName(int, Name) - Method in class textractor.xml.uniprot.xml.IsoformType

addName(Name) - Method in class textractor.xml.uniprot.xml.Organism

addName(int, Name) - Method in class textractor.xml.uniprot.xml.Organism

addName(Name) - Method in class textractor.xml.uniprot.xml.ProteinType

addName(int, Name) - Method in class textractor.xml.uniprot.xml.ProteinType

addName(String) - Method in class textractor.xml.uniprot.xml.Strain

addName(int, String) - Method in class textractor.xml.uniprot.xml.Strain

addName(String) - Method in class textractor.xml.yapex.xml.ProteinNames

Method addName

addName(int, String) - Method in class textractor.xml.yapex.xml.ProteinNames

Method addName

addNameListTypeItem(NameListTypeItem) - Method in class textractor.xml.uniprot.xml.NameListType

addNameListTypeItem(int, NameListTypeItem) - Method in class textractor.xml.uniprot.xml.NameListType

addNameOfSubstanceItem(NameOfSubstanceItem) - Method in class textractor.xml.pubmed.xml.NameOfSubstance

addNameOfSubstanceItem(int, NameOfSubstanceItem) - Method in class textractor.xml.pubmed.xml.NameOfSubstance

addNameOfSubstanceItem(NameOfSubstanceItem) - Method in class textractor.xml.pubmedabstracts.xml.NameOfSubstance

addNameOfSubstanceItem(int, NameOfSubstanceItem) - Method in class textractor.xml.pubmedabstracts.xml.NameOfSubstance

addNameQualifierItem(NameQualifierItem) - Method in class textractor.xml.pubmed.xml.NameQualifier

addNameQualifierItem(int, NameQualifierItem) - Method in class textractor.xml.pubmed.xml.NameQualifier

addNameQualifierItem(NameQualifierItem) - Method in class textractor.xml.pubmedabstracts.xml.NameQualifier

addNameQualifierItem(int, NameQualifierItem) - Method in class textractor.xml.pubmedabstracts.xml.NameQualifier

addNlmDcmsIDItem(NlmDcmsIDItem) - Method in class textractor.xml.pubmed.xml.NlmDcmsID

addNlmDcmsIDItem(int, NlmDcmsIDItem) - Method in class textractor.xml.pubmed.xml.NlmDcmsID

addNlmDcmsIDItem(NlmDcmsIDItem) - Method in class textractor.xml.pubmedabstracts.xml.NlmDcmsID

addNlmDcmsIDItem(int, NlmDcmsIDItem) - Method in class textractor.xml.pubmedabstracts.xml.NlmDcmsID

addNlmUniqueIDItem(NlmUniqueIDItem) - Method in class textractor.xml.pubmed.xml.NlmUniqueID

addNlmUniqueIDItem(int, NlmUniqueIDItem) - Method in class textractor.xml.pubmed.xml.NlmUniqueID

addNlmUniqueIDItem(NlmUniqueIDItem) - Method in class textractor.xml.pubmedabstracts.xml.NlmUniqueID

addNlmUniqueIDItem(int, NlmUniqueIDItem) - Method in class textractor.xml.pubmedabstracts.xml.NlmUniqueID

addNoteItem(NoteItem) - Method in class textractor.xml.pubmed.xml.Note

addNoteItem(int, NoteItem) - Method in class textractor.xml.pubmed.xml.Note

addNoteItem(NoteItem) - Method in class textractor.xml.pubmedabstracts.xml.Note

addNoteItem(int, NoteItem) - Method in class textractor.xml.pubmedabstracts.xml.Note

addNumberOfReferencesItem(NumberOfReferencesItem) - Method in class textractor.xml.pubmed.xml.NumberOfReferences

addNumberOfReferencesItem(int, NumberOfReferencesItem) - Method in class textractor.xml.pubmed.xml.NumberOfReferences

addNumberOfReferencesItem(NumberOfReferencesItem) - Method in class textractor.xml.pubmedabstracts.xml.NumberOfReferences

addNumberOfReferencesItem(int, NumberOfReferencesItem) - Method in class textractor.xml.pubmedabstracts.xml.NumberOfReferences

addOrganism(Organism) - Method in class textractor.xml.uniprot.xml.EntryType

addOrganism(int, Organism) - Method in class textractor.xml.uniprot.xml.EntryType

addOriginalReportIn(OriginalReportIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addOriginalReportIn(int, OriginalReportIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addOriginalReportIn(OriginalReportIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addOriginalReportIn(int, OriginalReportIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addOtherAbstract(OtherAbstract) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addOtherAbstract(int, OtherAbstract) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addOtherAbstract(OtherAbstract) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addOtherAbstract(int, OtherAbstract) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addOtherID(OtherID) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addOtherID(int, OtherID) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addOtherID(OtherID) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addOtherID(int, OtherID) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addOtherIDItem(OtherIDItem) - Method in class textractor.xml.pubmed.xml.OtherID

addOtherIDItem(int, OtherIDItem) - Method in class textractor.xml.pubmed.xml.OtherID

addOtherIDItem(OtherIDItem) - Method in class textractor.xml.pubmedabstracts.xml.OtherID

addOtherIDItem(int, OtherIDItem) - Method in class textractor.xml.pubmedabstracts.xml.OtherID

addOtherInformationItem(OtherInformationItem) - Method in class textractor.xml.pubmed.xml.OtherInformation

addOtherInformationItem(int, OtherInformationItem) - Method in class textractor.xml.pubmed.xml.OtherInformation

addOtherInformationItem(OtherInformationItem) - Method in class textractor.xml.pubmedabstracts.xml.OtherInformation

addOtherInformationItem(int, OtherInformationItem) - Method in class textractor.xml.pubmedabstracts.xml.OtherInformation

addPersonalNameSubject(PersonalNameSubject) - Method in class textractor.xml.pubmed.xml.PersonalNameSubjectList

addPersonalNameSubject(int, PersonalNameSubject) - Method in class textractor.xml.pubmed.xml.PersonalNameSubjectList

addPersonalNameSubject(PersonalNameSubject) - Method in class textractor.xml.pubmedabstracts.xml.PersonalNameSubjectList

addPersonalNameSubject(int, PersonalNameSubject) - Method in class textractor.xml.pubmedabstracts.xml.PersonalNameSubjectList

addPlace(Place) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addPlace(int, Place) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addPlace(Place) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addPlace(int, Place) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addPlaceCodeItem(PlaceCodeItem) - Method in class textractor.xml.pubmed.xml.PlaceCode

addPlaceCodeItem(int, PlaceCodeItem) - Method in class textractor.xml.pubmed.xml.PlaceCode

addPlaceCodeItem(PlaceCodeItem) - Method in class textractor.xml.pubmedabstracts.xml.PlaceCode

addPlaceCodeItem(int, PlaceCodeItem) - Method in class textractor.xml.pubmedabstracts.xml.PlaceCode

addPlaceItem(PlaceItem) - Method in class textractor.xml.pubmed.xml.Place

addPlaceItem(int, PlaceItem) - Method in class textractor.xml.pubmed.xml.Place

addPlaceItem(PlaceItem) - Method in class textractor.xml.pubmedabstracts.xml.Place

addPlaceItem(int, PlaceItem) - Method in class textractor.xml.pubmedabstracts.xml.Place

addPMID(PMID) - Method in class textractor.xml.pubmed.xml.DeleteCitation

addPMID(int, PMID) - Method in class textractor.xml.pubmed.xml.DeleteCitation

addPMID(PMID) - Method in class textractor.xml.pubmedabstracts.xml.DeleteCitation

addPMID(int, PMID) - Method in class textractor.xml.pubmedabstracts.xml.DeleteCitation

addPMIDItem(PMIDItem) - Method in class textractor.xml.pubmed.xml.PMID

addPMIDItem(int, PMIDItem) - Method in class textractor.xml.pubmed.xml.PMID

addPMIDItem(PMIDItem) - Method in class textractor.xml.pubmedabstracts.xml.PMID

addPMIDItem(int, PMIDItem) - Method in class textractor.xml.pubmedabstracts.xml.PMID

addProjectedPublicationDateItem(ProjectedPublicationDateItem) - Method in class textractor.xml.pubmed.xml.ProjectedPublicationDate

addProjectedPublicationDateItem(int, ProjectedPublicationDateItem) - Method in class textractor.xml.pubmed.xml.ProjectedPublicationDate

addProjectedPublicationDateItem(ProjectedPublicationDateItem) - Method in class textractor.xml.pubmedabstracts.xml.ProjectedPublicationDate

addProjectedPublicationDateItem(int, ProjectedPublicationDateItem) - Method in class textractor.xml.pubmedabstracts.xml.ProjectedPublicationDate

addProperty(Property) - Method in class textractor.xml.uniprot.xml.DbReferenceType

addProperty(int, Property) - Method in class textractor.xml.uniprot.xml.DbReferenceType

addPublicationEndYearItem(PublicationEndYearItem) - Method in class textractor.xml.pubmed.xml.PublicationEndYear

addPublicationEndYearItem(int, PublicationEndYearItem) - Method in class textractor.xml.pubmed.xml.PublicationEndYear

addPublicationEndYearItem(PublicationEndYearItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationEndYear

addPublicationEndYearItem(int, PublicationEndYearItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationEndYear

addPublicationFirstYearItem(PublicationFirstYearItem) - Method in class textractor.xml.pubmed.xml.PublicationFirstYear

addPublicationFirstYearItem(int, PublicationFirstYearItem) - Method in class textractor.xml.pubmed.xml.PublicationFirstYear

addPublicationFirstYearItem(PublicationFirstYearItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationFirstYear

addPublicationFirstYearItem(int, PublicationFirstYearItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationFirstYear

addPublicationStatusItem(PublicationStatusItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationStatus

addPublicationStatusItem(int, PublicationStatusItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationStatus

addPublicationType(PublicationType) - Method in class textractor.xml.pubmed.xml.PublicationTypeList

addPublicationType(int, PublicationType) - Method in class textractor.xml.pubmed.xml.PublicationTypeList

addPublicationType(PublicationType) - Method in class textractor.xml.pubmedabstracts.xml.PublicationTypeList

addPublicationType(int, PublicationType) - Method in class textractor.xml.pubmedabstracts.xml.PublicationTypeList

addPublicationTypeItem(PublicationTypeItem) - Method in class textractor.xml.pubmed.xml.PublicationType

addPublicationTypeItem(int, PublicationTypeItem) - Method in class textractor.xml.pubmed.xml.PublicationType

addPublicationTypeItem(PublicationTypeItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationType

addPublicationTypeItem(int, PublicationTypeItem) - Method in class textractor.xml.pubmedabstracts.xml.PublicationType

addPublisher(Publisher) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addPublisher(int, Publisher) - Method in class textractor.xml.pubmed.xml.PublicationInfo

addPublisher(Publisher) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addPublisher(int, Publisher) - Method in class textractor.xml.pubmedabstracts.xml.PublicationInfo

addPublisherItem(PublisherItem) - Method in class textractor.xml.pubmed.xml.Publisher

addPublisherItem(int, PublisherItem) - Method in class textractor.xml.pubmed.xml.Publisher

addPublisherItem(PublisherItem) - Method in class textractor.xml.pubmedabstracts.xml.Publisher

addPublisherItem(int, PublisherItem) - Method in class textractor.xml.pubmedabstracts.xml.Publisher

addPubmedArticleSetItem(PubmedArticleSetItem) - Method in class textractor.xml.pubmedabstracts.xml.PubmedArticleSet

addPubmedArticleSetItem(int, PubmedArticleSetItem) - Method in class textractor.xml.pubmedabstracts.xml.PubmedArticleSet

addPubMedPubDate(PubMedPubDate) - Method in class textractor.xml.pubmedabstracts.xml.History

addPubMedPubDate(int, PubMedPubDate) - Method in class textractor.xml.pubmedabstracts.xml.History

addQualifierName(QualifierName) - Method in class textractor.xml.pubmed.xml.MeshHeading

addQualifierName(int, QualifierName) - Method in class textractor.xml.pubmed.xml.MeshHeading

addQualifierName(QualifierName) - Method in class textractor.xml.pubmedabstracts.xml.MeshHeading

addQualifierName(int, QualifierName) - Method in class textractor.xml.pubmedabstracts.xml.MeshHeading

addQualifierNameItem(QualifierNameItem) - Method in class textractor.xml.pubmed.xml.QualifierName

addQualifierNameItem(int, QualifierNameItem) - Method in class textractor.xml.pubmed.xml.QualifierName

addQualifierNameItem(QualifierNameItem) - Method in class textractor.xml.pubmedabstracts.xml.QualifierName

addQualifierNameItem(int, QualifierNameItem) - Method in class textractor.xml.pubmedabstracts.xml.QualifierName

addReference(Reference) - Method in class textractor.xml.uniprot.xml.EntryType

addReference(int, Reference) - Method in class textractor.xml.uniprot.xml.EntryType

addRefSourceItem(RefSourceItem) - Method in class textractor.xml.pubmed.xml.RefSource

addRefSourceItem(int, RefSourceItem) - Method in class textractor.xml.pubmed.xml.RefSource

addRefSourceItem(RefSourceItem) - Method in class textractor.xml.pubmedabstracts.xml.RefSource

addRefSourceItem(int, RefSourceItem) - Method in class textractor.xml.pubmedabstracts.xml.RefSource

addRegistryNumberItem(RegistryNumberItem) - Method in class textractor.xml.pubmed.xml.RegistryNumber

addRegistryNumberItem(int, RegistryNumberItem) - Method in class textractor.xml.pubmed.xml.RegistryNumber

addRegistryNumberItem(RegistryNumberItem) - Method in class textractor.xml.pubmedabstracts.xml.RegistryNumber

addRegistryNumberItem(int, RegistryNumberItem) - Method in class textractor.xml.pubmedabstracts.xml.RegistryNumber

addReprintIn(ReprintIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addReprintIn(int, ReprintIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addReprintIn(ReprintIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addReprintIn(int, ReprintIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addReprintOf(ReprintOf) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addReprintOf(int, ReprintOf) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addReprintOf(ReprintOf) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addReprintOf(int, ReprintOf) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRepublishedFrom(RepublishedFrom) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRepublishedFrom(int, RepublishedFrom) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRepublishedFrom(RepublishedFrom) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRepublishedFrom(int, RepublishedFrom) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRepublishedIn(RepublishedIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRepublishedIn(int, RepublishedIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRepublishedIn(RepublishedIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRepublishedIn(int, RepublishedIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRetractionIn(RetractionIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRetractionIn(int, RetractionIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRetractionIn(RetractionIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRetractionIn(int, RetractionIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRetractionOf(RetractionOf) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRetractionOf(int, RetractionOf) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addRetractionOf(RetractionOf) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addRetractionOf(int, RetractionOf) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addScope(String) - Method in class textractor.xml.uniprot.xml.SptrCitationGroup

addScope(int, String) - Method in class textractor.xml.uniprot.xml.SptrCitationGroup

addSeasonItem(SeasonItem) - Method in class textractor.xml.pubmed.xml.Season

addSeasonItem(int, SeasonItem) - Method in class textractor.xml.pubmed.xml.Season

addSeasonItem(SeasonItem) - Method in class textractor.xml.pubmedabstracts.xml.Season

addSeasonItem(int, SeasonItem) - Method in class textractor.xml.pubmedabstracts.xml.Season

addSecondItem(SecondItem) - Method in class textractor.xml.pubmed.xml.Second

addSecondItem(int, SecondItem) - Method in class textractor.xml.pubmed.xml.Second

addSecondItem(SecondItem) - Method in class textractor.xml.pubmedabstracts.xml.Second

addSecondItem(int, SecondItem) - Method in class textractor.xml.pubmedabstracts.xml.Second

addSentenceProcessedListener(SentenceProcessedListener) - Method in class textractor.sentence.AbstractSentenceProcessor

Add a SentenceProcessedListener to the listener list.

addSentenceProcessedListener(SentenceProcessedListener) - Method in interface textractor.sentence.SentenceProcessor

Adds an event listener to be invoked whenever a sentence is processed.

addSentenceProcessingCompleteListener(SentenceProcessingCompleteListener) - Method in class textractor.sentence.AbstractSentenceProcessor

Add a SentenceProcessingCompleteListener to the listener list.

addSentenceProcessingCompleteListener(SentenceProcessingCompleteListener) - Method in interface textractor.sentence.SentenceProcessor

Adds an event listener to be invoked when sentence processing is complete.

addSourceDataTypeItem(SourceDataTypeItem) - Method in class textractor.xml.uniprot.xml.SourceDataType

addSourceDataTypeItem(int, SourceDataTypeItem) - Method in class textractor.xml.uniprot.xml.SourceDataType

addSpaceFlightMission(SpaceFlightMission) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addSpaceFlightMission(int, SpaceFlightMission) - Method in class textractor.xml.pubmed.xml.MedlineCitation

addSpaceFlightMission(SpaceFlightMission) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addSpaceFlightMission(int, SpaceFlightMission) - Method in class textractor.xml.pubmedabstracts.xml.MedlineCitation

addSpaceFlightMissionItem(SpaceFlightMissionItem) - Method in class textractor.xml.pubmed.xml.SpaceFlightMission

addSpaceFlightMissionItem(int, SpaceFlightMissionItem) - Method in class textractor.xml.pubmed.xml.SpaceFlightMission

addSpaceFlightMissionItem(SpaceFlightMissionItem) - Method in class textractor.xml.pubmedabstracts.xml.SpaceFlightMission

addSpaceFlightMissionItem(int, SpaceFlightMissionItem) - Method in class textractor.xml.pubmedabstracts.xml.SpaceFlightMission

addStartPageItem(StartPageItem) - Method in class textractor.xml.pubmed.xml.StartPage

addStartPageItem(int, StartPageItem) - Method in class textractor.xml.pubmed.xml.StartPage

addStartPageItem(StartPageItem) - Method in class textractor.xml.pubmedabstracts.xml.StartPage

addStartPageItem(int, StartPageItem) - Method in class textractor.xml.pubmedabstracts.xml.StartPage

addSuffixItem(SuffixItem) - Method in class textractor.xml.pubmed.xml.Suffix

addSuffixItem(int, SuffixItem) - Method in class textractor.xml.pubmed.xml.Suffix

addSuffixItem(SuffixItem) - Method in class textractor.xml.pubmedabstracts.xml.Suffix

addSuffixItem(int, SuffixItem) - Method in class textractor.xml.pubmedabstracts.xml.Suffix

addSummaryForPatientsIn(SummaryForPatientsIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addSummaryForPatientsIn(int, SummaryForPatientsIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addSummaryForPatientsIn(SummaryForPatientsIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addSummaryForPatientsIn(int, SummaryForPatientsIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addSupportToWord(int, int) - Method in class textractor.tools.expansion.CandidateExpansion

addTaxon(String) - Method in class textractor.xml.uniprot.xml.Lineage

addTaxon(int, String) - Method in class textractor.xml.uniprot.xml.Lineage

addTerm(String) - Method in class textractor.caseInsensitive.CaseInsensitiveStore

Try to add a term to the CaseInsensitiveStore.

addTermOccurrence(TermOccurrence) - Method in class textractor.datamodel.Article

addTermPredictionStatistic(TermPredictionStatistics) - Method in class textractor.datamodel.Article

addTerms(Collection<String>) - Method in class textractor.tools.lookup.Dictionary

Add additional term list to existing dictionary.

addTitleAssociatedWithNameItem(TitleAssociatedWithNameItem) - Method in class textractor.xml.pubmed.xml.TitleAssociatedWithName

addTitleAssociatedWithNameItem(int, TitleAssociatedWithNameItem) - Method in class textractor.xml.pubmed.xml.TitleAssociatedWithName

addTitleAssociatedWithNameItem(TitleAssociatedWithNameItem) - Method in class textractor.xml.pubmedabstracts.xml.TitleAssociatedWithName

addTitleAssociatedWithNameItem(int, TitleAssociatedWithNameItem) - Method in class textractor.xml.pubmedabstracts.xml.TitleAssociatedWithName

addTitleItem(TitleItem) - Method in class textractor.xml.pubmed.xml.Title

addTitleItem(int, TitleItem) - Method in class textractor.xml.pubmed.xml.Title

addTitleItem(TitleItem) - Method in class textractor.xml.pubmedabstracts.xml.Title

addTitleItem(int, TitleItem) - Method in class textractor.xml.pubmedabstracts.xml.Title

addToTermPredictionCount(int) - Method in class textractor.datamodel.TermPredictionStatistics

addUpdateIn(UpdateIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addUpdateIn(int, UpdateIn) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addUpdateIn(UpdateIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addUpdateIn(int, UpdateIn) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addUpdateOf(UpdateOf) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addUpdateOf(int, UpdateOf) - Method in class textractor.xml.pubmed.xml.CommentsCorrections

addUpdateOf(UpdateOf) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addUpdateOf(int, UpdateOf) - Method in class textractor.xml.pubmedabstracts.xml.CommentsCorrections

addURLItem(URLItem) - Method in class textractor.xml.pubmedabstracts.xml.URL

addURLItem(int, URLItem) - Method in class textractor.xml.pubmedabstracts.xml.URL

addVariation(String) - Method in class textractor.xml.uniprot.xml.FeatureType

addVariation(int, String) - Method in class textractor.xml.uniprot.xml.FeatureType

addVernacularTitleItem(VernacularTitleItem) - Method in class textractor.xml.pubmed.xml.VernacularTitle

addVernacularTitleItem(int, VernacularTitleItem) - Method in class textractor.xml.pubmed.xml.VernacularTitle

addVernacularTitleItem(VernacularTitleItem) - Method in class textractor.xml.pubmedabstracts.xml.VernacularTitle

addVernacularTitleItem(int, VernacularTitleItem) - Method in class textractor.xml.pubmedabstracts.xml.VernacularTitle

addVmax(String) - Method in class textractor.xml.uniprot.xml.Kinetics

addVmax(int, String) - Method in class textractor.xml.uniprot.xml.Kinetics

addVolumeItem(VolumeItem) - Method in class textractor.xml.pubmed.xml.Volume

addVolumeItem(int, VolumeItem) - Method in class textractor.xml.pubmed.xml.Volume

addVolumeItem(VolumeItem) - Method in class textractor.xml.pubmedabstracts.xml.Volume

addVolumeItem(int, VolumeItem) - Method in class textractor.xml.pubmedabstracts.xml.Volume

addWordsToTerms(int[], int, int, int[]) - Method in class textractor.datamodel.SingleBagOfWordFeatureCreationParameters

To find out what terms are in the window and add them to the non-redundant termsInWindows.

addYearItem(YearItem) - Method in class textractor.xml.pubmed.xml.Year

addYearItem(int, YearItem) - Method in class textractor.xml.pubmed.xml.Year

addYearItem(YearItem) - Method in class textractor.xml.pubmedabstracts.xml.Year

addYearItem(int, YearItem) - Method in class textractor.xml.pubmedabstracts.xml.Year

adjust(int, float, int) - Method in class textractor.tools.expansion.CandidateExpansion

AF - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The instance of the AF type

AF_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The AF type

Affiliation - Class in textractor.xml.pubmed.xml

Class Affiliation.

Affiliation() - Constructor for class textractor.xml.pubmed.xml.Affiliation

Affiliation - Class in textractor.xml.pubmedabstracts.xml

Class Affiliation.

Affiliation() - Constructor for class textractor.xml.pubmedabstracts.xml.Affiliation

AffiliationDescriptor - Class in textractor.xml.pubmed.xml

Class AffiliationDescriptor.

AffiliationDescriptor() - Constructor for class textractor.xml.pubmed.xml.AffiliationDescriptor

AffiliationDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AffiliationDescriptor.

AffiliationDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AffiliationDescriptor

AffiliationItem - Class in textractor.xml.pubmed.xml

Class AffiliationItem.

AffiliationItem() - Constructor for class textractor.xml.pubmed.xml.AffiliationItem

AffiliationItem - Class in textractor.xml.pubmedabstracts.xml

Class AffiliationItem.

AffiliationItem() - Constructor for class textractor.xml.pubmedabstracts.xml.AffiliationItem

AffiliationItemDescriptor - Class in textractor.xml.pubmed.xml

Class AffiliationItemDescriptor.

AffiliationItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.AffiliationItemDescriptor

AffiliationItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AffiliationItemDescriptor.

AffiliationItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AffiliationItemDescriptor

Agency - Class in textractor.xml.pubmed.xml

Class Agency.

Agency() - Constructor for class textractor.xml.pubmed.xml.Agency

Agency - Class in textractor.xml.pubmedabstracts.xml

Class Agency.

Agency() - Constructor for class textractor.xml.pubmedabstracts.xml.Agency

AgencyDescriptor - Class in textractor.xml.pubmed.xml

Class AgencyDescriptor.

AgencyDescriptor() - Constructor for class textractor.xml.pubmed.xml.AgencyDescriptor

AgencyDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AgencyDescriptor.

AgencyDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AgencyDescriptor

AgencyItem - Class in textractor.xml.pubmed.xml

Class AgencyItem.

AgencyItem() - Constructor for class textractor.xml.pubmed.xml.AgencyItem

AgencyItem - Class in textractor.xml.pubmedabstracts.xml

Class AgencyItem.

AgencyItem() - Constructor for class textractor.xml.pubmedabstracts.xml.AgencyItem

AgencyItemDescriptor - Class in textractor.xml.pubmed.xml

Class AgencyItemDescriptor.

AgencyItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.AgencyItemDescriptor

AgencyItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AgencyItemDescriptor.

AgencyItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AgencyItemDescriptor

AHEADOFPRINT - Static variable in class textractor.xml.pubmedabstracts.xml.types.PubMedPubDatePubStatusType

The instance of the aheadofprint type

AHEADOFPRINT_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.PubMedPubDatePubStatusType

The aheadofprint type

AIDS - Static variable in class textractor.xml.pubmed.xml.types.OtherAbstractTypeType

The instance of the AIDS type

AIDS - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherAbstractTypeType

The instance of the AIDS type

AIDS_TYPE - Static variable in class textractor.xml.pubmed.xml.types.OtherAbstractTypeType

The AIDS type

AIDS_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherAbstractTypeType

The AIDS type

ALLERGEN - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The instance of the allergen type

ALLERGEN_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The allergen type

allocate(int) - Method in class textractor.database.TermDocumentPositions

Allocate storage for a given number of documents.

allocateNumDocForTerm() - Method in class textractor.tfidf.TfIdfCalculator

Return the NumDocForTerm array.

ALTERNATIVE_INITIATION - Static variable in class textractor.xml.uniprot.xml.types.EventTypeTypeType

The instance of the alternative initiation type

ALTERNATIVE_INITIATION_TYPE - Static variable in class textractor.xml.uniprot.xml.types.EventTypeTypeType

The alternative initiation type

ALTERNATIVE_PRODUCTS - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The instance of the alternative products type

ALTERNATIVE_PRODUCTS_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The alternative products type

ALTERNATIVE_PROMOTER - Static variable in class textractor.xml.uniprot.xml.types.EventTypeTypeType

The instance of the alternative promoter type

ALTERNATIVE_PROMOTER_TYPE - Static variable in class textractor.xml.uniprot.xml.types.EventTypeTypeType

The alternative promoter type

ALTERNATIVE_SPLICING - Static variable in class textractor.xml.uniprot.xml.types.EventTypeTypeType

The instance of the alternative splicing type

ALTERNATIVE_SPLICING_TYPE - Static variable in class textractor.xml.uniprot.xml.types.EventTypeTypeType

The alternative splicing type

AmbiguityDocumentIterator - Class in textractor.mg4j.document

Document iterator for ambiguity documents.

AmbiguityDocumentIterator(DbManager, SentenceFilter, DocumentFactory, int) - Constructor for class textractor.mg4j.document.AmbiguityDocumentIterator

AmbiguityDocumentIterator(DbManager, DocumentFactory, int) - Constructor for class textractor.mg4j.document.AmbiguityDocumentIterator

AmbiguityDocumentSequence - Class in textractor.mg4j.document

Created by IntelliJ IDEA.

AmbiguityDocumentSequence(DbManager, TextractorDocumentFactory, int, SentenceFilter) - Constructor for class textractor.mg4j.document.AmbiguityDocumentSequence

AmbiguityDocumentSequence(DbManager, TextractorDocumentFactory, int) - Constructor for class textractor.mg4j.document.AmbiguityDocumentSequence

AmbiguityDocumentSequence(TextractorDocumentFactory, int) - Constructor for class textractor.mg4j.document.AmbiguityDocumentSequence

AnalyzeQueries - Class in textractor.tools

User: Fabien Campagne Date: Jul 30, 2005 Time: 5:02:01 PM

AnalyzeQueries() - Constructor for class textractor.tools.AnalyzeQueries

AND - Static variable in interface textractor.parsers.extractor.ExtractionEngineConstants

AnnotatedTerm - Class in textractor.datamodel.annotation

Created by IntelliJ IDEA.

AnnotatedTerm() - Constructor for class textractor.datamodel.annotation.AnnotatedTerm

ANNOTATION_BIND - Static variable in class textractor.datamodel.annotation.DoubleTermAnnotation

ANNOTATION_MULTICLASS - Static variable in class textractor.datamodel.annotation.SingleTermAnnotation

ANNOTATION_MUTATION - Static variable in class textractor.datamodel.annotation.SingleTermAnnotation

ANNOTATION_PHOSPHORYLATE - Static variable in class textractor.datamodel.annotation.DoubleTermAnnotation

ANNOTATION_PROTEIN - Static variable in class textractor.datamodel.annotation.SingleTermAnnotation

AnnotationFormatReader - Class in textractor.learning

Reads text in a format suitable for human annotation and machine parsing.

AnnotationFormatReader(TextractorManager, Reader) - Constructor for class textractor.learning.AnnotationFormatReader

Constructs an instance to write the format to the given reader.

AnnotationFormatWriter - Class in textractor.learning

Writes text in a format suitable for human annotation and machine parsing.

AnnotationFormatWriter(DocumentIndexManager, Writer, boolean) - Constructor for class textractor.learning.AnnotationFormatWriter

Constructs an instance to write the format to the given writer.

annotationLabel(AnnotationSource) - Method in class textractor.learning.BagOfWordExporter

annotationLabel(AnnotationSource) - Method in class textractor.learning.MultiClassBagOfWordExporter

for multiclass input into SVM Light

annotationLabel(AnnotationSource) - Method in class textractor.learning.MutationBagOfWordExporter

annotationLabel(AnnotationSource) - Method in class textractor.learning.PhosphorylateBagOfWordExporter

annotationLabel(AnnotationSource) - Method in class textractor.learning.ProteinNameBagOfWordExporter

AnnotationSource - Interface in textractor.datamodel.annotation

A source of annotation information.

appendDocument(int, int[]) - Method in class textractor.mg4j.docstore.DocumentStoreWriter

Append a document to this docstore at the given document number.

appendDocument(int, int[]) - Method in class textractor.mg4j.docstore.TermDocumentFrequencyWriter

appendDocumentString(int, String) - Method in class textractor.mg4j.docstore.StringPerDocumentWriter

Append the string to external storage.

appendPositions(List<IntRange>) - Method in class textractor.mg4j.docstore.DocumentStoreWriter

Append position information to the document store.

appendSentencesInOneDocument - Variable in class textractor.chain.loader.AbstractFileLoader

Indicates that each article should produce a single sentence with all the article text.

appendSentencesInOneDocument - Variable in class textractor.html.AbstractHtml2Text

appendWithoutDuplication(String, String, String) - Static method in class textractor.chain.loader.SfnArticleLoader

AQuery - Class in textractor.tools.ambiguity

User: Fabien Campagne Date: Jul 31, 2005 Time: 5:42:50 PM

AQuery(String[]) - Constructor for class textractor.tools.ambiguity.AQuery

AR - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The instance of the AR type

AR_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The AR type

args - Variable in class textractor.tools.BuildDocumentIndexFromHTMLArticles

ARPL - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The instance of the ARPL type

ARPL - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The instance of the ARPL type

ARPL_TYPE - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The ARPL type

ARPL_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The ARPL type

article - Variable in class textractor.chain.ArticleSentencesPair

Article - Class in textractor.datamodel

Article() - Constructor for class textractor.datamodel.Article

Create a new article.

Article - Class in textractor.xml.pubmed.xml

Class Article.

Article() - Constructor for class textractor.xml.pubmed.xml.Article

Article - Class in textractor.xml.pubmedabstracts.xml

Class Article.

Article() - Constructor for class textractor.xml.pubmedabstracts.xml.Article

ArticleChoice - Class in textractor.xml.pubmed.xml

Class ArticleChoice.

ArticleChoice() - Constructor for class textractor.xml.pubmed.xml.ArticleChoice

ArticleChoice - Class in textractor.xml.pubmedabstracts.xml

Class ArticleChoice.

ArticleChoice() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleChoice

ArticleChoiceDescriptor - Class in textractor.xml.pubmed.xml

Class ArticleChoiceDescriptor.

ArticleChoiceDescriptor() - Constructor for class textractor.xml.pubmed.xml.ArticleChoiceDescriptor

ArticleChoiceDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleChoiceDescriptor.

ArticleChoiceDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleChoiceDescriptor

articleChunkSize - Variable in class textractor.html.AbstractHtml2Text

ArticleDate - Class in textractor.xml.pubmed.xml

Class ArticleDate.

ArticleDate() - Constructor for class textractor.xml.pubmed.xml.ArticleDate

ArticleDate - Class in textractor.xml.pubmedabstracts.xml

Class ArticleDate.

ArticleDate() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleDate

ArticleDateDescriptor - Class in textractor.xml.pubmed.xml

Class ArticleDateDescriptor.

ArticleDateDescriptor() - Constructor for class textractor.xml.pubmed.xml.ArticleDateDescriptor

ArticleDateDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleDateDescriptor.

ArticleDateDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleDateDescriptor

ArticleDateSequenceSequence - Class in textractor.xml.pubmed.xml

Class ArticleDateSequenceSequence.

ArticleDateSequenceSequence() - Constructor for class textractor.xml.pubmed.xml.ArticleDateSequenceSequence

ArticleDateSequenceSequence - Class in textractor.xml.pubmedabstracts.xml

Class ArticleDateSequenceSequence.

ArticleDateSequenceSequence() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleDateSequenceSequence

ArticleDateSequenceSequenceDescriptor - Class in textractor.xml.pubmed.xml

Class ArticleDateSequenceSequenceDescriptor.

ArticleDateSequenceSequenceDescriptor() - Constructor for class textractor.xml.pubmed.xml.ArticleDateSequenceSequenceDescriptor

ArticleDateSequenceSequenceDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleDateSequenceSequenceDescriptor.

ArticleDateSequenceSequenceDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleDateSequenceSequenceDescriptor

ArticleDateSequenceSequenceSequence - Class in textractor.xml.pubmed.xml

Class ArticleDateSequenceSequenceSequence.

ArticleDateSequenceSequenceSequence() - Constructor for class textractor.xml.pubmed.xml.ArticleDateSequenceSequenceSequence

ArticleDateSequenceSequenceSequence - Class in textractor.xml.pubmedabstracts.xml

Class ArticleDateSequenceSequenceSequence.

ArticleDateSequenceSequenceSequence() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleDateSequenceSequenceSequence

ArticleDateSequenceSequenceSequenceDescriptor - Class in textractor.xml.pubmed.xml

Class ArticleDateSequenceSequenceSequenceDescriptor.

ArticleDateSequenceSequenceSequenceDescriptor() - Constructor for class textractor.xml.pubmed.xml.ArticleDateSequenceSequenceSequenceDescriptor

ArticleDateSequenceSequenceSequenceDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleDateSequenceSequenceSequenceDescriptor.

ArticleDateSequenceSequenceSequenceDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleDateSequenceSequenceSequenceDescriptor

ArticleDescriptor - Class in textractor.xml.pubmed.xml

Class ArticleDescriptor.

ArticleDescriptor() - Constructor for class textractor.xml.pubmed.xml.ArticleDescriptor

ArticleDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleDescriptor.

ArticleDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleDescriptor

ArticleId - Class in textractor.xml.pubmedabstracts.xml

Class ArticleId.

ArticleId() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleId

ArticleIdDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleIdDescriptor.

ArticleIdDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleIdDescriptor

ArticleIdItem - Class in textractor.xml.pubmedabstracts.xml

Class ArticleIdItem.

ArticleIdItem() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleIdItem

ArticleIdItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleIdItemDescriptor.

ArticleIdItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleIdItemDescriptor

ArticleIdItemIdTypeType - Class in textractor.xml.pubmedabstracts.xml.types

Class ArticleIdItemIdTypeType.

ArticleIdItemIdTypeTypeDescriptor - Class in textractor.xml.pubmedabstracts.xml.types

Class ArticleIdItemIdTypeTypeDescriptor.

ArticleIdItemIdTypeTypeDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.types.ArticleIdItemIdTypeTypeDescriptor

ArticleIdList - Class in textractor.xml.pubmedabstracts.xml

Class ArticleIdList.

ArticleIdList() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleIdList

ArticleIdListDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleIdListDescriptor.

ArticleIdListDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleIdListDescriptor

ArticleInfo - Class in textractor.datamodel

ArticleInfo() - Constructor for class textractor.datamodel.ArticleInfo

articleParsed(Article, MutableString) - Method in class textractor.chain.loader.OmimArticleLoader

articleParsed(Article, MutableString) - Method in interface textractor.chain.loader.ParsedArticleHandler

ArticlePool - Class in textractor.datamodel

Created by IntelliJ IDEA.

ArticlePool() - Constructor for class textractor.datamodel.ArticlePool

articlePool - Variable in class textractor.tools.BuildDocumentIndexFromHTMLArticles

articleProcessed(ProcessingEvent<ArticleProcessor, Article>) - Method in interface textractor.event.article.ArticleProcessedListener

This method gets called when a sentence is processed.

ArticleProcessedListener - Interface in textractor.event.article

A "SentenceProcessed" event gets fired whenever a SentenceProcessor processes a Sentence.

ArticleProcessingCompleteEvent - Class in textractor.event.article

Events associated with sentence processing.

ArticleProcessingCompleteEvent(SentenceProcessor) - Constructor for class textractor.event.article.ArticleProcessingCompleteEvent

Creates a new event object.

ArticleProcessingCompleteListener - Interface in textractor.event.article

A "SentenceProcessingComplete" event gets fired whenever a SentenceProcessor has finished processing Sentences.

ArticleProcessor - Interface in textractor.article

Implementations of this class perform operations on Articles.

ArticleProducer - Interface in textractor.article

Classes that implement this interface are capable of creating new Article objects on demand.

ArticlePubModelType - Class in textractor.xml.pubmed.xml.types

Class ArticlePubModelType.

ArticlePubModelType - Class in textractor.xml.pubmedabstracts.xml.types

Class ArticlePubModelType.

ArticlePubModelTypeDescriptor - Class in textractor.xml.pubmed.xml.types

Class ArticlePubModelTypeDescriptor.

ArticlePubModelTypeDescriptor() - Constructor for class textractor.xml.pubmed.xml.types.ArticlePubModelTypeDescriptor

ArticlePubModelTypeDescriptor - Class in textractor.xml.pubmedabstracts.xml.types

Class ArticlePubModelTypeDescriptor.

ArticlePubModelTypeDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.types.ArticlePubModelTypeDescriptor

ArticleSentencesPair - Class in textractor.chain

A container used to group sentences together with the article they relate to.

ArticleSentencesPair(Article, Collection<Sentence>) - Constructor for class textractor.chain.ArticleSentencesPair

ArticleSingleTermAnnotationIterator - Class in textractor.datamodel.annotation

Created by IntelliJ IDEA.

ArticleSingleTermAnnotationIterator(TextractorManager, DocumentIndexManager, Article, int[]) - Constructor for class textractor.datamodel.annotation.ArticleSingleTermAnnotationIterator

Creates an iterator to iterate through annotations that would be produced from an article and a term.

ArticleSingleTermAnnotationSource - Class in textractor.datamodel.annotation

This implementation acts like an annotation without storing one persistently.

ArticleSingleTermAnnotationSource(Sentence, int[], String, int) - Constructor for class textractor.datamodel.annotation.ArticleSingleTermAnnotationSource

ArticleTermCount - Class in textractor.tools

This class determines the frequency of all terms in an Article, and adds the most common terms as an array of TermOccurrence to the relevant Article.

ArticleTermCount() - Constructor for class textractor.tools.ArticleTermCount

Create a new ArticleTermCount object.

ArticleTermCount(String[]) - Constructor for class textractor.tools.ArticleTermCount

ArticleTitle - Class in textractor.xml.pubmed.xml

Class ArticleTitle.

ArticleTitle() - Constructor for class textractor.xml.pubmed.xml.ArticleTitle

ArticleTitle - Class in textractor.xml.pubmedabstracts.xml

Class ArticleTitle.

ArticleTitle() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleTitle

ArticleTitleDescriptor - Class in textractor.xml.pubmed.xml

Class ArticleTitleDescriptor.

ArticleTitleDescriptor() - Constructor for class textractor.xml.pubmed.xml.ArticleTitleDescriptor

ArticleTitleDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleTitleDescriptor.

ArticleTitleDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleTitleDescriptor

ArticleTitleItem - Class in textractor.xml.pubmed.xml

Class ArticleTitleItem.

ArticleTitleItem() - Constructor for class textractor.xml.pubmed.xml.ArticleTitleItem

ArticleTitleItem - Class in textractor.xml.pubmedabstracts.xml

Class ArticleTitleItem.

ArticleTitleItem() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleTitleItem

ArticleTitleItemDescriptor - Class in textractor.xml.pubmed.xml

Class ArticleTitleItemDescriptor.

ArticleTitleItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.ArticleTitleItemDescriptor

ArticleTitleItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ArticleTitleItemDescriptor.

ArticleTitleItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ArticleTitleItemDescriptor

AS - Static variable in interface textractor.parsers.extractor.ExtractionEngineConstants

asCharSequence(Object) - Static method in class textractor.chain.docstore.DocumentStoreBuilder

Of obj is a CharSequence, this will return obj casted to a CharSequence.

assureFieldType(TextractorFieldInfo, Object) - Static method in class textractor.chain.indexer.Indexer

Assure that value is appropriate for fieldInfo.type.

attributesMap - Variable in class textractor.chain.loader.XmlElement

Author - Class in textractor.datamodel

An author for an Article.

Author(String, String, String) - Constructor for class textractor.datamodel.Author

Constructor.

Author(String) - Constructor for class textractor.datamodel.Author

An author will full name such as "Michael J.

Author - Class in textractor.xml.pubmed.xml

Class Author.

Author() - Constructor for class textractor.xml.pubmed.xml.Author

Author - Class in textractor.xml.pubmedabstracts.xml

Class Author.

Author() - Constructor for class textractor.xml.pubmedabstracts.xml.Author

AuthorChoice - Class in textractor.xml.pubmed.xml

Class AuthorChoice.

AuthorChoice() - Constructor for class textractor.xml.pubmed.xml.AuthorChoice

AuthorChoice - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoice.

AuthorChoice() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoice

AuthorChoiceChoiceSequence - Class in textractor.xml.pubmed.xml

Class AuthorChoiceChoiceSequence.

AuthorChoiceChoiceSequence() - Constructor for class textractor.xml.pubmed.xml.AuthorChoiceChoiceSequence

AuthorChoiceChoiceSequence - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoiceChoiceSequence.

AuthorChoiceChoiceSequence() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoiceChoiceSequence

AuthorChoiceChoiceSequenceChoice - Class in textractor.xml.pubmed.xml

Class AuthorChoiceChoiceSequenceChoice.

AuthorChoiceChoiceSequenceChoice() - Constructor for class textractor.xml.pubmed.xml.AuthorChoiceChoiceSequenceChoice

AuthorChoiceChoiceSequenceChoice - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoiceChoiceSequenceChoice.

AuthorChoiceChoiceSequenceChoice() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoiceChoiceSequenceChoice

AuthorChoiceChoiceSequenceChoiceDescriptor - Class in textractor.xml.pubmed.xml

Class AuthorChoiceChoiceSequenceChoiceDescriptor.

AuthorChoiceChoiceSequenceChoiceDescriptor() - Constructor for class textractor.xml.pubmed.xml.AuthorChoiceChoiceSequenceChoiceDescriptor

AuthorChoiceChoiceSequenceChoiceDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoiceChoiceSequenceChoiceDescriptor.

AuthorChoiceChoiceSequenceChoiceDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoiceChoiceSequenceChoiceDescriptor

AuthorChoiceChoiceSequenceChoiceSequence - Class in textractor.xml.pubmed.xml

Class AuthorChoiceChoiceSequenceChoiceSequence.

AuthorChoiceChoiceSequenceChoiceSequence() - Constructor for class textractor.xml.pubmed.xml.AuthorChoiceChoiceSequenceChoiceSequence

AuthorChoiceChoiceSequenceChoiceSequence - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoiceChoiceSequenceChoiceSequence.

AuthorChoiceChoiceSequenceChoiceSequence() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoiceChoiceSequenceChoiceSequence

AuthorChoiceChoiceSequenceChoiceSequenceDescriptor - Class in textractor.xml.pubmed.xml

Class AuthorChoiceChoiceSequenceChoiceSequenceDescriptor.

AuthorChoiceChoiceSequenceChoiceSequenceDescriptor() - Constructor for class textractor.xml.pubmed.xml.AuthorChoiceChoiceSequenceChoiceSequenceDescriptor

AuthorChoiceChoiceSequenceChoiceSequenceDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoiceChoiceSequenceChoiceSequenceDescriptor.

AuthorChoiceChoiceSequenceChoiceSequenceDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoiceChoiceSequenceChoiceSequenceDescriptor

AuthorChoiceChoiceSequenceDescriptor - Class in textractor.xml.pubmed.xml

Class AuthorChoiceChoiceSequenceDescriptor.

AuthorChoiceChoiceSequenceDescriptor() - Constructor for class textractor.xml.pubmed.xml.AuthorChoiceChoiceSequenceDescriptor

AuthorChoiceChoiceSequenceDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoiceChoiceSequenceDescriptor.

AuthorChoiceChoiceSequenceDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoiceChoiceSequenceDescriptor

AuthorChoiceDescriptor - Class in textractor.xml.pubmed.xml

Class AuthorChoiceDescriptor.

AuthorChoiceDescriptor() - Constructor for class textractor.xml.pubmed.xml.AuthorChoiceDescriptor

AuthorChoiceDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AuthorChoiceDescriptor.

AuthorChoiceDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorChoiceDescriptor

AuthorDescriptor - Class in textractor.xml.pubmed.xml

Class AuthorDescriptor.

AuthorDescriptor() - Constructor for class textractor.xml.pubmed.xml.AuthorDescriptor

AuthorDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AuthorDescriptor.

AuthorDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorDescriptor

AuthorList - Class in textractor.xml.pubmed.xml

Class AuthorList.

AuthorList() - Constructor for class textractor.xml.pubmed.xml.AuthorList

AuthorList - Class in textractor.xml.pubmedabstracts.xml

Class AuthorList.

AuthorList() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorList

AuthorList - Class in textractor.xml.uniprot.xml

The authors of the citation.

AuthorList() - Constructor for class textractor.xml.uniprot.xml.AuthorList

AuthorListCompleteYNType - Class in textractor.xml.pubmed.xml.types

Class AuthorListCompleteYNType.

AuthorListCompleteYNType - Class in textractor.xml.pubmedabstracts.xml.types

Class AuthorListCompleteYNType.

AuthorListCompleteYNTypeDescriptor - Class in textractor.xml.pubmed.xml.types

Class AuthorListCompleteYNTypeDescriptor.

AuthorListCompleteYNTypeDescriptor() - Constructor for class textractor.xml.pubmed.xml.types.AuthorListCompleteYNTypeDescriptor

AuthorListCompleteYNTypeDescriptor - Class in textractor.xml.pubmedabstracts.xml.types

Class AuthorListCompleteYNTypeDescriptor.

AuthorListCompleteYNTypeDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.types.AuthorListCompleteYNTypeDescriptor

AuthorListDescriptor - Class in textractor.xml.pubmed.xml

Class AuthorListDescriptor.

AuthorListDescriptor() - Constructor for class textractor.xml.pubmed.xml.AuthorListDescriptor

AuthorListDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class AuthorListDescriptor.

AuthorListDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.AuthorListDescriptor

AuthorListDescriptor - Class in textractor.xml.uniprot.xml

Class AuthorListDescriptor.

AuthorListDescriptor() - Constructor for class textractor.xml.uniprot.xml.AuthorListDescriptor

AuthorsWordReader - Class in textractor.mg4j.io

PubMedExtractor creates a specifically formatted "authorsIndexText" string.

AuthorsWordReader() - Constructor for class textractor.mg4j.io.AuthorsWordReader

AuthorValidYNType - Class in textractor.xml.pubmed.xml.types

Class AuthorValidYNType.

AuthorValidYNType - Class in textractor.xml.pubmedabstracts.xml.types

Class AuthorValidYNType.

AuthorValidYNTypeDescriptor - Class in textractor.xml.pubmed.xml.types

Class AuthorValidYNTypeDescriptor.

AuthorValidYNTypeDescriptor() - Constructor for class textractor.xml.pubmed.xml.types.AuthorValidYNTypeDescriptor

AuthorValidYNTypeDescriptor - Class in textractor.xml.pubmedabstracts.xml.types

Class AuthorValidYNTypeDescriptor.

AuthorValidYNTypeDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.types.AuthorValidYNTypeDescriptor

AZ - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The instance of the AZ type

AZ_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The AZ type

B

BagOfWordExporter - Class in textractor.learning

Created by IntelliJ IDEA.

BagOfWordExporter() - Constructor for class textractor.learning.BagOfWordExporter

basenameFromAlias(String, String) - Static method in class textractor.database.IndexDetails

batchId - Variable in class textractor.tools.io.ExportRecords

begin() - Method in class textractor.database.JDOArticleProducer

Begin the interaction with this processor.

begin() - Method in class textractor.database.JDOSentenceProducer

begin() - Method in class textractor.html.DatabaseTextConsumer

Begin the interaction with this processor.

begin() - Method in class textractor.html.QueueTextConsumer

Begin the interaction with this consumer.

begin() - Method in interface textractor.TransactionalProcessor

Begin the interaction with this processor.

Begin - Class in textractor.xml.uniprot.xml

Class Begin.

Begin() - Constructor for class textractor.xml.uniprot.xml.Begin

beginColumn - Variable in class textractor.parsers.extractor.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

BeginDescriptor - Class in textractor.xml.uniprot.xml

Class BeginDescriptor.

BeginDescriptor() - Constructor for class textractor.xml.uniprot.xml.BeginDescriptor

beginIteration(int) - Method in class textractor.chain.loader.AbstractFileLoader

Called at the start of an iteration.

beginIteration(int) - Method in class textractor.chain.loader.PubmedArticleLoader

Called at the start of an iteration.

beginLine - Variable in class textractor.parsers.extractor.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

beginTxn() - Method in class textractor.database.DbManager

Begin a transaction.

beginTxn() - Method in interface textractor.database.TransactionManager

Begin a transaction.

bestMatchFile(String, String[]) - Static method in class textractor.query.clustering.TermCoOccurenceLoader

Find the best match file for term co-occurences.

bestScoresFavorLarge(float[], int) - Static method in class textractor.tfidf.TfIdfCalculator

Returns the indices of the n best scores in scoresInput.

bestScoresFavorSmall(float[], int) - Static method in class textractor.tfidf.TfIdfCalculator

BG - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The instance of the BG type

BG_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.URLItemLangType

The BG type

bind(Object) - Method in class textractor.database.DbManager

Same as makePersistent

bind(Object, String) - Method in class textractor.database.DbManager

Binds a transient object to a name and make it persistent.

bind(Object, String) - Method in class textractor.database.NamingManager

BINDING_SITE - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The instance of the binding site type

BINDING_SITE_TYPE - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The binding site type

BIOPHYSICOCHEMICAL_PROPERTIES - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The instance of the biophysicochemical properties type

BIOPHYSICOCHEMICAL_PROPERTIES_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The biophysicochemical properties type

BioSequenceWordReader - Class in textractor.mg4j.io

A word reader that splits a biological sequence into overlapping n-grams.

BioSequenceWordReader() - Constructor for class textractor.mg4j.io.BioSequenceWordReader

BioStemmer - Class in textractor.tools.biostems

Removes word prefix and suffixes leveraging a large word dictionary.

BioStemmer(DidYouMeanI) - Constructor for class textractor.tools.biostems.BioStemmer

BIOTECHNOLOGY - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The instance of the biotechnology type

BIOTECHNOLOGY_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The biotechnology type

Book - Class in textractor.xml.pubmed.xml

Class Book.

Book() - Constructor for class textractor.xml.pubmed.xml.Book

Book - Class in textractor.xml.pubmedabstracts.xml

Class Book.

Book() - Constructor for class textractor.xml.pubmedabstracts.xml.Book

BOOK - Static variable in class textractor.xml.uniprot.xml.types.CitationTypeTypeType

The instance of the book type

BOOK_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CitationTypeTypeType

The book type

BookDescriptor - Class in textractor.xml.pubmed.xml

Class BookDescriptor.

BookDescriptor() - Constructor for class textractor.xml.pubmed.xml.BookDescriptor

BookDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class BookDescriptor.

BookDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.BookDescriptor

BpcCommentGroup - Class in textractor.xml.uniprot.xml

Class BpcCommentGroup.

BpcCommentGroup() - Constructor for class textractor.xml.uniprot.xml.BpcCommentGroup

BpcCommentGroupDescriptor - Class in textractor.xml.uniprot.xml

Class BpcCommentGroupDescriptor.

BpcCommentGroupDescriptor() - Constructor for class textractor.xml.uniprot.xml.BpcCommentGroupDescriptor

BroadJournalHeading - Class in textractor.xml.pubmed.xml

Class BroadJournalHeading.

BroadJournalHeading() - Constructor for class textractor.xml.pubmed.xml.BroadJournalHeading

BroadJournalHeading - Class in textractor.xml.pubmedabstracts.xml

Class BroadJournalHeading.

BroadJournalHeading() - Constructor for class textractor.xml.pubmedabstracts.xml.BroadJournalHeading

BroadJournalHeadingDescriptor - Class in textractor.xml.pubmed.xml

Class BroadJournalHeadingDescriptor.

BroadJournalHeadingDescriptor() - Constructor for class textractor.xml.pubmed.xml.BroadJournalHeadingDescriptor

BroadJournalHeadingDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class BroadJournalHeadingDescriptor.

BroadJournalHeadingDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.BroadJournalHeadingDescriptor

BroadJournalHeadingItem - Class in textractor.xml.pubmed.xml

Class BroadJournalHeadingItem.

BroadJournalHeadingItem() - Constructor for class textractor.xml.pubmed.xml.BroadJournalHeadingItem

BroadJournalHeadingItem - Class in textractor.xml.pubmedabstracts.xml

Class BroadJournalHeadingItem.

BroadJournalHeadingItem() - Constructor for class textractor.xml.pubmedabstracts.xml.BroadJournalHeadingItem

BroadJournalHeadingItemDescriptor - Class in textractor.xml.pubmed.xml

Class BroadJournalHeadingItemDescriptor.

BroadJournalHeadingItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.BroadJournalHeadingItemDescriptor

BroadJournalHeadingItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class BroadJournalHeadingItemDescriptor.

BroadJournalHeadingItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.BroadJournalHeadingItemDescriptor

BroadJournalHeadingList - Class in textractor.xml.pubmed.xml

Class BroadJournalHeadingList.

BroadJournalHeadingList() - Constructor for class textractor.xml.pubmed.xml.BroadJournalHeadingList

BroadJournalHeadingList - Class in textractor.xml.pubmedabstracts.xml

Class BroadJournalHeadingList.

BroadJournalHeadingList() - Constructor for class textractor.xml.pubmedabstracts.xml.BroadJournalHeadingList

BroadJournalHeadingListDescriptor - Class in textractor.xml.pubmed.xml

Class BroadJournalHeadingListDescriptor.

BroadJournalHeadingListDescriptor() - Constructor for class textractor.xml.pubmed.xml.BroadJournalHeadingListDescriptor

BroadJournalHeadingListDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class BroadJournalHeadingListDescriptor.

BroadJournalHeadingListDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.BroadJournalHeadingListDescriptor

build() - Method in class textractor.caseInsensitive.CaseInsensitiveBuilder

Build the CaseInsensetiveStore.

BuildDocStore - Class in textractor.tools.docstore

Construct a document store from documents in the database.

BuildDocStore() - Constructor for class textractor.tools.docstore.BuildDocStore

BuildDocStoreFromPubmedArticles - Class in textractor.tools

Pass over a document collection to create a document store.

BuildDocStoreFromPubmedArticles(String[]) - Constructor for class textractor.tools.BuildDocStoreFromPubmedArticles

BuildDocumentIndex - Class in textractor.tools

Prints documents from the database into the MG document format.

BuildDocumentIndex() - Constructor for class textractor.tools.BuildDocumentIndex

BuildDocumentIndexFromDB - Class in textractor.tools

Used to builds a the document index from the database.

BuildDocumentIndexFromDB() - Constructor for class textractor.tools.BuildDocumentIndexFromDB

BuildDocumentIndexFromDocumentSequence - Class in textractor.tools

User: campagne Date: Nov 8, 2005 Time: 3:01:44 PM

BuildDocumentIndexFromDocumentSequence(String, DocumentSequence) - Constructor for class textractor.tools.BuildDocumentIndexFromDocumentSequence

BuildDocumentIndexFromGenbankFiles - Class in textractor.tools.genbank

User: Fabien Campagne Date: Oct 17, 2004 Time: 1:19:53 PM

BuildDocumentIndexFromGenbankFiles(String[], String, boolean) - Constructor for class textractor.tools.genbank.BuildDocumentIndexFromGenbankFiles

BuildDocumentIndexFromGenbankFiles(String) - Constructor for class textractor.tools.genbank.BuildDocumentIndexFromGenbankFiles

BuildDocumentIndexFromGenbankFiles(String, boolean) - Constructor for class textractor.tools.genbank.BuildDocumentIndexFromGenbankFiles

BuildDocumentIndexFromHTMLArticles - Class in textractor.tools

User: Fabien Campagne Date: Oct 17, 2004 Time: 1:19:53 PM

BuildDocumentIndexFromHTMLArticles(String) - Constructor for class textractor.tools.BuildDocumentIndexFromHTMLArticles

BuildDocumentIndexFromHTMLArticles(String[], String, boolean) - Constructor for class textractor.tools.BuildDocumentIndexFromHTMLArticles

BuildDocumentIndexFromHTMLArticles(String, boolean) - Constructor for class textractor.tools.BuildDocumentIndexFromHTMLArticles

BuildDocumentIndexFromPubmedArticles - Class in textractor.tools

Builds a document index directly from a set of pubmed articles.

BuildDocumentIndexFromPubmedArticles(String[]) - Constructor for class textractor.tools.BuildDocumentIndexFromPubmedArticles

BuildDocumentIndexFromTextDocuments - Class in textractor.tools

BuildDocumentIndexFromTextDocuments(String) - Constructor for class textractor.tools.BuildDocumentIndexFromTextDocuments

C

CALCIUM_BINDING_REGION - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The instance of the calcium-binding region type

CALCIUM_BINDING_REGION_TYPE - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The calcium-binding region type

calculate(TermSimilarityMatrix, int[]) - Method in class textractor.query.clustering.TermCoOccurenceCalculator

calculate(String[]) - Method in class textractor.query.clustering.TermDependencyCalculator

calculate(int[], String[]) - Method in class textractor.query.clustering.TermDependencyCalculator

calculate(TermSimilarityMatrix, int[]) - Method in class textractor.query.clustering.TermDependencyCalculator

calculateMaxWindowWidth(int, int, int) - Method in class textractor.datamodel.SingleBagOfWordFeatureCreationParameters

calculateMinWindowIndex(int) - Method in class textractor.datamodel.SingleBagOfWordFeatureCreationParameters

calculatePartial(Map<String, Integer>, Map<String, Integer>) - Method in class textractor.tools.lookup.LookupProteinnameStandalone

Calculate the occurence of a term as a part of the other term e.g.

calculateTfIdfScore(float[], float[]) - Method in class textractor.tfidf.TfIdfCalculator

Retuns the tf-idf score based on two tf-idf vectors.

call() - Method in class textractor.chain.AbstractSentenceConsumer

call() - Method in class textractor.chain.AbstractSentenceTransformer

call() - Method in class textractor.chain.loader.AbstractFileLoader

Thread that will process a file, directory or list of files.

call() - Method in class textractor.chain.producer.StringArrayProducer

Thread that will process a array of strings.

CandidateAcronym - Class in textractor.tools.expansion

User: Fabien Campagne Date: Nov 6, 2004 Time: 2:44:29 PM

CandidateAcronym(String) - Constructor for class textractor.tools.expansion.CandidateAcronym

CandidateExpansion - Class in textractor.tools.expansion

Created by IntelliJ IDEA.

CandidateExpansion() - Constructor for class textractor.tools.expansion.CandidateExpansion

CandidateExpansion(List<String>) - Constructor for class textractor.tools.expansion.CandidateExpansion

CaseInsensitiveBuilder - Class in textractor.caseInsensitive

Class to build the CaseInsensetiveStore.

CaseInsensitiveBuilder(DocumentIndexManager) - Constructor for class textractor.caseInsensitive.CaseInsensitiveBuilder

Contractor to use to build the CaseInsensitiveStore.

CaseInsensitiveStore - Class in textractor.caseInsensitive

The Textractor index for Twease is case insensitive for large words but for small words it is case sensitive.

CaseInsensitiveStore(DocumentIndexManager) - Constructor for class textractor.caseInsensitive.CaseInsensitiveStore

This version of the constructor is used when creating a CaseInsensitiveStore and should only be used during the indexing phase, not during application runtime.

CaseInsensitiveStore(DocumentIndexManager, String) - Constructor for class textractor.caseInsensitive.CaseInsensitiveStore

This version of the constructor is used during application runtime.

CaseInsensitiveStoreReader - Interface in textractor.caseInsensitive

Interface to read information in a CaseInsensitiveStore.

CATALYTIC_ACTIVITY - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The instance of the catalytic activity type

CATALYTIC_ACTIVITY_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The catalytic activity type

CAUTION - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The instance of the caution type

CAUTION_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The caution type

CERTAIN - Static variable in class textractor.xml.uniprot.xml.types.PositionTypeStatusType

The instance of the certain type

CERTAIN_TYPE - Static variable in class textractor.xml.uniprot.xml.types.PositionTypeStatusType

The certain type

CHAIN - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The instance of the chain type

CHAIN_TYPE - Static variable in class textractor.xml.uniprot.xml.types.FeatureTypeTypeType

The chain type

ChainExecutor - Class in textractor.tools.chain

ChainExecutor(URL) - Constructor for class textractor.tools.chain.ChainExecutor

ChainExecutor(Catalog) - Constructor for class textractor.tools.chain.ChainExecutor

characterIsDelimiter(char) - Method in class textractor.mg4j.io.ProteinWordSplitterReader

Check if the character is a word delimiter.

characterIsNonDelimiter(char) - Method in class textractor.mg4j.io.ProteinWordSplitterReader

Check if the character is a word delimiter.

characterIsNonDelimiter(char) - Method in class textractor.mg4j.io.TweaseWordReader2

Check if the character can be part of a word.

characterIsPunctuation(char) - Static method in class textractor.util.TextractorUtils

characterIsSentenceTerminator(char) - Static method in class textractor.util.TextractorUtils

characters(char[], int, int, boolean) - Method in class textractor.chain.loader.SimplifiedDefaultCallback

Process (more) characters between start and end elements.

characters(char[], int, int, boolean) - Method in class textractor.parsers.PubmedExtractor

Received XML characters.

characters(char[], int, int) - Method in class textractor.tools.expansion.ExpansionHandler

check() - Method in class textractor.util.TermChecker

Build the CaseInsensetiveStore.

checkAndRemoveRedundancy - Variable in class textractor.tools.lookup.AbstractLookupProteinname

checkConsisentcyWithSearchTerm(String) - Method in class textractor.mg4j.docstore.DocumentStoreConsistencyChecker

CheckpointCallback - Interface in textractor.html

Created by IntelliJ IDEA.

checkpointCallback() - Method in interface textractor.html.CheckpointCallback

checkpointCallback() - Method in class textractor.html.DatabaseTextConsumer

checkpointCallback() - Method in class textractor.html.PubmedAbstracts2Text2DB

checkpointTxn() - Method in class textractor.database.DbManager

Checkpoints a transaction.

Chemical - Class in textractor.xml.pubmed.xml

Class Chemical.

Chemical() - Constructor for class textractor.xml.pubmed.xml.Chemical

Chemical - Class in textractor.xml.pubmedabstracts.xml

Class Chemical.

Chemical() - Constructor for class textractor.xml.pubmedabstracts.xml.Chemical

ChemicalDescriptor - Class in textractor.xml.pubmed.xml

Class ChemicalDescriptor.

ChemicalDescriptor() - Constructor for class textractor.xml.pubmed.xml.ChemicalDescriptor

ChemicalDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ChemicalDescriptor.

ChemicalDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ChemicalDescriptor

ChemicalList - Class in textractor.xml.pubmed.xml

Class ChemicalList.

ChemicalList() - Constructor for class textractor.xml.pubmed.xml.ChemicalList

ChemicalList - Class in textractor.xml.pubmedabstracts.xml

Class ChemicalList.

ChemicalList() - Constructor for class textractor.xml.pubmedabstracts.xml.ChemicalList

ChemicalListDescriptor - Class in textractor.xml.pubmed.xml

Class ChemicalListDescriptor.

ChemicalListDescriptor() - Constructor for class textractor.xml.pubmed.xml.ChemicalListDescriptor

ChemicalListDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class ChemicalListDescriptor.

ChemicalListDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.ChemicalListDescriptor

CHLOROPLAST - Static variable in class textractor.xml.uniprot.xml.types.GeneLocationTypeTypeType

The instance of the chloroplast type

CHLOROPLAST_TYPE - Static variable in class textractor.xml.uniprot.xml.types.GeneLocationTypeTypeType

The chloroplast type

chunkSize - Variable in class textractor.database.TextractorDBDocumentIterator

chunkSize - Variable in class textractor.database.TextractorDBDocumentSequence

Citation - Class in textractor.xml.uniprot.xml

Class Citation.

Citation() - Constructor for class textractor.xml.uniprot.xml.Citation

CitationDescriptor - Class in textractor.xml.uniprot.xml

Class CitationDescriptor.

CitationDescriptor() - Constructor for class textractor.xml.uniprot.xml.CitationDescriptor

CitationSubset - Class in textractor.xml.pubmed.xml

Class CitationSubset.

CitationSubset() - Constructor for class textractor.xml.pubmed.xml.CitationSubset

CitationSubset - Class in textractor.xml.pubmedabstracts.xml

Class CitationSubset.

CitationSubset() - Constructor for class textractor.xml.pubmedabstracts.xml.CitationSubset

CitationSubsetDescriptor - Class in textractor.xml.pubmed.xml

Class CitationSubsetDescriptor.

CitationSubsetDescriptor() - Constructor for class textractor.xml.pubmed.xml.CitationSubsetDescriptor

CitationSubsetDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CitationSubsetDescriptor.

CitationSubsetDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CitationSubsetDescriptor

CitationSubsetItem - Class in textractor.xml.pubmed.xml

Class CitationSubsetItem.

CitationSubsetItem() - Constructor for class textractor.xml.pubmed.xml.CitationSubsetItem

CitationSubsetItem - Class in textractor.xml.pubmedabstracts.xml

Class CitationSubsetItem.

CitationSubsetItem() - Constructor for class textractor.xml.pubmedabstracts.xml.CitationSubsetItem

CitationSubsetItemDescriptor - Class in textractor.xml.pubmed.xml

Class CitationSubsetItemDescriptor.

CitationSubsetItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.CitationSubsetItemDescriptor

CitationSubsetItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CitationSubsetItemDescriptor.

CitationSubsetItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CitationSubsetItemDescriptor

CitationType - Class in textractor.xml.uniprot.xml

The citation type stores all information about a citation.

CitationType() - Constructor for class textractor.xml.uniprot.xml.CitationType

CitationTypeDescriptor - Class in textractor.xml.uniprot.xml

Class CitationTypeDescriptor.

CitationTypeDescriptor() - Constructor for class textractor.xml.uniprot.xml.CitationTypeDescriptor

CitationTypeTypeType - Class in textractor.xml.uniprot.xml.types

Class CitationTypeTypeType.

CitationTypeTypeTypeDescriptor - Class in textractor.xml.uniprot.xml.types

Class CitationTypeTypeTypeDescriptor.

CitationTypeTypeTypeDescriptor() - Constructor for class textractor.xml.uniprot.xml.types.CitationTypeTypeTypeDescriptor

CitingCitation - Class in textractor.xml.uniprot.xml

Used by type: unpublished results.

CitingCitation() - Constructor for class textractor.xml.uniprot.xml.CitingCitation

CitingCitationDescriptor - Class in textractor.xml.uniprot.xml

Class CitingCitationDescriptor.

CitingCitationDescriptor() - Constructor for class textractor.xml.uniprot.xml.CitingCitationDescriptor

classesNames - Variable in class textractor.tools.io.ExportImport

cleanData(BufferedReader) - Method in class textractor.util.CleanRatioData

CleanRatioData - Class in textractor.util

Used to clean the results from the ImportSVMResultsByAnnotation class.

CleanRatioData() - Constructor for class textractor.util.CleanRatioData

cleanTermPredictionStats - Variable in class textractor.tools.io.ImportSVMResults

clear() - Method in class textractor.tools.Features

Clears the features.

clear_abstract() - Method in class textractor.xml.yapex.xml.Abstracts

Method clear_abstract

clearCache(boolean) - Method in class textractor.database.NamingManager

Removes the persistent object references from the cache This must be done always after commiting a transaction.

clearName() - Method in class textractor.xml.yapex.xml.ProteinNames

Method clearName

clearTerms() - Method in class textractor.datamodel.DoubleBagOfWordFeatureCreationParameters

clearTerms() - Method in class textractor.datamodel.FeatureCreationParameters

Clear the terms stored in this parameter.

clearTerms() - Method in class textractor.datamodel.SingleBagOfWordFeatureCreationParameters

clip(DocumentIndexManager) - Method in class textractor.tools.expansion.ClipExpansions

ClipExpansions - Class in textractor.tools.expansion

Class removes commonly occuring words from collected expansions.

ClipExpansions(float) - Constructor for class textractor.tools.expansion.ClipExpansions

ClippedExpansionXMLWriter - Class in textractor.tools.expansion

ClippedExpansionXMLWriter(String) - Constructor for class textractor.tools.expansion.ClippedExpansionXMLWriter

CLML - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The instance of the CLML type

CLML - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The instance of the CLML type

CLML_TYPE - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The CLML type

CLML_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The CLML type

close() - Method in class textractor.crf.CRFDatasetWriter

close() - Method in class textractor.crf.MalletDatasetWriter

close() - Method in class textractor.database.DocumentIndexManager

Close all loaded indexes.

close() - Method in class textractor.database.TextractorDBDocumentIterator

close() - Method in class textractor.database.TextractorDBDocumentSequence

Releases database resources.

close() - Method in class textractor.didyoumean.DidYouMeanDocument

close() - Method in class textractor.didyoumean.DidYouMeanDocumentSequence

close() - Method in class textractor.html.PubmedAbstracts2Text2DB

close() - Method in class textractor.learning.AnnotationFormatReader

close() - Method in class textractor.mg4j.docstore.DocumentStoreConsistencyChecker

Closes this stream and releases any system resources associated with it.

close() - Method in class textractor.mg4j.docstore.DocumentStoreReader

Closes this reader and releases any system resources associated with it.

close() - Method in class textractor.mg4j.docstore.DocumentStoreWriter

Close.

close() - Method in class textractor.mg4j.docstore.StringPerDocumentReader

Closes this reader and releases any system resources associated with it.

close() - Method in class textractor.mg4j.docstore.StringPerDocumentWriter

close() - Method in class textractor.mg4j.docstore.TermDocumentFrequencyReader

Closes this reader and releases any system resources associated with it.

close() - Method in class textractor.mg4j.docstore.TermDocumentFrequencyWriter

close() - Method in class textractor.mg4j.document.DocStoreDocumentCollection

Closes this stream and releases any system resources associated with it.

close() - Method in class textractor.mg4j.document.TextractorQueueDocumentIterator

Closes this document iterator, releasing all resources.

close() - Method in class textractor.mg4j.document.TextractorQueueDocumentSequence

Closes this document sequence, releasing all resources.

close() - Method in class textractor.mg4j.index.TermIterator

Closes this iterator.

close() - Method in class textractor.tools.lookup.LookupProteinname

CLOSEPAREN - Static variable in interface textractor.parsers.extractor.ExtractionEngineConstants

ClusterTool - Class in textractor.tools.clustering

This is a class to test clustering using MutualInformation.

ClusterTool() - Constructor for class textractor.tools.clustering.ClusterTool

Coden - Class in textractor.xml.pubmed.xml

Class Coden.

Coden() - Constructor for class textractor.xml.pubmed.xml.Coden

Coden - Class in textractor.xml.pubmedabstracts.xml

Class Coden.

Coden() - Constructor for class textractor.xml.pubmedabstracts.xml.Coden

CodenDescriptor - Class in textractor.xml.pubmed.xml

Class CodenDescriptor.

CodenDescriptor() - Constructor for class textractor.xml.pubmed.xml.CodenDescriptor

CodenDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CodenDescriptor.

CodenDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CodenDescriptor

CodenItem - Class in textractor.xml.pubmed.xml

Class CodenItem.

CodenItem() - Constructor for class textractor.xml.pubmed.xml.CodenItem

CodenItem - Class in textractor.xml.pubmedabstracts.xml

Class CodenItem.

CodenItem() - Constructor for class textractor.xml.pubmedabstracts.xml.CodenItem

CodenItemDescriptor - Class in textractor.xml.pubmed.xml

Class CodenItemDescriptor.

CodenItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.CodenItemDescriptor

CodenItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CodenItemDescriptor.

CodenItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CodenItemDescriptor

COFACTOR - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The instance of the cofactor type

COFACTOR_TYPE - Static variable in class textractor.xml.uniprot.xml.types.CommentTypeTypeType

The cofactor type

CollectExpansions - Class in textractor.tools.expansion

Collect potential expansions of a list of abbreviations or acronyms.

CollectExpansions() - Constructor for class textractor.tools.expansion.CollectExpansions

collectFiles(String) - Method in class textractor.util.HTMLByteLocator

CollectionTitle - Class in textractor.xml.pubmed.xml

Class CollectionTitle.

CollectionTitle() - Constructor for class textractor.xml.pubmed.xml.CollectionTitle

CollectionTitle - Class in textractor.xml.pubmedabstracts.xml

Class CollectionTitle.

CollectionTitle() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectionTitle

CollectionTitleDescriptor - Class in textractor.xml.pubmed.xml

Class CollectionTitleDescriptor.

CollectionTitleDescriptor() - Constructor for class textractor.xml.pubmed.xml.CollectionTitleDescriptor

CollectionTitleDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CollectionTitleDescriptor.

CollectionTitleDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectionTitleDescriptor

CollectionTitleItem - Class in textractor.xml.pubmed.xml

Class CollectionTitleItem.

CollectionTitleItem() - Constructor for class textractor.xml.pubmed.xml.CollectionTitleItem

CollectionTitleItem - Class in textractor.xml.pubmedabstracts.xml

Class CollectionTitleItem.

CollectionTitleItem() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectionTitleItem

CollectionTitleItemDescriptor - Class in textractor.xml.pubmed.xml

Class CollectionTitleItemDescriptor.

CollectionTitleItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.CollectionTitleItemDescriptor

CollectionTitleItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CollectionTitleItemDescriptor.

CollectionTitleItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectionTitleItemDescriptor

CollectiveName - Class in textractor.xml.pubmed.xml

Class CollectiveName.

CollectiveName() - Constructor for class textractor.xml.pubmed.xml.CollectiveName

CollectiveName - Class in textractor.xml.pubmedabstracts.xml

Class CollectiveName.

CollectiveName() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectiveName

CollectiveNameDescriptor - Class in textractor.xml.pubmed.xml

Class CollectiveNameDescriptor.

CollectiveNameDescriptor() - Constructor for class textractor.xml.pubmed.xml.CollectiveNameDescriptor

CollectiveNameDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CollectiveNameDescriptor.

CollectiveNameDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectiveNameDescriptor

CollectiveNameItem - Class in textractor.xml.pubmed.xml

Class CollectiveNameItem.

CollectiveNameItem() - Constructor for class textractor.xml.pubmed.xml.CollectiveNameItem

CollectiveNameItem - Class in textractor.xml.pubmedabstracts.xml

Class CollectiveNameItem.

CollectiveNameItem() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectiveNameItem

CollectiveNameItemDescriptor - Class in textractor.xml.pubmed.xml

Class CollectiveNameItemDescriptor.

CollectiveNameItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.CollectiveNameItemDescriptor

CollectiveNameItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CollectiveNameItemDescriptor.

CollectiveNameItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CollectiveNameItemDescriptor

COMMA - Static variable in interface textractor.parsers.extractor.ExtractionEngineConstants

commands - Variable in class textractor.chain.AbstractSentenceProducer

The list of Commands configured for this Chain, in the order in which they may delegate processing to the remainder of the Chain.

commands - Variable in class textractor.chain.AbstractSentenceTransformer

The list of Commands configured for this Chain, in the order in which they may delegate processing to the remainder of the Chain.

Comment - Class in textractor.xml.uniprot.xml

Class Comment.

Comment() - Constructor for class textractor.xml.uniprot.xml.Comment

CommentDescriptor - Class in textractor.xml.uniprot.xml

Class CommentDescriptor.

CommentDescriptor() - Constructor for class textractor.xml.uniprot.xml.CommentDescriptor

CommentIn - Class in textractor.xml.pubmed.xml

Class CommentIn.

CommentIn() - Constructor for class textractor.xml.pubmed.xml.CommentIn

CommentIn - Class in textractor.xml.pubmedabstracts.xml

Class CommentIn.

CommentIn() - Constructor for class textractor.xml.pubmedabstracts.xml.CommentIn

CommentInDescriptor - Class in textractor.xml.pubmed.xml

Class CommentInDescriptor.

CommentInDescriptor() - Constructor for class textractor.xml.pubmed.xml.CommentInDescriptor

CommentInDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CommentInDescriptor.

CommentInDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CommentInDescriptor

CommentOn - Class in textractor.xml.pubmed.xml

Class CommentOn.

CommentOn() - Constructor for class textractor.xml.pubmed.xml.CommentOn

CommentOn - Class in textractor.xml.pubmedabstracts.xml

Class CommentOn.

CommentOn() - Constructor for class textractor.xml.pubmedabstracts.xml.CommentOn

CommentOnDescriptor - Class in textractor.xml.pubmed.xml

Class CommentOnDescriptor.

CommentOnDescriptor() - Constructor for class textractor.xml.pubmed.xml.CommentOnDescriptor

CommentOnDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CommentOnDescriptor.

CommentOnDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CommentOnDescriptor

CommentsCorrections - Class in textractor.xml.pubmed.xml

Class CommentsCorrections.

CommentsCorrections() - Constructor for class textractor.xml.pubmed.xml.CommentsCorrections

CommentsCorrections - Class in textractor.xml.pubmedabstracts.xml

Class CommentsCorrections.

CommentsCorrections() - Constructor for class textractor.xml.pubmedabstracts.xml.CommentsCorrections

CommentsCorrectionsDescriptor - Class in textractor.xml.pubmed.xml

Class CommentsCorrectionsDescriptor.

CommentsCorrectionsDescriptor() - Constructor for class textractor.xml.pubmed.xml.CommentsCorrectionsDescriptor

CommentsCorrectionsDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CommentsCorrectionsDescriptor.

CommentsCorrectionsDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CommentsCorrectionsDescriptor

CommentType - Class in textractor.xml.uniprot.xml

The comment element stores all information found in the CC lines of the flatfile format.

CommentType() - Constructor for class textractor.xml.uniprot.xml.CommentType

CommentTypeChoice - Class in textractor.xml.uniprot.xml

Class CommentTypeChoice.

CommentTypeChoice() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoice

CommentTypeChoiceDescriptor - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceDescriptor.

CommentTypeChoiceDescriptor() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceDescriptor

CommentTypeChoiceSequence - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequence.

CommentTypeChoiceSequence() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequence

CommentTypeChoiceSequence2 - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequence2.

CommentTypeChoiceSequence2() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequence2

CommentTypeChoiceSequence2Descriptor - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequence2Descriptor.

CommentTypeChoiceSequence2Descriptor() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequence2Descriptor

CommentTypeChoiceSequence3 - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequence3.

CommentTypeChoiceSequence3() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequence3

CommentTypeChoiceSequence3Descriptor - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequence3Descriptor.

CommentTypeChoiceSequence3Descriptor() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequence3Descriptor

CommentTypeChoiceSequence4 - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequence4.

CommentTypeChoiceSequence4() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequence4

CommentTypeChoiceSequence4Descriptor - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequence4Descriptor.

CommentTypeChoiceSequence4Descriptor() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequence4Descriptor

CommentTypeChoiceSequenceDescriptor - Class in textractor.xml.uniprot.xml

Class CommentTypeChoiceSequenceDescriptor.

CommentTypeChoiceSequenceDescriptor() - Constructor for class textractor.xml.uniprot.xml.CommentTypeChoiceSequenceDescriptor

CommentTypeDescriptor - Class in textractor.xml.uniprot.xml

Class CommentTypeDescriptor.

CommentTypeDescriptor() - Constructor for class textractor.xml.uniprot.xml.CommentTypeDescriptor

CommentTypeTypeType - Class in textractor.xml.uniprot.xml.types

Class CommentTypeTypeType.

CommentTypeTypeTypeDescriptor - Class in textractor.xml.uniprot.xml.types

Class CommentTypeTypeTypeDescriptor.

CommentTypeTypeTypeDescriptor() - Constructor for class textractor.xml.uniprot.xml.types.CommentTypeTypeTypeDescriptor

commitTxn() - Method in class textractor.database.DbManager

Commit a transaction.

commitTxn() - Method in interface textractor.database.TransactionManager

Commit a transaction.

COMMON - Static variable in class textractor.xml.uniprot.xml.types.OrganismNameTypeTypeType

The instance of the common type

COMMON_TYPE - Static variable in class textractor.xml.uniprot.xml.types.OrganismNameTypeTypeType

The common type

compare(ScoredResult, ScoredResult) - Method in class textractor.scoredresult.ScoredResultComparator

compare(ScoredTerm, ScoredTerm) - Method in class textractor.tools.biostems.ScoredTermComparator

compareAcronymsWith(ExpansionAnalyser) - Method in class textractor.tools.expansion.ExpansionAnalyser

compareLongFormsWith(ExpansionAnalyser) - Method in class textractor.tools.expansion.ExpansionAnalyser

compareTo(TextSegment) - Method in class textractor.crf.TextSegment

compareTo(TermOccurrence) - Method in class textractor.datamodel.TermOccurrence

Natural ordering of TermOccurrence - by term count.

compareTo(ScoredResult) - Method in class textractor.scoredresult.ScoredResult

compareTo(OrthogonalKeywordSets) - Method in class textractor.tools.ambiguity.OrthogonalKeywordSets

Compares this object with the specified object for order.

compareTo(ScoredTerm) - Method in class textractor.tools.biostems.ScoredTerm

COMPLETED - Static variable in class textractor.xml.pubmed.xml.types.MedlineCitationStatusType

The instance of the Completed type

COMPLETED - Static variable in class textractor.xml.pubmedabstracts.xml.types.MedlineCitationStatusType

The instance of the Completed type

COMPLETED_TYPE - Static variable in class textractor.xml.pubmed.xml.types.MedlineCitationStatusType

The Completed type

COMPLETED_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.MedlineCitationStatusType

The Completed type

Component - Class in textractor.xml.uniprot.xml

The component list is equivalent to the CONTAINS section of the DE line.

Component() - Constructor for class textractor.xml.uniprot.xml.Component

ComponentDescriptor - Class in textractor.xml.uniprot.xml

Class ComponentDescriptor.

ComponentDescriptor() - Constructor for class textractor.xml.uniprot.xml.ComponentDescriptor

CompressionAdaptor - Class in textractor.mg4j.docstore

Created by IntelliJ IDEA.

CompressionAdaptor(OutputBitStream) - Constructor for class textractor.mg4j.docstore.CompressionAdaptor

CompressionAdaptorDelta - Class in textractor.mg4j.docstore

Writes with DELTA coding.

CompressionAdaptorDelta(OutputBitStream) - Constructor for class textractor.mg4j.docstore.CompressionAdaptorDelta

CompressionAdaptorGamma - Class in textractor.mg4j.docstore

Writes with GAMMA coding.

CompressionAdaptorGamma(OutputBitStream) - Constructor for class textractor.mg4j.docstore.CompressionAdaptorGamma

ConfigurableTextractorDocumentFactory - Class in textractor.mg4j.document

A factory that can produce MG4J documents from Textractor sentences.

ConfigurableTextractorDocumentFactory(String, Reference2ObjectMap<Enum<?>, Object>) - Constructor for class textractor.mg4j.document.ConfigurableTextractorDocumentFactory

Construct a new DocumentFactory.

ConfigurableTextractorDocumentFactory(String, Properties) - Constructor for class textractor.mg4j.document.ConfigurableTextractorDocumentFactory

Construct a new DocumentFactory.

ConfigurableTextractorDocumentFactory.MetadataKeys - Enum in textractor.mg4j.document

Case-insensitive keys for metadata passed to DocumentFactory.getDocument( java.io.InputStream,it.unimi.dsi.fastutil.objects.Reference2ObjectMap).

configure(BulletParser) - Method in class textractor.chain.loader.OmimExtractor

Specify the elements we want to parse from the XML file.

configure(Properties) - Method in class textractor.mg4j.io.AuthorsWordReader

configure(Properties) - Method in class textractor.mg4j.io.BioSequenceWordReader

configure(Properties) - Method in class textractor.mg4j.io.ProteinWordSplitterReader

configure(Properties) - Method in interface textractor.mg4j.io.TextractorWordReader

Configure the word reader according to the textractor index properties.

configure(Properties) - Method in class textractor.mg4j.io.TweaseWordReader

configure(Properties) - Method in class textractor.mg4j.io.TweaseWordReader2

configure(BulletParser) - Method in class textractor.parsers.PubmedExtractor

Configure the parser to parse text.

configureFromCommandLine(String[]) - Method in class textractor.mg4j.io.AuthorsWordReader

configureFromCommandLine(String[]) - Method in class textractor.mg4j.io.BioSequenceWordReader

configureFromCommandLine(String[]) - Method in class textractor.mg4j.io.ProteinWordSplitterReader

configureFromCommandLine(String[]) - Method in class textractor.mg4j.io.ShufflingBioSequenceWordReader

configureFromCommandLine(String[]) - Method in interface textractor.mg4j.io.TextractorWordReader

Let the word reader obtain its parameters from the command line.

configureFromCommandLine(String[]) - Method in class textractor.mg4j.io.TweaseWordReader

configureFromCommandLine(String[]) - Method in class textractor.mg4j.io.TweaseWordReader2

Consortium - Class in textractor.xml.uniprot.xml

Class Consortium.

Consortium() - Constructor for class textractor.xml.uniprot.xml.Consortium

ConsortiumDescriptor - Class in textractor.xml.uniprot.xml

Class ConsortiumDescriptor.

ConsortiumDescriptor() - Constructor for class textractor.xml.uniprot.xml.ConsortiumDescriptor

ConsortiumType - Class in textractor.xml.uniprot.xml

Class ConsortiumType.

ConsortiumType() - Constructor for class textractor.xml.uniprot.xml.ConsortiumType

ConsortiumTypeDescriptor - Class in textractor.xml.uniprot.xml

Class ConsortiumTypeDescriptor.

ConsortiumTypeDescriptor() - Constructor for class textractor.xml.uniprot.xml.ConsortiumTypeDescriptor

consume(Article, Collection<Sentence>) - Method in class textractor.chain.consumer.SentenceWriter

Print sentences along with their associated article.

consume(Article, Collection<Sentence>) - Method in class textractor.chain.docstore.DocumentStoreBuilder

Process sentences along with their associated article.

consume(Article, Collection<Sentence>) - Method in class textractor.chain.indexer.Indexer

Process sentences along with their associated article into individual sentences so that the IndexBuilder process can read them properly.

consume(Article, Collection<Sentence>) - Method in class textractor.html.DatabaseTextConsumer

consume(Article, Collection<Sentence>, CheckpointCallback) - Method in class textractor.html.DatabaseTextConsumer

consume(Article, Collection<Sentence>) - Method in class textractor.html.QueueTextConsumer

Process sentences along with their associated article.

consume(Article, Collection<Sentence>, CheckpointCallback) - Method in class textractor.html.QueueTextConsumer

Process sentences along with their associated article.

consume(Article, Collection<Sentence>) - Method in interface textractor.sentence.SentenceConsumer

Process sentences along with their associated article.

consumer - Variable in class textractor.html.Html2Text2DB

CONSUMER - Static variable in class textractor.xml.pubmed.xml.types.OtherAbstractTypeType

The instance of the Consumer type

CONSUMER - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherAbstractTypeType

The instance of the Consumer type

CONSUMER_TYPE - Static variable in class textractor.xml.pubmed.xml.types.OtherAbstractTypeType

The Consumer type

CONSUMER_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherAbstractTypeType

The Consumer type

containsVowel(String) - Method in class textractor.stemming.UnofficialPorterStemmer

Does string contain a vowel?

content(int) - Method in class textractor.didyoumean.DidYouMeanDocument

convert(MutableString, MutableString, MutableString, Map<String, Object>, String) - Method in class textractor.chain.loader.PubmedArticleLoader

"Convert" raw data from pubmed articles into internal textractor representation for further processing.

convert(MutableString, MutableString, MutableString, Map<String, Object>, String) - Method in class textractor.html.PubmedAbstracts2Text2DB

convert(MutableString, MutableString, MutableString, Map<String, Object>, String) - Method in interface textractor.parsers.PubmedLoader

"Convert" raw data from pubmed articles into internal textractor representation for further processing.

convert(String, FSMSymbols) - Static method in class textractor.tools.biostems.FSMPrefixSuffix

convertDistanceTypeToString(FisherDistanceCalculator.DistanceType) - Static method in class textractor.tools.clustering.FisherDistanceCalculator

convertEntryToArticle(DbManager, Entry) - Method in class textractor.html.SwissProtNames2DB

convertStringToDistanceType(String) - Static method in class textractor.tools.clustering.FisherDistanceCalculator

convertThreeLetterMonthToDigits(MutableString) - Static method in class textractor.util.ICBMutableStringUtils

Take a three letter month and conver it to digits.

convertToTermOccurrence(Map<String, Integer>) - Static method in class textractor.util.ParseOutput

copy() - Method in class textractor.didyoumean.DidYouMeanDocumentFactory

copy() - Method in class textractor.mg4j.document.ConfigurableTextractorDocumentFactory

Creates a copy of this factory.

copy() - Method in class textractor.mg4j.document.DocStoreDocumentCollection

Make a copy of this DocStoreDocumentCollection.

copy() - Method in class textractor.mg4j.document.SfnDocumentFactory

Creates a copy of this factory.

copy() - Method in class textractor.mg4j.document.TextractorDocumentFactory

Creates a copy of this factory.

copy() - Method in class textractor.mg4j.index.LowercaseTermProcessor

copy() - Method in class textractor.mg4j.index.TweaseTermProcessor

copy() - Method in class textractor.mg4j.io.ProteinWordSplitterReader

copy() - Method in class textractor.mg4j.io.TweaseWordReader2

copy() - Method in class textractor.scorers.PubDateScorer

copy() - Method in class textractor.tools.TFIDFScorer

CopyrightInformation - Class in textractor.xml.pubmed.xml

Class CopyrightInformation.

CopyrightInformation() - Constructor for class textractor.xml.pubmed.xml.CopyrightInformation

CopyrightInformation - Class in textractor.xml.pubmedabstracts.xml

Class CopyrightInformation.

CopyrightInformation() - Constructor for class textractor.xml.pubmedabstracts.xml.CopyrightInformation

CopyrightInformationDescriptor - Class in textractor.xml.pubmed.xml

Class CopyrightInformationDescriptor.

CopyrightInformationDescriptor() - Constructor for class textractor.xml.pubmed.xml.CopyrightInformationDescriptor

CopyrightInformationDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CopyrightInformationDescriptor.

CopyrightInformationDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CopyrightInformationDescriptor

CopyrightInformationItem - Class in textractor.xml.pubmed.xml

Class CopyrightInformationItem.

CopyrightInformationItem() - Constructor for class textractor.xml.pubmed.xml.CopyrightInformationItem

CopyrightInformationItem - Class in textractor.xml.pubmedabstracts.xml

Class CopyrightInformationItem.

CopyrightInformationItem() - Constructor for class textractor.xml.pubmedabstracts.xml.CopyrightInformationItem

CopyrightInformationItemDescriptor - Class in textractor.xml.pubmed.xml

Class CopyrightInformationItemDescriptor.

CopyrightInformationItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.CopyrightInformationItemDescriptor

CopyrightInformationItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CopyrightInformationItemDescriptor.

CopyrightInformationItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CopyrightInformationItemDescriptor

count - Variable in class textractor.database.TextractorDBDocumentIterator

CountNGramOccurences - Class in textractor.tools

A tool to count how many times n grams listed in a file occur in the corpus.

CountNGramOccurences() - Constructor for class textractor.tools.CountNGramOccurences

Country - Class in textractor.xml.pubmed.xml

Class Country.

Country() - Constructor for class textractor.xml.pubmed.xml.Country

Country - Class in textractor.xml.pubmedabstracts.xml

Class Country.

Country() - Constructor for class textractor.xml.pubmedabstracts.xml.Country

CountryDescriptor - Class in textractor.xml.pubmed.xml

Class CountryDescriptor.

CountryDescriptor() - Constructor for class textractor.xml.pubmed.xml.CountryDescriptor

CountryDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CountryDescriptor.

CountryDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CountryDescriptor

CountryItem - Class in textractor.xml.pubmed.xml

Class CountryItem.

CountryItem() - Constructor for class textractor.xml.pubmed.xml.CountryItem

CountryItem - Class in textractor.xml.pubmedabstracts.xml

Class CountryItem.

CountryItem() - Constructor for class textractor.xml.pubmedabstracts.xml.CountryItem

CountryItemDescriptor - Class in textractor.xml.pubmed.xml

Class CountryItemDescriptor.

CountryItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.CountryItemDescriptor

CountryItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CountryItemDescriptor.

CountryItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CountryItemDescriptor

CountTissueOccurencesInEntries - Class in textractor.tools.genbank

A tool to count how many different tissues are listed in Genbank entries.

CountTissueOccurencesInEntries() - Constructor for class textractor.tools.genbank.CountTissueOccurencesInEntries

Coverage - Class in textractor.xml.pubmed.xml

Class Coverage.

Coverage() - Constructor for class textractor.xml.pubmed.xml.Coverage

Coverage - Class in textractor.xml.pubmedabstracts.xml

Class Coverage.

Coverage() - Constructor for class textractor.xml.pubmedabstracts.xml.Coverage

CoverageDescriptor - Class in textractor.xml.pubmed.xml

Class CoverageDescriptor.

CoverageDescriptor() - Constructor for class textractor.xml.pubmed.xml.CoverageDescriptor

CoverageDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CoverageDescriptor.

CoverageDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CoverageDescriptor

CoverageItem - Class in textractor.xml.pubmed.xml

Class CoverageItem.

CoverageItem() - Constructor for class textractor.xml.pubmed.xml.CoverageItem

CoverageItem - Class in textractor.xml.pubmedabstracts.xml

Class CoverageItem.

CoverageItem() - Constructor for class textractor.xml.pubmedabstracts.xml.CoverageItem

CoverageItemDescriptor - Class in textractor.xml.pubmed.xml

Class CoverageItemDescriptor.

CoverageItemDescriptor() - Constructor for class textractor.xml.pubmed.xml.CoverageItemDescriptor

CoverageItemDescriptor - Class in textractor.xml.pubmedabstracts.xml

Class CoverageItemDescriptor.

CoverageItemDescriptor() - Constructor for class textractor.xml.pubmedabstracts.xml.CoverageItemDescriptor

CPC - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The instance of the CPC type

CPC - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The instance of the CPC type

CPC_TYPE - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The CPC type

CPC_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The CPC type

CPFH - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The instance of the CPFH type

CPFH - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The instance of the CPFH type

CPFH_TYPE - Static variable in class textractor.xml.pubmed.xml.types.OtherIDItemSourceType

The CPFH type

CPFH_TYPE - Static variable in class textractor.xml.pubmedabstracts.xml.types.OtherIDItemSourceType

The CPFH type

createAnnotatedTerm() - Method in class textractor.datamodel.annotation.TextFragmentAnnotation

createArticle() - Method in interface textractor.article.ArticleProducer

Creates an article.

createArticle() - Method in class textractor.article.DefaultArticleProducer

Creates a new Article.

createArticle(long, String) - Method in class textractor.chain.loader.PubmedArticleLoader

Create an Article using the given parameters.

createArticle() - Method in class textractor.database.JDOArticleProducer

Create a new persistent Article.

createArticle() - Method in class textractor.database.TextractorManager

Creates an article.

createArticle() - Method in class textractor.html.DatabaseTextConsumer

createArticle(long, String) - Method in class textractor.html.PubmedAbstracts2Text2DB

createArticle() - Method in class textractor.html.QueueTextConsumer

Creates an article.

createArticle(long, String) - Method in interface textractor.parsers.PubmedLoader

Create an Article using the given parameters.

createDocument(Reference2ObjectMap<Enum<?>, Object>, String) - Method in class textractor.mg4j.document.AbstractTextractorDocumentIterator

createDoubleTermAnnotation(int) - Method in class textractor.database.TextractorManager

createDummyTextSegment(int) - Method in class textractor.util.HTMLByteLocator

Creates a new dummy TextSegment when there are no entries for a specific topicId.

createFeatureCreationParameters() - Method in class textractor.learning.DoubleBagOfWordExporter

createFeatureCreationParameters() - Method in class textractor.learning.SingleBagOfWordExporter

createFeatureCreationParameters() - Method in interface textractor.learning.SVMFeatureExporter

Return corresponding type of FeatureCreationParameters.

createFrequencyStorage() - Method in class textractor.mg4j.docstore.TermDocumentFrequencyReader

Create storage for frequency information.

createIndexedTerms(DocumentIndexManager) - Method in interface textractor.datamodel.annotation.AnnotationSource

Instructs this annotation to created indexed terms if they do not already exist.

createIndexedTerms(DocumentIndexManager) - Method in class textractor.datamodel.annotation.ArticleSingleTermAnnotationSource

createIndexedTerms(DocumentIndexManager) - Method in class textractor.datamodel.annotation.TextFragmentAnnotation

Instructs this annotation to created indexed terms if they do not already exist.

createNew() - Method in class textractor.tools.BuildDocumentIndex

Factory method.