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

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SemanticType - Class in gov.nih.nlm.nls.tc.Sti

This class is the Semantic Type Java object

SemanticType() - Constructor for class gov.nih.nlm.nls.tc.Sti.SemanticType

Create a Semantic Type object (defualt).

SemanticType(String, String) - Constructor for class gov.nih.nlm.nls.tc.Sti.SemanticType

Create a Semantic Type object by specifying TUI and ST name.

SemanticType(int, String, String) - Constructor for class gov.nih.nlm.nls.tc.Sti.SemanticType

Create a Semantic Type object by specifying index, TUI, and ST name.

SemanticType(int, String, String, String) - Constructor for class gov.nih.nlm.nls.tc.Sti.SemanticType

Create a Semantic Type object by specifying index, tui, ST abbreviation, and ST name.

SemanticTypeComparator<T> - Class in gov.nih.nlm.nls.tc.Sti

This class provides methods to compare Semantic Type.

SemanticTypeComparator() - Constructor for class gov.nih.nlm.nls.tc.Sti.SemanticTypeComparator

SemanticTypes - Class in gov.nih.nlm.nls.tc.Sti

This class is to load Semantic Types from a flat file.

SemanticTypes(String) - Constructor for class gov.nih.nlm.nls.tc.Sti.SemanticTypes

Create the Semantic Types list object by specifying the input file.

SemanticTypes(String, boolean) - Constructor for class gov.nih.nlm.nls.tc.Sti.SemanticTypes

Create the Semantic Types list object by specifying the input file and flag of verbose.

SentenceTokenizer - Class in gov.nih.nlm.nls.tc.FilterApi

This class provides methods to tokenize sentence.

SentenceTokenizer() - Constructor for class gov.nih.nlm.nls.tc.FilterApi.SentenceTokenizer

SetAbbr(String) - Method in class gov.nih.nlm.nls.tc.Sti.SemanticType

Set the ST abbreviation

SetAbbreviation(String) - Method in class gov.nih.nlm.nls.tc.Jdi.Subheading

Set MeSH subheading abbreviation

SetCandidates(Vector<String>) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the candidate for display

SetClusterInc(float) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the value of the increment of cluster

SetClusterNum(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the value of the number of cluster

SetCompareField(String) - Method in class gov.nih.nlm.nls.tc.MedLine.CitationComparator

Set the comparing flag

SetCompareFlag(int) - Method in class gov.nih.nlm.nls.tc.Jdi.Count1fJdComparator

Set the comparing flag

SetCompareFlag(int) - Method in class gov.nih.nlm.nls.tc.Jdi.Count2fJdComparator

Set the comparing flag

SetCompareFlag(int) - Method in class gov.nih.nlm.nls.tc.Lib.Count1fComparator

Set the comparing flag

SetCompareFlag(int) - Method in class gov.nih.nlm.nls.tc.Lib.Count2fComparator

Set the comparing flag

SetCompareFlag(int) - Method in class gov.nih.nlm.nls.tc.Sti.Count2fStComparator

Set the comparing flag

SetCompareFlag(int) - Method in class gov.nih.nlm.nls.tc.Sti.SemanticTypeComparator

Set the comparing flag

SetCompareFlag(int) - Method in class gov.nih.nlm.nls.tc.Stri.Count1fStComparator

Set the comparing flag

SetCompareLengthFlag(boolean) - Method in class gov.nih.nlm.nls.tc.MedLine.CitationComparator

Set the flag of copareing length

SetCount1(float) - Method in class gov.nih.nlm.nls.tc.Lib.Count1f

Set the score of the Count1f object.

SetCount1(float) - Method in class gov.nih.nlm.nls.tc.Lib.Count2f

Set the count1 of the Count2f object.

SetCount2(float) - Method in class gov.nih.nlm.nls.tc.Lib.Count2f

Set the count2 of the Count2f object.

SetDc(int) - Method in class gov.nih.nlm.nls.tc.Jdi.WordSignalWcDc

Set document count

SetFieldSeparator(String) - Static method in class gov.nih.nlm.nls.tc.Util.GlobalVars

Set field separator

SetFullName(String) - Method in class gov.nih.nlm.nls.tc.Jdi.Subheading

Set MeSH subheading abbreviation

SetId(String) - Method in class gov.nih.nlm.nls.tc.Sti.SemanticType

Set the ST id

SetIndex(int) - Method in class gov.nih.nlm.nls.tc.Jdi.JournalDescriptor

Set the JD index

SetIndex(int) - Method in class gov.nih.nlm.nls.tc.Sti.SemanticType

Set the ST index

SetJdid(String) - Method in class gov.nih.nlm.nls.tc.Jdi.JournalDescriptor

Set the JD id

SetJds(Vector<String>) - Method in class gov.nih.nlm.nls.tc.Jdi.JidTaJd

Set journal descriptors.

SetJdScores(Vector<Count2f>) - Method in class gov.nih.nlm.nls.tc.Stri.StJd

Set the Jd scores

SetJid(String) - Method in class gov.nih.nlm.nls.tc.Jdi.JidTaJd

Set journal id.

SetJid(String) - Method in class gov.nih.nlm.nls.tc.MedLine.MltObj

Set Journal id of the tokenized MEDLINE citation

SetJournalDescriptors(JournalDescriptors) - Method in class gov.nih.nlm.nls.tc.Jdi.Count1fJdComparator

Set the Journal Descriptors

SetJournalDescriptors(JournalDescriptors) - Method in class gov.nih.nlm.nls.tc.Jdi.Count2fJdComparator

Set the Journal Descriptors

SetKey(K) - Method in class gov.nih.nlm.nls.tc.Lib.KeyValueObj

Set key to a key-value object.

SetLegalWordsOption(LegalWordsOption) - Method in class gov.nih.nlm.nls.tc.FilterApi.InputFilterOption

Set options of legal words

SetMaxSignal(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set value of max.

SetMaxSignal(String) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

SetMinDc(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set value of min.

SetMinLength(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set value of min.

SetMinSignal(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set value of min.

SetMinWc(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set value of min.

SetName(String) - Method in class gov.nih.nlm.nls.tc.Jdi.JournalDescriptor

Set the JD name

SetName(String) - Method in class gov.nih.nlm.nls.tc.Lib.Countf

Set the name of the Count1f object.

SetName(String) - Method in class gov.nih.nlm.nls.tc.Sti.SemanticType

Set the ST name

SetNoOutputMsg(String) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the message for no output.

SetOutputFieldList(Vector<Integer>) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the output fields list

SetOutputNum(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the number of output result to display.

SetPmid(String) - Method in class gov.nih.nlm.nls.tc.MedLine.MltObj

Set pmid of the tokenized MEDLINE citation

SetPropertiesInConfig(String) - Method in class gov.nih.nlm.nls.tc.Lib.TcSystemOption

SetRemoveStopWord(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set flag of removing stopwords

SetResultType(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the value of type for the overall result pick.

SetRoundOffDecimals(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the decimals to round off

SetScoreMultiplyFactor(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the value of score multiply factor.

SetSemanticTypes(SemanticTypes) - Method in class gov.nih.nlm.nls.tc.Sti.Count2fStComparator

Set the Semantic Types

SetSemanticTypes(SemanticTypes) - Method in class gov.nih.nlm.nls.tc.Stri.Count1fStComparator

Set the Semantic Types

SetShortName(String) - Method in class gov.nih.nlm.nls.tc.Jdi.Subheading

Set MeSH subheading abbreviation

SetShowResult(int) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the value of type for the shown result.

SetSignal(double) - Method in class gov.nih.nlm.nls.tc.Jdi.WordSignalWcDc

Set normalized signal

SetStatus(String) - Method in class gov.nih.nlm.nls.tc.Jdi.JournalDescriptor

Set the JD status

SetTa(String) - Method in class gov.nih.nlm.nls.tc.Jdi.JidTaJd

Set journal title.

SetTokenizedText(String) - Method in class gov.nih.nlm.nls.tc.MedLine.MltObj

Set tokenized text of the tokenized MEDLINE citation

SetTui(String) - Method in class gov.nih.nlm.nls.tc.Stri.StJd

Set the St index

SetUseAcronymFilter(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.InputFilterOption

Set flag of using acronym filter

SetUseCluster(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the boolean flag to display results in cluster.

SetUseDebugMsg(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.InputFilterOption

Set flag of using Debug Message

SetUseLegalWordsMsg(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.InputFilterOption

Set flag of using legal wrods in debug Message

SetUseMaxSignal(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set flag of using max.

SetUseMinDc(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set flag of using min.

SetUseMinLength(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set flag of using min.

SetUseMinSignal(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set flag of using min.

SetUseMinWc(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set flag of using min.

SetUseNoOutputMsg(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.OutputFilterOption

Set the boolean flag to show no output message.

SetUseRestrictWord(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.LegalWordsOption

Set flag of using restrictwords only

SetUseUniqueWord(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.InputFilterOption

Set flag of using word extraction filter

SetUseWordExtractionFilter(boolean) - Method in class gov.nih.nlm.nls.tc.FilterApi.InputFilterOption

Set flag of using word extraction filter

SetValue(V) - Method in class gov.nih.nlm.nls.tc.Lib.KeyValueObj

Set value to a key-value object.

SetVerbose(boolean) - Method in class gov.nih.nlm.nls.tc.Jdi.Count2fJdComparator

Set verbose flag for reading in JD file

SetVerbose(boolean) - Method in class gov.nih.nlm.nls.tc.MedLine.CitationObjs

Set verbose flag for message.

SetVerbose(boolean) - Method in class gov.nih.nlm.nls.tc.Sti.Count2fStComparator

Set verbose flag for reading in ST file

SetVerbose(boolean) - Method in class gov.nih.nlm.nls.tc.Sti.SemanticTypeComparator

Set verbose flag for reading in ST file

SetVerbose(boolean) - Method in class gov.nih.nlm.nls.tc.Stri.Count1fStComparator

Set verbose flag for reading in ST file

SetWc(int) - Method in class gov.nih.nlm.nls.tc.Jdi.WordSignalWcDc

Set word count

SetWord(String) - Method in class gov.nih.nlm.nls.tc.Jdi.WordSignalWcDc

Set word

ShowJds(BufferedWriter, boolean) - Method in class gov.nih.nlm.nls.tc.Jdi.JournalDescriptors

Show index, id, and name of all Journal descriptors.

ShowSts(BufferedWriter, boolean) - Method in class gov.nih.nlm.nls.tc.Sti.SemanticTypes

Show index, abbreviation, and full name of all Semantic Types.

shs_ - Variable in class gov.nih.nlm.nls.tc.Api.JdiApi

SimilarityApi - Class in gov.nih.nlm.nls.tc.Api

This class provides APIs for calculate similarity value for JD vectors and ST vectors.

SimilarityApi() - Constructor for class gov.nih.nlm.nls.tc.Api.SimilarityApi

Creates an SimilarityApi object.

ST_FILE - Static variable in class gov.nih.nlm.nls.tc.Lib.Configuration

key for the path of STs file defined in conf file

ST_JD_FILE - Static variable in class gov.nih.nlm.nls.tc.Lib.Configuration

key for the path of ST-JD file defined in conf file

Standardize(Vector<Count1f>, SemanticTypes) - Static method in class gov.nih.nlm.nls.tc.Lib.Count1fOperator

Standardize the order of ST scores.

Standardize(Vector<Count1f>, JournalDescriptors) - Static method in class gov.nih.nlm.nls.tc.Lib.Count1fOperator

Standardize the Count1f Vector by rearrnging the vector in index order and fill 0 in empty elements.

Standardize(Vector<Count2f>, SemanticTypes) - Static method in class gov.nih.nlm.nls.tc.Lib.Count2fOperator

Standardize the order of ST scores.

Standardize(Vector<Count2f>, JournalDescriptors) - Static method in class gov.nih.nlm.nls.tc.Lib.Count2fOperator

Standardize the Count2f Vector by rearrnging the vector in index order and fill 0 in empty elements.

Sti - Class in gov.nih.nlm.nls.tc.Tools

This class provides St index tool

Sti() - Constructor for class gov.nih.nlm.nls.tc.Tools.Sti

Create a STI tool object (default).

Sti(String) - Constructor for class gov.nih.nlm.nls.tc.Tools.Sti

Create a STI tool object by specifying option string.

StiApi - Class in gov.nih.nlm.nls.tc.Api

This class provides Semantic Type Indexing API.

StiApi(Configuration) - Constructor for class gov.nih.nlm.nls.tc.Api.StiApi

Creates an StiApi object and initiate related data, using a specified configuration object.

StiApi(String) - Constructor for class gov.nih.nlm.nls.tc.Api.StiApi

Creates an StiApi object and initiate related data, using a specified configuration file.

StiApi(Connection) - Constructor for class gov.nih.nlm.nls.tc.Api.StiApi

Creates an StiApi object and initiate related data, using a specified database connection object.

StiApi(Hashtable<String, String>) - Constructor for class gov.nih.nlm.nls.tc.Api.StiApi

Creates an StiApi object and initiate related data, using a specified properties to be overwritten in configuration.

StiApi(Configuration, SemanticTypes) - Constructor for class gov.nih.nlm.nls.tc.Api.StiApi

Creates an StiApi object and initiate related data, using a specified configuration object and semantic types object.

StiApi(Connection, SemanticTypes) - Constructor for class gov.nih.nlm.nls.tc.Api.StiApi

Creates an StiApi object and initiate related data, using a specified database connection object and semantic types object.

StiHelp - Class in gov.nih.nlm.nls.tc.Tools

This class is to print out ST index help menu.

StiHelp() - Constructor for class gov.nih.nlm.nls.tc.Tools.StiHelp

StiHelp(BufferedWriter, boolean) - Static method in class gov.nih.nlm.nls.tc.Tools.StiHelp

Print out Sti system help menu.

StJd - Class in gov.nih.nlm.nls.tc.Stri

This class provides St-Jd score object

StJd() - Constructor for class gov.nih.nlm.nls.tc.Stri.StJd

Create a St-Jd score (Count2f) object (defualt).

StJdComparator<T> - Class in gov.nih.nlm.nls.tc.Stri

This class provides methods to compare StJd object.

StJdComparator() - Constructor for class gov.nih.nlm.nls.tc.Stri.StJdComparator

StJds - Class in gov.nih.nlm.nls.tc.Stri

This class provides St-Jd scores Objects from a flat file

StJds(String) - Constructor for class gov.nih.nlm.nls.tc.Stri.StJds

Create the St-Jd scores (Count2f) objects (default).

StJds(String, boolean) - Constructor for class gov.nih.nlm.nls.tc.Stri.StJds

Create the St-Jd scores (Count2f) objects by specifying the StJd file and flag of verbose.

StJds(Configuration, boolean) - Constructor for class gov.nih.nlm.nls.tc.Stri.StJds

Create the St-Jd scores (Count2f) objects by specifying the configuration object and flag of verbose.

StJds(SemanticTypes, JournalDescriptors, String, boolean) - Constructor for class gov.nih.nlm.nls.tc.Stri.StJds

Create the St-Jd scores (Count2f) objects by specifying the semantic types list object, journal descriptors list object, and flag of verbose.

STOP_WORDS_FILE - Static variable in class gov.nih.nlm.nls.tc.Lib.Configuration

key for the path of stopwords file defined in conf file

Str - Class in gov.nih.nlm.nls.tc.Util

This class provides methods of string related operations.

Str() - Constructor for class gov.nih.nlm.nls.tc.Util.Str

Stri - Class in gov.nih.nlm.nls.tc.Tools

This class provides ST real-time index tool

Stri() - Constructor for class gov.nih.nlm.nls.tc.Tools.Stri

Create a STRI tool object (default).

Stri(String) - Constructor for class gov.nih.nlm.nls.tc.Tools.Stri

Create a STRI tool object by specifying option string.

StriApi - Class in gov.nih.nlm.nls.tc.Api

This class provides Semantic Type Realtime Indexing API.

StriApi(Configuration) - Constructor for class gov.nih.nlm.nls.tc.Api.StriApi

Creates an StriApi object and initiate related data, using a specified configuration object.

StriApi(String) - Constructor for class gov.nih.nlm.nls.tc.Api.StriApi

Creates an StriApi object and initiate related data, using a specified configuration file.

StriApi(Connection) - Constructor for class gov.nih.nlm.nls.tc.Api.StriApi

Creates an StriApi object and initiate related data, using a specified database connection object.

StriApi(Hashtable<String, String>) - Constructor for class gov.nih.nlm.nls.tc.Api.StriApi

Creates an StriApi object and initiate related data, using a specified properties to be overwritten in configuration.

StriApi(Configuration, JournalDescriptors, Subheadings) - Constructor for class gov.nih.nlm.nls.tc.Api.StriApi

Creates an StriApi object and initiate related data, using a specified configuration object, journal descritor object, and subHeadings object.

StriApi(Configuration, JournalDescriptors, Subheadings, SemanticTypes) - Constructor for class gov.nih.nlm.nls.tc.Api.StriApi

Creates an StriApi object and initiate related data, using a specified configuration object, journal descritor object, subHeadings object, and semantic types object.

StriApi(Connection, JournalDescriptors, Subheadings) - Constructor for class gov.nih.nlm.nls.tc.Api.StriApi

Creates an StriApi object and initiate related data, using a specified db connection object, journal descritor object, and subHeadings object.

StriHelp - Class in gov.nih.nlm.nls.tc.Tools

This class is to print out ST real-time index help menu.

StriHelp() - Constructor for class gov.nih.nlm.nls.tc.Tools.StriHelp

StriHelp(BufferedWriter, boolean) - Static method in class gov.nih.nlm.nls.tc.Tools.StriHelp

Print out LexAccess system help menu.

sts_ - Variable in class gov.nih.nlm.nls.tc.Api.StiApi

sts_ - Variable in class gov.nih.nlm.nls.tc.Api.StWsdApi

StWsd - Class in gov.nih.nlm.nls.tc.Tools

This class provides St-Wsd tool

StWsd() - Constructor for class gov.nih.nlm.nls.tc.Tools.StWsd

Create a STI tool object (default).

StWsd(String) - Constructor for class gov.nih.nlm.nls.tc.Tools.StWsd

Create a STI tool object by specifying option string.

StWsdApi - Class in gov.nih.nlm.nls.tc.Api

This class provides Word Sense Disambiguation Tool API using STI.

StWsdApi(Configuration) - Constructor for class gov.nih.nlm.nls.tc.Api.StWsdApi

Creates an WsdApi object and initiate related data, using a specified configuration object.

StWsdApi(String) - Constructor for class gov.nih.nlm.nls.tc.Api.StWsdApi

Creates an WsdApi object and initiate related data, using a specified configuration file.

StWsdApi(Connection) - Constructor for class gov.nih.nlm.nls.tc.Api.StWsdApi

Creates an WsdApi object and initiate related data, using a specified database connection object.

StWsdApi(Hashtable<String, String>) - Constructor for class gov.nih.nlm.nls.tc.Api.StWsdApi

Creates an WsdApi object and initiate related data, using a specified properties to be overwritten in configuration.

StWsdApi(Configuration, SemanticTypes, JournalDescriptors) - Constructor for class gov.nih.nlm.nls.tc.Api.StWsdApi

Creates an WsdApi object and initiate related data, using a specified configuration object and semantic types object.

StWsdApi(Connection, SemanticTypes, JournalDescriptors) - Constructor for class gov.nih.nlm.nls.tc.Api.StWsdApi

Creates an WsdApi object and initiate related data, using a specified database connection object and semantic types object.

StWsdHelp - Class in gov.nih.nlm.nls.tc.Tools

This class is to print out ST-WSD Tool help menu.

StWsdHelp() - Constructor for class gov.nih.nlm.nls.tc.Tools.StWsdHelp

StWsdHelp(BufferedWriter, boolean) - Static method in class gov.nih.nlm.nls.tc.Tools.StWsdHelp

Print out StWsd system help menu.

SUB_HEADINGS_FILE - Static variable in class gov.nih.nlm.nls.tc.Lib.Configuration

key for the path of Subheadings file defined in conf file

Subheading - Class in gov.nih.nlm.nls.tc.Jdi

This class is the Subheading Java object

Subheading() - Constructor for class gov.nih.nlm.nls.tc.Jdi.Subheading

Create a MeSH subheading object (default).

Subheading(String, String, String) - Constructor for class gov.nih.nlm.nls.tc.Jdi.Subheading

Create a MeSH subheading object by specifying abbreviation, short name, and full name.

Subheadings - Class in gov.nih.nlm.nls.tc.Jdi

This class is to load MeSH Subheadings from a flat file.

Subheadings(String) - Constructor for class gov.nih.nlm.nls.tc.Jdi.Subheadings

Create the MeSH Subheadings List object by specifying the input file.

Subheadings(String, boolean) - Constructor for class gov.nih.nlm.nls.tc.Jdi.Subheadings

Create the MeSH Subheadings List object by specifying the input file and flag of verbose.