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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.
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2011 Version
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