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

a() - Method in class com.aliasi.util.Pair

Return the first value of the pair.

A - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element a.

a() - Method in class com.aliasi.xml.XHtmlWriter

Start an a element with no attributes.

a(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an a element with the specified attributes.

a(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an a element with the specified attribute and value.

a(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an a element with the specified attributes and values.

a(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an a element with the specified attributes and values.

a(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an a element with the specified attributes and values.

ABBR - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element abbr.

abbr() - Method in class com.aliasi.xml.XHtmlWriter

Start an abbr element with no attributes.

abbr(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an abbr element with the specified attributes.

abbr(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an abbr element with the specified attribute and value.

abbr(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an abbr element with the specified attributes and values.

abbr(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an abbr element with the specified attributes and values.

abbr(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an abbr element with the specified attributes and values.

ABBR_ATT - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the abbr attribute.

Abstract - Class in com.aliasi.medline

An Abstract represents the abstract of a MEDLINE document.

ABSTRACT_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The Abstract element.

ABSTRACT_TEXT_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The AbstractText element.

AbstractCharLmRescoringChunker<B extends NBestChunker,O extends LanguageModel.Process,C extends LanguageModel.Sequence> - Class in com.aliasi.chunk

An AbstractCharLmRescoringChunker provides the basic character language-model rescoring model used by the trainable CharLmRescoringChunker and its compiled version.

AbstractCharLmRescoringChunker(B, int, O, Map<String, Character>, Map<String, C>) - Constructor for class com.aliasi.chunk.AbstractCharLmRescoringChunker

Construct a rescoring chunker based on the specified underlying chunker, with the specified number of underlying chunkings rescored, based on the models and type encodings provided in the last three arguments.

AbstractCommand - Class in com.aliasi.util

A CommandLineArguments object represents a the command-line arguments.

AbstractCommand(String[]) - Constructor for class com.aliasi.util.AbstractCommand

Constructs a command-line arguments object from the specified arguments list using no default values.

AbstractCommand(String[], Properties) - Constructor for class com.aliasi.util.AbstractCommand

Constructs a command-line arguments object from the specified arguments using the specified properties as default values.

AbstractDictionary<C> - Class in com.aliasi.dict

An AbstractDictionary is a dictionary with convenience implementations of most methods.

AbstractDictionary() - Constructor for class com.aliasi.dict.AbstractDictionary

Construct an abstract dictionary.

AbstractDiscreteDistribution - Class in com.aliasi.stats

An AbstractDiscreteDistribution provides a default abstract implementation of discrete distributions.

AbstractDiscreteDistribution() - Constructor for class com.aliasi.stats.AbstractDiscreteDistribution

Construct an abstract discrete distribution.

AbstractExternalizable - Class in com.aliasi.util

The AbstractExternalizer is an adapter for read resolved externalizables.

AbstractExternalizable() - Constructor for class com.aliasi.util.AbstractExternalizable

Construct an abstract externalizable.

AbstractHierarchicalClusterer<E> - Class in com.aliasi.cluster

An AbstractHierachicalClusterer provides an adapter for clustering for hierarchical clusterers.

AbstractHierarchicalClusterer(double, Distance<? super E>) - Constructor for class com.aliasi.cluster.AbstractHierarchicalClusterer

Construct an abstract hierarchical clusterer with the specified maximum distance.

AbstractHmm - Class in com.aliasi.hmm

An AbstractHmm is an abstract implementation of a hidden Markov model which manages a symbol table and defines the basic methods in terms of the symbolic linear probability methods.

AbstractHmm(SymbolTable) - Constructor for class com.aliasi.hmm.AbstractHmm

Construct an HMM with the specified symbol table.

AbstractHmmEstimator - Class in com.aliasi.hmm

An HmmEstimator may be used to train a hidden Markov model (HMM).

AbstractHmmEstimator(SymbolTable) - Constructor for class com.aliasi.hmm.AbstractHmmEstimator

Construct an HMM estimator with the specified tag symbol table.

AbstractMatrix - Class in com.aliasi.matrix

An AbstractMatrix implements most of a matrix's functionality in terms of methods for accessing numbers of rows and columns and values.

AbstractMatrix() - Constructor for class com.aliasi.matrix.AbstractMatrix

Construct an abstract matrix.

AbstractMedTagParser - Class in com.aliasi.corpus.parsers

The AbstractMedTagParser class provides an adapter for NCBI's MedTag corpora, including GeneTag and MedPost.

AbstractMedTagParser() - Constructor for class com.aliasi.corpus.parsers.AbstractMedTagParser

Construct an abstract MedTag parser with no handler specified.

AbstractMedTagParser(TagHandler) - Constructor for class com.aliasi.corpus.parsers.AbstractMedTagParser

Construct an abstract MedTag parser with the specified tag handler.

AbstractMentionChain - Class in com.aliasi.coref

An abstract implementation of a mention chain in terms of matching and killing functions.

AbstractMentionChain(Mention, int, int) - Constructor for class com.aliasi.coref.AbstractMentionChain

AbstractMentionFactory - Class in com.aliasi.coref

The AbstractMentionFactory class implements the mention factory interface using linguistically-motivated abstract methods.

AbstractMentionFactory(TokenizerFactory) - Constructor for class com.aliasi.coref.AbstractMentionFactory

Construct an abstract mention factory with the specified tokenizer factory.

AbstractSentenceModel - Class in com.aliasi.sentences

An AbstractSentenceModel implements a sentence model in terms of the method that adds indices to the collection.

AbstractSentenceModel() - Constructor for class com.aliasi.sentences.AbstractSentenceModel

Construct an abstract sentence model.

AbstractVector - Class in com.aliasi.matrix

An AbstractVector implements most of a vector's functionality in terms of methods for dimensionality and values.

AbstractVector() - Constructor for class com.aliasi.matrix.AbstractVector

Construct an abstract vector.

abstrct() - Method in class com.aliasi.medline.Article

Returns the abstract for this article, or null if there is no abstract.

accept(String) - Method in class com.aliasi.io.FileExtensionFilter

Returns true if the specified file name has an acceptable suffix as specified in the constructor.

accept(File) - Method in class com.aliasi.io.FileNameFilter

Return true if a file is acceptable to this filter.

accept(String) - Method in class com.aliasi.io.FileNameFilter

Return true if files with the specified name should be accepted.

accept(E) - Method in class com.aliasi.util.Iterators.Filter

Returns true for objects returned by the contained iterator that should be returned by this iterator.

ACCEPT - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the accept attribute.

ACCEPT_CHARSET - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the accept-charset attribute.

acceptCategory() - Method in class com.aliasi.classify.BinaryLMClassifier

Returns the category assigned to matching/accepted cases.

ACCESSION_NUMBER_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The AccessionNumber element.

accessionNumbers() - Method in class com.aliasi.medline.DataBank

Returns the list of accession numbers for molecular sequences in this database.

ACCESSKEY - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the accesskey attribute.

accuracy() - Method in class com.aliasi.classify.PrecisionRecallEvaluation

Returns the sample accuracy of the responses.

accuracyDeviation() - Method in class com.aliasi.classify.PrecisionRecallEvaluation

Returns the standard deviation of the accuracy.

acronym() - Method in class com.aliasi.medline.Grant

Returns a two-letter acronym for the type of this grant, or the empty (zero length) string if none was provided.

ACRONYM - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element acronym.

acronym() - Method in class com.aliasi.xml.XHtmlWriter

Start an acronym element with no attributes.

acronym(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an acronym element with the specified attributes.

acronym(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an acronym element with the specified attribute and value.

acronym(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an acronym element with the specified attributes and values.

acronym(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an acronym element with the specified attributes and values.

acronym(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an acronym element with the specified attributes and values.

ACRONYM_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The Acronym element.

ACTION - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the action attribute.

add(Chunk) - Method in class com.aliasi.chunk.ChunkingImpl

Add a chunk this this chunking.

add(Mention, int) - Method in class com.aliasi.coref.AbstractMentionChain

Adds the specified mention appearing at the specified sentence offset to this mention chain, and calls the method AbstractMentionChain.add(Mention), which may be overridden by subclasses to carry out additional bookkeeping when new mentions are added.

add(Mention) - Method in class com.aliasi.coref.AbstractMentionChain

Adds the specified mention appearing at the specified sentence offset to this mention chain.

add(Mention, int) - Method in interface com.aliasi.coref.MentionChain

Adds the specified mention appearing at the specified sentence offset to this mention chain.

add(Mention) - Method in class com.aliasi.coref.MentionChainImpl

Adds the specified mention appearing at the specified sentence offset to this mention chain.

add(Vector) - Method in class com.aliasi.matrix.AbstractVector

Returns the result of adding the specified vector to this vector.

add(Vector) - Method in class com.aliasi.matrix.DenseVector

add(Vector) - Method in class com.aliasi.matrix.SparseFloatVector

add(Vector) - Method in interface com.aliasi.matrix.Vector

Returns a new vector that is the reuslt of adding this vector to the specified vector.

add(char, char[]) - Static method in class com.aliasi.util.Arrays

Return the result of adding the specified character to the specified sorted character array.

add(E) - Method in class com.aliasi.util.BoundedPriorityQueue

Conditionally add the specified element to this queue.

add(E) - Method in class com.aliasi.util.MinMaxHeap

Add the element to the heap.

add(E) - Method in class com.aliasi.util.NBestSet

Add the specified object to this n-best set.

addAll(Collection) - Method in class com.aliasi.chunk.ChunkingImpl

Adds all of the chunks in the specified collection to this chunking.

addAll(Collection<? super E>, E[]) - Static method in class com.aliasi.util.Collections

Adds the elements from the specified array to the specified collection.

addAll(Collection<? extends E>) - Method in class com.aliasi.util.NBestSet

Add the elements of the collection one by one.

addCase(Chunking, Chunking) - Method in class com.aliasi.chunk.ChunkingEvaluation

Add an evaluation case consisting of a reference chunk set and a response chunk set.

addCase(String, E) - Method in class com.aliasi.classify.ClassifierEvaluator

Adds a test case for the specified input with the specified reference category.

addCase(boolean, boolean) - Method in class com.aliasi.classify.PrecisionRecallEvaluation

Adds a case with the specified reference and response classifications.

addCase(boolean, double) - Method in class com.aliasi.classify.ScoredPrecisionRecallEvaluation

Add a case with the specified correctness and response score.

addCase(String[], String[], String[], TagWordLattice, Iterator<ScoredObject<String[]>>) - Method in class com.aliasi.hmm.HmmEvaluation

Adds a complete response case for evaluation, consisting of the specified tokens, reference tags, first-best response tags, lattice of forward-backward confidence-based scores, and an iterator over the n-best list.

addCase(Chunking, Chunking) - Method in class com.aliasi.sentences.SentenceEvaluation

Add the case corresponding to the specified reference and response chunkings.

addCase(String, String) - Method in class com.aliasi.spell.SpellEvaluator

Adds a training case to the spelling evaluator in the form of input text and its corrected form.

addClassification(String, Classification) - Method in class com.aliasi.classify.ClassifierEvaluator

Adds the specified classification as a response for the specified reference category.

addDefaultProperty(String, String) - Method in class com.aliasi.util.AbstractCommand

Adds the specified key and value as default arguments.

addEntry(DictionaryEntry<C>) - Method in class com.aliasi.dict.AbstractDictionary

Adds the specified dictionary entry to the dictionary.

addEntry(DictionaryEntry<C>) - Method in interface com.aliasi.dict.Dictionary

Adds the specified dictionary entry to the dictionary.

addEntry(DictionaryEntry<C>) - Method in class com.aliasi.dict.MapDictionary

addEntry(DictionaryEntry<C>) - Method in class com.aliasi.dict.TrieDictionary

Equal entries will be ignored.

addFirstBestCase(String[], String[], String[]) - Method in class com.aliasi.hmm.HmmEvaluation

Adds a first-best response case with the specified tokens, reference tags, and first-best response tags.

addKnownToken(String) - Method in class com.aliasi.hmm.HmmEvaluation

Adds the specified token to the set of known tokens.

addLatticeCase(String[], String[], TagWordLattice) - Method in class com.aliasi.hmm.HmmEvaluation

Add a lattice-based response case with the specified tokens, reference tags and lattice.

addMember(K, M) - Method in class com.aliasi.util.ObjectToSet

Add a member to the value of the set mapped to by the specified key.

addMembers(K, Set<? extends M>) - Method in class com.aliasi.util.ObjectToSet

Adds a set of members to the value of the set mapped to by the specified key.

addNBestCase(String[], String[], Iterator<ScoredObject<String[]>>) - Method in class com.aliasi.hmm.HmmEvaluation

Add an n-best response case with the specified tokens, reference tags and n-best iterator.

ADDRESS - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element address.

address() - Method in class com.aliasi.xml.XHtmlWriter

Start an address element with no attributes.

address(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an address element with the specified attributes.

address(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an address element with the specified attribute and value.

address(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an address element with the specified attributes and values.

address(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an address element with the specified attributes and values.

address(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an address element with the specified attributes and values.

addSimpleAttribute(AttributesImpl, String, String) - Static method in class com.aliasi.xml.SimpleElementHandler

Add a local name and value to an attributes implementation as type "CDATA".

addState(String) - Method in class com.aliasi.hmm.AbstractHmm

Adds the state with the specified name to this hidden Markov model.

addSymbol(String) - Method in class com.aliasi.symbol.SymbolTableCompiler

Add a symbol to the symbol table to be compiled.

addSynonym(String, String) - Method in class com.aliasi.coref.matchers.SynonymMatch

Adds the two phrases as synonyms for one another.

affiliation() - Method in class com.aliasi.medline.Article

Returns the affiliation for the the first author of this article.

affiliation() - Method in class com.aliasi.medline.Author

Returns the affiliation for this author.

affiliation() - Method in class com.aliasi.medline.Investigator

Returns the affiliation of this investigator, or the empty (zero length) string if none was provided.

AFFILIATION_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The Affiliation element.

agency() - Method in class com.aliasi.medline.Grant

Returns a three-letter acronym for the agency providing this grant, or the empty (zero length) string if none was provided.

AGENCY_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The Agency element.

ALIGN - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the align attribute.

allDigits(String) - Static method in class com.aliasi.util.Strings

Returns true if all of the characters making up the specified string are digits.

allDigits(char[], int, int) - Static method in class com.aliasi.util.Strings

Returns true if all of the characters in the specified range are digits.

allLetters(char[]) - Static method in class com.aliasi.util.Strings

Returns true if all of the characters in the specified array are letters.

allLowerCase(char[]) - Static method in class com.aliasi.util.Strings

Returns true if all of the characters in the specified array are lower case letters.

allLowerCase(CharSequence) - Static method in class com.aliasi.util.Strings

Returns true if the specified character sequence contains only lowercase letters.

allowDelete() - Method in class com.aliasi.spell.CompiledSpellChecker

Returns true if this spell checker allows deletions.

allowInsert() - Method in class com.aliasi.spell.CompiledSpellChecker

Returns true if this spell checker allows insertions.

allowMatch() - Method in class com.aliasi.spell.CompiledSpellChecker

Returns true if this spell checker allows matches.

allowSubstitute() - Method in class com.aliasi.spell.CompiledSpellChecker

Returns true if this spell checker allows substitutions.

allowTranspose() - Method in class com.aliasi.spell.CompiledSpellChecker

Returns true if this spell checker allows transpositions.

allPunctuation(char[]) - Static method in class com.aliasi.util.Strings

Returns true if all of the characters in the specified array are punctuation as specified by Strings.isPunctuation(char).

allPunctuation(String) - Static method in class com.aliasi.util.Strings

Returns true if all of the characters in the specified string are punctuation as specified by Strings.isPunctuation(char).

allSymbols(char[]) - Static method in class com.aliasi.util.Strings

Returns true if none of the characters in the specified array are letters or digits.

allUpperCase(char[]) - Static method in class com.aliasi.util.Strings

Returns true if all of the characters in the specified array are upper case letters.

allWhitespace(StringBuffer) - Static method in class com.aliasi.util.Strings

Returns true if the specified buffer contains only whitespace characters.

allWhitespace(String) - Static method in class com.aliasi.util.Strings

Returns true if the specified string contains only whitespace characters.

allWhitespace(char[], int, int) - Static method in class com.aliasi.util.Strings

Returns true if the specified range of the specified character array only whitespace characters, as defined for characters by Strings.isWhitespace(char c).

ALT - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the alt attribute.

AnnealingSchedule - Class in com.aliasi.stats

An AnnealingSchedule instance implements a method to return the learning rate for a specified epoch.

AnnealingSchedule() - Constructor for class com.aliasi.stats.AnnealingSchedule

Do-nothing constructor to be used by concrete implementations.

APPLET - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element applet.

applet() - Method in class com.aliasi.xml.XHtmlWriter

Start an applet element with no attributes.

applet(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an applet element with the specified attributes.

applet(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an applet element with the specified attribute and value.

applet(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an applet element with the specified attributes and values.

applet(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an applet element with the specified attributes and values.

applet(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an applet element with the specified attributes and values.

ApproxDictionaryChunker - Class in com.aliasi.dict

An ApproxDictionaryChunker implements a chunker that produces chunks based on weighted edit distance of strings from dictionary entries.

ApproxDictionaryChunker(TrieDictionary<String>, TokenizerFactory, WeightedEditDistance, double) - Constructor for class com.aliasi.dict.ApproxDictionaryChunker

Construct an approximate dictionary chunker from the specified dictionary, tokenizer factory, weighted edit distance and distance bound.

ARCHIVE - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the archive attribute.

AREA - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element area.

area() - Method in class com.aliasi.xml.XHtmlWriter

Start an area element with no attributes.

area(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an area element with the specified attributes.

area(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an area element with the specified attribute and value.

area(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an area element with the specified attributes and values.

area(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an area element with the specified attributes and values.

area(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an area element with the specified attributes and values.

areaUnderPrCurve(boolean) - Method in class com.aliasi.classify.ScoredPrecisionRecallEvaluation

Returns the area under the recall-precision curve with interpolation as specified.

areaUnderRocCurve(boolean) - Method in class com.aliasi.classify.ScoredPrecisionRecallEvaluation

Returns the area under the receiver operating characteristic (ROC) curve.

Arrays - Class in com.aliasi.util

Static utility methods for processing arrays.

arrayToCSV(String[][]) - Static method in class com.aliasi.util.Arrays

Converts the two-dimensional array of strings to comma-separated value notaiton.

arrayToCSV(Object[]) - Static method in class com.aliasi.util.Arrays

Converts an array of objects to comma-separated values notation.

arrayToString(Object[]) - Static method in class com.aliasi.util.Arrays

Returns the concatenation of the string representations of the specified objects separated by commas, with the whole surrounded by square brackets and separated by a comma.

arrayToStringBuffer(StringBuffer, Object[]) - Static method in class com.aliasi.util.Arrays

Appends to the string buffer the concatenation of the string representations of the specified objects separated by commas, with the whole surrounded by square brackets and separated by a comma.

Article - Class in com.aliasi.medline

An Article represents the content of the Article element of a MEDLINE citation.

article() - Method in class com.aliasi.medline.MedlineCitation

Returns the article for this citation, containing the information derived from the cited article itself.

ARTICLE_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The Article element.

ARTICLE_TITLE_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The ArticleTitle element.

articleDate() - Method in class com.aliasi.medline.Article

Returns the date on which the publisher released an electronic version of this article.

ArticleDate - Class in com.aliasi.medline

An ArticleDate represents the date on which the publisher created an electronic version of an article.

articleTitle() - Method in class com.aliasi.medline.Article

Returns the title of this article.

articleTitleText() - Method in class com.aliasi.medline.Article

Return the article title without any brackets that may have been added to indicate translation and without any indication of the author having translated it.

articleTranslated() - Method in class com.aliasi.medline.Article

Returns true if the article has been translated from a language other than English.

assertFiniteNonNegative(String, double) - Static method in class com.aliasi.util.Math

Throws an illegal argument exception if the specified double value is not a finite non-negative number.

Author - Class in com.aliasi.medline

An instance of Author represents an author of a paper, including information about name, affiliation, title, and various qualifiers and dates.

AUTHOR_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The Author element.

AUTHOR_LIST_ELT - Static variable in class com.aliasi.medline.MedlineCitationSet

The AuthorList element.

authorList() - Method in class com.aliasi.medline.Article

Returns the author list for this article.

AuthorList - Class in com.aliasi.medline

An AuthorList represents the authors of a particular article.

authors() - Method in class com.aliasi.medline.AuthorList

Returns the authors of this article.

available() - Method in class com.aliasi.io.BitInput

Returns number of bits available for reading without blocking.

availableTopics() - Static method in class com.aliasi.corpus.parsers.Reuters21578Parser

Returns an array consisting of all of the available topics in the Reuters collection.

averageConditionalProbability(String, String) - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average conditional probability of the specified response category for test cases with the specified reference category.

averageConditionalProbabilityReference() - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average over all test cases of the conditional probability of the response that matches the reference category.

averageLog2JointProbability(String, String) - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average log (base 2) joint probability of the response category for cases of the specified reference category.

averageLog2JointProbabilityReference() - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average over all test cases of the joint log (base 2) probability of the response that matches the reference category.

averagePrecision() - Method in class com.aliasi.classify.ScoredPrecisionRecallEvaluation

Returns point-wise average precision of points on the uninterpolated precision-recall curve.

averageRank(String, String) - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average rank of the specified response category for test cases with the specified reference category.

averageRankReference() - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average over all test samples of the rank of the the response that matches the reference category.

averageScore(String, String) - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average score of the specified response category for test cases with the specified reference category.

averageScoreReference() - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the average over all test cases of the score of the response that matches the reference category.

AXIS - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the axis attribute.

B

b() - Method in class com.aliasi.util.Pair

Return the second value of the pair.

B - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element b.

b() - Method in class com.aliasi.xml.XHtmlWriter

Start an b element with no attributes.

b(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an b element with the specified attributes.

b(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an b element with the specified attribute and value.

b(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an b element with the specified attributes and values.

b(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an b element with the specified attributes and values.

b(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an b element with the specified attributes and values.

b3ClusterF() - Method in class com.aliasi.cluster.ClusterScore

Returns the F₁ measure of the B³ precision and recall metrics with equal cluster weighting.

b3ClusterPrecision() - Method in class com.aliasi.cluster.ClusterScore

Returns the precision as defined by B³ metric with equal cluster weighting.

b3ClusterRecall() - Method in class com.aliasi.cluster.ClusterScore

Returns the recall as defined by B³ metric with equal cluster weighting.

b3ElementF() - Method in class com.aliasi.cluster.ClusterScore

Returns the F₁ measure of the B³ precision and recall metrics with equal element weighting.

b3ElementPrecision() - Method in class com.aliasi.cluster.ClusterScore

Returns the precision as defined by B³ metric with equal element weighting.

b3ElementRecall() - Method in class com.aliasi.cluster.ClusterScore

Returns the recall as defined by B³ metric with equal element weighting.

B_GENE_TAG - Static variable in class com.aliasi.corpus.parsers.GeneTagParser

The tag used to start gene spans, "B-GENE".

backward(int, int) - Method in class com.aliasi.hmm.TagWordLattice

Returns the backward probability up to the token of the specified index and for the tag of the specified identifier.

balanceParens() - Method in class com.aliasi.sentences.HeuristicSentenceModel

Returns true if this model does parenthesis balancing.

BARE_ARG_PREFIX - Static variable in class com.aliasi.util.AbstractCommand

The string prefixed before a number to indicate bare arguments.

bareArguments() - Method in class com.aliasi.util.AbstractCommand

Returns the array of bare arguments, in order, supplied on the command line.

BASE - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element base.

base() - Method in class com.aliasi.xml.XHtmlWriter

Start an base element with no attributes.

base(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an base element with the specified attributes.

base(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an base element with the specified attribute and value.

base(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an base element with the specified attributes and values.

base(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an base element with the specified attributes and values.

base(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an base element with the specified attributes and values.

baseChunker() - Method in class com.aliasi.chunk.RescoringChunker

The base chunker that generates hypotheses to rescore.

BASEFONT - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element basefont.

basefont() - Method in class com.aliasi.xml.XHtmlWriter

Start an basefont element with no attributes.

basefont(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an basefont element with the specified attributes.

basefont(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an basefont element with the specified attribute and value.

basefont(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an basefont element with the specified attributes and values.

basefont(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an basefont element with the specified attributes and values.

basefont(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an basefont element with the specified attributes and values.

baseName(File) - Static method in class com.aliasi.util.Files

Returns prefix of the file's name.

basisDistribution() - Method in class com.aliasi.stats.MultinomialDistribution

Returns the multivariate distribution that forms the basis of this multinomial distribution.

BDO - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element bdo.

bdo() - Method in class com.aliasi.xml.XHtmlWriter

Start an bdo element with no attributes.

bdo(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an bdo element with the specified attributes.

bdo(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an bdo element with the specified attribute and value.

bdo(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an bdo element with the specified attributes and values.

bdo(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an bdo element with the specified attributes and values.

bdo(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an bdo element with the specified attributes and values.

BEGIN_TAG_PREFIX - Static variable in class com.aliasi.corpus.ChunkTagHandlerAdapter

The prefix to which a tag is appended to produce a begin tag, namely "B-".

BernoulliClassifier<E> - Class in com.aliasi.classify

A BernoulliClassifier provides a feature-based classifier where feature values are reduced to booleans based on a specified threshold.

BernoulliClassifier(FeatureExtractor) - Constructor for class com.aliasi.classify.BernoulliClassifier

Construct a Bernoulli classifier with the specified feature extractor and the default feature activation threshold of 0.0.

BernoulliClassifier(FeatureExtractor, double) - Constructor for class com.aliasi.classify.BernoulliClassifier

Construct a Bernoulli classifier with the specified feature extractor and specified feature activation threshold.

BernoulliConstant - Class in com.aliasi.stats

A BernoulliConstant implements a Bernoulli distribution with a constant probability of success.

BernoulliConstant(double) - Constructor for class com.aliasi.stats.BernoulliConstant

Construct a constant Bernoulli distribution with the specified success probability.

BernoulliDistribution - Class in com.aliasi.stats

A BernoulliDistribution is a multivariate distribution with two outcomes, 0 (labeled "failure") and 1 (labeled "success").

BernoulliDistribution() - Constructor for class com.aliasi.stats.BernoulliDistribution

Construct a Bernoulli distribution.

bernoulliDistribution() - Method in class com.aliasi.stats.BinomialDistribution

Returns the underlying Bernoulli (two outcome) distribution underlying this binomial distribution.

BernoulliEstimator - Class in com.aliasi.stats

A BernoulliEstimator provides a maximum likelihood estimate of a Bernoulli distribution.

BernoulliEstimator() - Constructor for class com.aliasi.stats.BernoulliEstimator

Construct a Bernoulli estimator with zero counts.

bestCategory() - Method in class com.aliasi.classify.Classification

Returns the best-scoring category.

bestForwardBackward() - Method in class com.aliasi.hmm.TagWordLattice

Returns the array of tags with the best forward-backward probabilities for each token position.

BIG - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element big.

big() - Method in class com.aliasi.xml.XHtmlWriter

Start an big element with no attributes.

big(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an big element with the specified attributes.

big(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an big element with the specified attribute and value.

big(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an big element with the specified attributes and values.

big(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an big element with the specified attributes and values.

big(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an big element with the specified attributes and values.

BinaryLMClassifier - Class in com.aliasi.classify

A BinaryLMClassifier is a boolean dynamic language model classifier based on a single language model and cross-entropy threshold.

BinaryLMClassifier(LanguageModel.Dynamic, double) - Constructor for class com.aliasi.classify.BinaryLMClassifier

Construct a binary character sequence classifier that accepts or rejects inputs based on their cross-entropy being above or below a fixed cross-entropy threshold.

BinaryLMClassifier(LanguageModel.Dynamic, double, String, String) - Constructor for class com.aliasi.classify.BinaryLMClassifier

Construct a binary character sequence classifier that accepts or rejects inputs based on their cross-entropy being above or below a fixed cross-entropy threshold.

BinomialDistribution - Class in com.aliasi.stats

A BinomialDistribution is a discrete distribution over the number of successes given a fixed number of Bernoulli trials.

BinomialDistribution(BernoulliDistribution, int) - Constructor for class com.aliasi.stats.BinomialDistribution

Construct a binomial distribution that samples from the specified Bernoulli distribution the specified number of times.

BitInput - Class in com.aliasi.io

A BitInput wraps an underlying input stream to provide bit-level input.

BitInput(InputStream) - Constructor for class com.aliasi.io.BitInput

Constructs a bit input wrapping the specified input stream.

BitOutput - Class in com.aliasi.io

A BitOutput wraps an underlying output stream to provide bit-level output.

BitOutput(OutputStream) - Constructor for class com.aliasi.io.BitOutput

Construct a bit output wrapping the specified output stream.

BitTrieReader - Class in com.aliasi.lm

A BitTrieReader provides a trie reader that wraps a bit-level input.

BitTrieReader(BitInput) - Constructor for class com.aliasi.lm.BitTrieReader

Construct a bit trie reader from the specified bit input.

BitTrieWriter - Class in com.aliasi.lm

A BitTrieWriter provides a trie writer that wraps a bit-level output.

BitTrieWriter(BitOutput) - Constructor for class com.aliasi.lm.BitTrieWriter

Construct a bit trie writer from the specified bit output with the specified maximum n-gram.

BLOCKQUOTE - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element blockquote.

blockquote() - Method in class com.aliasi.xml.XHtmlWriter

Start an blockquote element with no attributes.

blockquote(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an blockquote element with the specified attributes.

blockquote(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an blockquote element with the specified attribute and value.

blockquote(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an blockquote element with the specified attributes and values.

blockquote(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an blockquote element with the specified attributes and values.

blockquote(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an blockquote element with the specified attributes and values.

BODY - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element body.

body() - Method in class com.aliasi.xml.XHtmlWriter

Start an body element with no attributes.

body(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an body element with the specified attributes.

body(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an body element with the specified attribute and value.

body(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an body element with the specified attributes and values.

body(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an body element with the specified attributes and values.

body(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an body element with the specified attributes and values.

BooleanMatcherAdapter - Class in com.aliasi.coref

Provides a means of implementing a Matcher that returns a constant value if a boolean condition is satisifed and the no-match score otherwise.

BooleanMatcherAdapter(int) - Constructor for class com.aliasi.coref.BooleanMatcherAdapter

Construct a boolean matcher adapter that returns the specified score.

BORDER - Static variable in class com.aliasi.xml.XHtmlWriter

A constant for the border attribute.

boundaryIndices(String[], String[]) - Method in class com.aliasi.sentences.AbstractSentenceModel

Returns an array of indices of sentence-final tokens.

boundaryIndices(String[], String[], int, int) - Method in class com.aliasi.sentences.AbstractSentenceModel

Returns an array of indices of sentence-final tokens for the slice of the token and whitespace arrays specified.

boundaryIndices(String[], String[], int, int, Collection<Integer>) - Method in class com.aliasi.sentences.AbstractSentenceModel

Adds the sentence final token indices as Integer instances to the specified collection, only considering tokens between index start and end-1 inclusive.

boundaryIndices(String[], String[], int, int, Collection<Integer>) - Method in class com.aliasi.sentences.HeuristicSentenceModel

Adds the sentence final token indices as Integer instances to the specified collection, only considering tokens between index start and end-1 inclusive.

boundaryIndices(String[], String[]) - Method in interface com.aliasi.sentences.SentenceModel

Returns an array of indices of sentence-final tokens.

boundaryIndices(String[], String[], int, int, Collection<Integer>) - Method in interface com.aliasi.sentences.SentenceModel

Adds the sentence final token indices as Integer instances to the specified collection, only considering tokens between index start and end-1 inclusive.

BoundedPriorityQueue<E> - Class in com.aliasi.util

A BoundedPriorityQueue implements a priority queue with an upper bound on the number of elements.

BoundedPriorityQueue(Comparator<? super E>, int) - Constructor for class com.aliasi.util.BoundedPriorityQueue

Construct a bounded priority queue which uses the specified comparator to order elements and allows up to the specified maximum number of elements.

BR - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element br.

br() - Method in class com.aliasi.xml.XHtmlWriter

Start an br element with no attributes.

br(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an br element with the specified attributes.

br(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an br element with the specified attribute and value.

br(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an br element with the specified attributes and values.

br(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an br element with the specified attributes and values.

br(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an br element with the specified attributes and values.

BrownPosParser - Class in com.aliasi.corpus.parsers

The BrownPosParser class provides a parser for the NLTK distribution of the Brown Corpus.

BrownPosParser() - Constructor for class com.aliasi.corpus.parsers.BrownPosParser

Construct a Brown corpus part-of-speech tag parser with no handler specified.

BrownPosParser(TagHandler) - Constructor for class com.aliasi.corpus.parsers.BrownPosParser

Construct a Brown corpus part-of-speech tag parser with the specified tag handler.

BrownTextParser - Class in com.aliasi.corpus.parsers

The BrownTextParser parses the Natural Language Toolkit (NLTK) distribution of the Brown Corpus.

BrownTextParser() - Constructor for class com.aliasi.corpus.parsers.BrownTextParser

Construct a Brown text parser with a null text handler.

BrownTextParser(TextHandler) - Constructor for class com.aliasi.corpus.parsers.BrownTextParser

Construct a Brown text parser with the specified text handler.

bufferNext() - Method in class com.aliasi.util.Iterators.Buffered

Returns the next object for this iterator, or null if there are no more objects.

BUTTON - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element button.

button() - Method in class com.aliasi.xml.XHtmlWriter

Start an button element with no attributes.

button(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an button element with the specified attributes.

button(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an button element with the specified attribute and value.

button(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an button element with the specified attributes and values.

button(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an button element with the specified attributes and values.

button(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an button element with the specified attributes and values.

byteAsUnsigned(byte) - Static method in class com.aliasi.util.Math

Returns the integer value of reading the specified byte as an unsigned value.

bytesToHex(byte[]) - Static method in class com.aliasi.util.Strings

Returns a hexadecimal string-based representation of the specified byte array.

byteToHex(byte) - Static method in class com.aliasi.util.Strings

Converts the specified byte into a two-digit hexadecimal string representation.

C

CachedMention - Class in com.aliasi.coref

A CachedMention stores all of the retun values specified by the Mention interface.

CachedMention(String, String, Set<String>, String[], String, boolean) - Constructor for class com.aliasi.coref.CachedMention

Construct a cached mention from the specified return values.

capitalized(char[]) - Static method in class com.aliasi.util.Strings

Returns true if the first character in the specified array is an upper case letter and all subsequent characters are lower case letters.

CAPTION - Static variable in class com.aliasi.xml.XHtmlWriter

Constant for element caption.

caption() - Method in class com.aliasi.xml.XHtmlWriter

Start an caption element with no attributes.

caption(Attributes) - Method in class com.aliasi.xml.XHtmlWriter

Start an caption element with the specified attributes.

caption(String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an caption element with the specified attribute and value.

caption(String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an caption element with the specified attributes and values.

caption(String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an caption element with the specified attributes and values.

caption(String, String, String, String, String, String, String, String) - Method in class com.aliasi.xml.XHtmlWriter

Start an caption element with the specified attributes and values.

CASE_RESTORING - Static variable in class com.aliasi.spell.CompiledSpellChecker

A weighted edit distance ordered by similarity that treats case variants as zero cost and all other edits as infinite cost.

caseAccuracy() - Method in class com.aliasi.hmm.HmmEvaluation

Returns the accuracy measured over entire cases.

cases() - Method in class com.aliasi.chunk.ChunkingEvaluation

Return the set of cases consisting of pairs of reference and response chunkings.

caseSensitive() - Method in class com.aliasi.dict.ExactDictionaryChunker

Returns true if this dictionary chunker is case sensitive.

categories() - Method in class com.aliasi.classify.BernoulliClassifier

Returns the categories for this classifier.

categories() - Method in class com.aliasi.classify.ClassifierEvaluator

Returns the categories for which this evaluator stores results.

categories() - Method in class com.aliasi.classify.ConfusionMatrix

Return the array of categories for this confusion matrix.

categories() - Method in class com.aliasi.classify.LMClassifier

Returns the array of categories for this classifier.

categories() - Method in class com.aliasi.classify.TfIdfClassifierTrainer

Return the set of categories for which at least one training instance has been seen.

categories() - Method in class com.aliasi.classify.XValidatingClassificationCorpus

Returns the categories found in the cases for this corpus sorted into ascending order.

categories() - Method in class com.aliasi.tokenizer.CharacterTokenCategorizer

Returns the array of categories used by this categorizer.

categories() - Method in class com.aliasi.tokenizer.IndoEuropeanTokenCategorizer

Returns an array of strings representing all the categories produced by this categorizer.

categories() - Method in interface com.aliasi.tokenizer.TokenCategorizer

Returns an array of all available categories produced by this categorizer.

categorize(String) - Method in class com.aliasi.tokenizer.CharacterTokenCategorizer

Returns the category of the specified token.

categorize(String) - Method in class com.aliasi.tokenizer.IndoEuropeanTokenCategorizer

Returns the type of a token, based on its structure or other information.

categorize(String) - Method in interface com.aliasi.tokenizer.TokenCategorizer

Returns the category string for the specified token.

CATEGORIZER - Static variable in class com.aliasi.tokenizer.IndoEuropeanTokenCategorizer

This is a constant Indo-European token categorizer.

category(int) - Method in class com.aliasi.classify.RankedClassification

Returns the category with the specified rank in the classification.

category() - Method in class com.aliasi.dict.DictionaryEntry

Returns the category for this dictionary entry.

categoryDistribution() - Method in class com.aliasi.classify.LMClassifier

Returns a multivariate distribution over categories for this classifier.

categoryEntries(C) - Method in class com.aliasi.dict.AbstractDictionary

Returns the dictionary entries with the specified category.

categoryEntries(C) - Method in interface com.aliasi.dict.Dictionary

Returns the dictionary entries with the specified category.

categoryEntryIt(C) - Method in class com.aliasi.dict.AbstractDictionary

Returns an iterator over the dictionary entries with the specified category.

categoryEntryIt(C) - Method in interface com.aliasi.dict.Dictionary

Returns an iterator over the dictionary entries with the specified category.

categoryEstimator() - Method in class com.aliasi.classify.DynamicLMClassifier

Deprecated. As of 3.0, use general method LMClassifier.categoryDistribution().

categorySymbols() - Method in class com.aliasi.classify.LogisticRegressionClassifier

Returns the category symbols used by this classifier.

cauchy(double, boolean) - Static method in class com.aliasi.stats.RegressionPrior

Returns the Cauchy