Deprecated List (LingPipe API)

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Deprecated Interfaces
Deprecated Classes
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Deprecated Interfaces
com.aliasi.corpus.ChunkHandler Use `ObjectHandler<Chunking>` instead.
com.aliasi.corpus.ClassificationHandler Use `ObjectHandler` with subclass of `Classified<E>` instead.
com.aliasi.classify.Classifier Use `BaseClassifier` or one if its subinterfaces.
com.aliasi.corpus.IntArrayHandler Use `ObjectHandler<int[]>` instead.
com.aliasi.util.PriorityQueue Use one of the implementations in applications, or `Queue` for the interface.
com.aliasi.corpus.StringArrayHandler Use `ObjectHandler<String[]>` instead.
com.aliasi.corpus.TagHandler Use `ObjectHandler` with generic type `Tagging` if no whitespace is involved or `StringTagging` if whitespace is required.
com.aliasi.corpus.TextHandler Use `ObjectHandler` with generic type `CharSequence` instead.

Deprecated Classes
com.aliasi.medline.Abstract Moved to lingmed sandbox project.
com.aliasi.corpus.parsers.AbstractMedTagParser This class will move to the demos in 4.0.
com.aliasi.medline.Article Moved to lingmed sandbox project.
com.aliasi.medline.ArticleDate Moved to lingmed sandbox project.
com.aliasi.medline.Author Moved to lingmed sandbox project.
com.aliasi.medline.AuthorList Moved to lingmed sandbox project.
com.aliasi.corpus.parsers.BrownPosParser This class will move to the demos in 4.0.
com.aliasi.corpus.parsers.BrownTextParser This class will move to the demos in 4.0.
com.aliasi.medline.Chemical Moved to lingmed sandbox project.
com.aliasi.corpus.ChunkHandlerAdapter Use `TagChunkCodecAdapters.taggingToChunking(TagChunkCodec,ObjectHandler)` instead.
com.aliasi.corpus.ChunkTagHandlerAdapter Use `TagChunkCodecAdapters.chunkingToStringTagging(TagChunkCodec,ObjectHandler)` instead.
com.aliasi.classify.ClassifierEvaluator Use `BaseClassifierEvaluator` or one of its subclasses.
com.aliasi.util.Collections Use methods as indicated on a per-method basis.
com.aliasi.medline.CommentOrCorrection Moved to lingmed sandbox project.
com.aliasi.xml.CompositeFilter Plug filters together directly.
com.aliasi.medline.DataBank Moved to lingmed sandbox project.
com.aliasi.medline.DataBankList Moved to lingmed sandbox project.
com.aliasi.medline.ELocationId Moved to lingmed sandbox project.
com.aliasi.tokenizer.EnglishStopListFilterTokenizer Use `EnglishStopTokenizerFactory` instead.
com.aliasi.io.FileNameFilter Implement filters directly.
com.aliasi.util.FilterComparator Build your own from scratch, this is a very simple filter.
com.aliasi.tokenizer.FilterTokenizer Use `ModifiedTokenizerFactory` instead.
com.aliasi.medline.GeneralNote Moved to lingmed sandbox project.
com.aliasi.corpus.parsers.GeneTagChunkParser This class will move to the demos in 4.0.
com.aliasi.corpus.parsers.GeneTagParser This class will move to the demos in 4.0.
com.aliasi.corpus.parsers.GeniaEntityChunkParser This class will move to the demos in 4.0.
com.aliasi.corpus.parsers.GeniaPosParser This class will move to the demos in 4.0.
com.aliasi.corpus.parsers.GeniaSentenceParser This class will move to the demos in 4.0.
com.aliasi.corpus.parsers.GigawordTextParser This class will move to the demos in 4.0.
com.aliasi.medline.Grant Moved to lingmed sandbox project.
com.aliasi.medline.GrantList Moved to lingmed sandbox project.
com.aliasi.hmm.HmmEvaluation Use `TaggerEvaluator`, `MarginalTaggerEvaluator` and `NBestTaggerEvaluator` instead.
com.aliasi.hmm.HmmEvaluator Use `TaggerEvaluator`, `MarginalTaggerEvaluator` and `NBestTaggerEvaluator` instead.
com.aliasi.medline.Investigator Moved to lingmed sandbox project.
com.aliasi.util.Iterators.Array Construct with the static factory method `Iterators.array(Object[])` instead.
com.aliasi.util.Iterators.ArraySlice Use the static factory method `Iterators.arraySlice(Object[],int,int)` instead.
com.aliasi.util.Iterators.Empty Use the static factory method `Iterators.empty()` instead.
com.aliasi.util.Iterators.Pair Use the static factory method `Iterators.pair(Object,Object)` instead.
com.aliasi.util.Iterators.Sequence Use the static factory method `Iterators.sequence(Iterator,Iterator)`, `Iterators.sequence(Iterator)`, or `Iterators.sequence(List)` instead.
com.aliasi.util.Iterators.Singleton Use the static factory method `Iterators.singleton(Object)` instead.
com.aliasi.medline.Journal Moved to lingmed sandbox project.
com.aliasi.medline.JournalInfo Moved to lingmed sandbox project.
com.aliasi.medline.JournalIssue Moved to lingmed sandbox project.
com.aliasi.medline.KeywordList Moved to lingmed sandbox project.
com.aliasi.tokenizer.LengthStopFilterTokenizer Use `TokenLengthTokenizerFactory` or `ModifyTokenTokenizerFactory.modify(Tokenizer)` instead.
com.aliasi.corpus.LineParser Implement directly.
com.aliasi.tokenizer.LowerCaseFilterTokenizer Use `LowerCaseTokenizerFactory` instead.
com.aliasi.medline.MedlineChars Moved to lingmed sandbox project.
com.aliasi.medline.MedlineCitation Moved to lingmed sandbox project.
com.aliasi.medline.MedlineCitationSet Moved to lingmed sandbox project.
com.aliasi.medline.MedlineParser Moved to lingmed sandbox project.
com.aliasi.corpus.parsers.MedlineTextParser This class will move to the demos in 4.0.
com.aliasi.corpus.parsers.MedPostPosParser This class will move to the demos in 4.0.
com.aliasi.medline.MeshHeading Moved to lingmed sandbox project.
com.aliasi.corpus.parsers.Muc6ChunkParser This class will move to the demos in 4.0.
com.aliasi.medline.Name Moved to lingmed sandbox project.
com.aliasi.medline.NameId Moved to lingmed sandbox project.
com.aliasi.util.NBestSet Use `BoundedPriorityQueue` or `ShortPriorityQueue` instead.
com.aliasi.tokenizer.NormalizeWhiteSpaceFilterTokenizer Use `WhitespaceNormTokenizerFactory` instead.
com.aliasi.medline.OtherAbstract Moved to lingmed sandbox project.
com.aliasi.medline.OtherID Moved to lingmed sandbox project.
com.aliasi.medline.PersonalNameSubject Moved to lingmed sandbox project.
com.aliasi.tokenizer.PorterStemmer Use `PorterStemmerTokenizerFactory.stem(String)` instead.
com.aliasi.tokenizer.PorterStemmerFilterTokenizer Use `PorterStemmerTokenizerFactory` instead.
com.aliasi.medline.PubDate Moved to lingmed sandbox project.
com.aliasi.tokenizer.PunctuationStopListTokenizer Use `RegExFilteredTokenizerFactory` with a pattern matching the characters specified in `Strings.allPunctuation(String)`.
com.aliasi.util.Reflection Use `java.lang.reflect` directly instead, as described on the individual methods.
com.aliasi.corpus.parsers.RegexLineTagParser Use `LineTaggingParser` instead.
com.aliasi.corpus.parsers.Reuters21578Parser This class will move to the demos in 4.0.
com.aliasi.util.ReversibleComparator Use `Collections.reverseOrder(Comparator)`.
com.aliasi.util.ReversibleMTFListComparator We'll put this in a demo if we ever need to build complex GUI table controls again.
com.aliasi.xml.SAXWriterFilter Not used anywhere.
com.aliasi.sentences.SentenceAnnotateFilter LingPipe is no longer supportintg direct XML annotation; see the generic demos for examples.
com.aliasi.util.SmallObjectToDoubleMap Use plain `ObjectToDoubleMap`.
com.aliasi.tokenizer.SoundexFilterTokenizer Use `SoundexTokenizerFactory` instead.
com.aliasi.tokenizer.StopFilterTokenizer Use `ModifyTokenTokenizerFactory` instead.
com.aliasi.tokenizer.StopListFilterTokenizer Use `StopTokenizerFactory` instead.
com.aliasi.corpus.parsers.SvmLightClassificationParser This class will move to the demos in 4.0.
com.aliasi.hmm.TagWordLattice Use `TagLattice` interface for return results, and `ForwardBackwardTagLattice` for construction.
com.aliasi.tokenizer.TokenFilterTokenizer Use `ModifyTokenTokenizerFactory` instead.
com.aliasi.medline.Topic Moved to lingmed sandbox project.
com.aliasi.xml.WellFormedFilter Use any old parser with appropriate properties.
com.aliasi.util.XML Implement functionality directly.
com.aliasi.classify.XValidatingClassificationCorpus Use `XValidatingObjectCorpus` with type `com.aliasi.corpus.ObjectHandler<Classified<E>>` instead.

Deprecated Fields
com.aliasi.util.Arrays.EMPTY_CHAR_ARRAY Use `Strings.EMPTY_CHAR_ARRAY` instead.
com.aliasi.util.Arrays.EMPTY_STRING_ARRAY Use `Strings.EMPTY_STRING_ARRAY` instead.
com.aliasi.tokenizer.IndoEuropeanTokenizerFactory.FACTORY Use `IndoEuropeanTokenizerFactory.INSTANCE` instead.
com.aliasi.tokenizer.CharacterTokenizerFactory.FACTORY Use `CharacterTokenizerFactory.INSTANCE` instead.
com.aliasi.coref.AbstractMentionChain.mEntityType Use `AbstractMentionChain.entityType()` or `AbstractMentionChain.setEntityType(String)` instead.
com.aliasi.coref.AbstractMentionChain.mGender Use `AbstractMentionChain.gender()` or `AbstractMentionChain.setGender(String)` instead.
com.aliasi.coref.AbstractMentionChain.mHonorifics Use `AbstractMentionChain.honorifics()` or `AbstractMentionChain.addHonorific(String)` instead.
com.aliasi.tokenizer.FilterTokenizer.mTokenizer Use the method `FilterTokenizer.baseTokenizer()` for reads and create a new instance of `FilterTokenizer` itself for different values.
com.aliasi.spell.TokenizedDistance.mTokenizerFactory Use `TokenizedDistance.tokenizerFactory()` instead.
com.aliasi.util.Scored.REVERSE_SCORE_COMPARATOR Use the static factory method `ScoredObject.reverseComparator()` instead.
com.aliasi.util.Scored.SCORE_COMPARATOR Use the static factory method `ScoredObject.comparator()` instead.
com.aliasi.util.Files.TEMP_DIRECTORY Use `new File(System.getProperty(TEMP_DIRECTORY_SYS_PROPERTY))` instead.
com.aliasi.util.XML.XERCES_BUFFER_SIZE_PROPERTY Configure Xerces on an ad-hoc basis as needed.

Deprecated Methods
com.aliasi.medline.Article.abstrct() See class documentation.
com.aliasi.util.ShortPriorityQueue.add(E) Use `ShortPriorityQueue.offer(Object)` instead.
com.aliasi.util.BoundedPriorityQueue.add(E) Use `BoundedPriorityQueue.offer(Object)` instead. In the next release, this will be redefined to match the collection interface.
com.aliasi.util.Collections.addAll(Collection, E[]) Use `java.util.Collections.addAll(Collection,Object[])` instead.
com.aliasi.hmm.HmmEvaluation.addCase(String[], String[], String[], TagWordLattice, Iterator>) See class documentation.
com.aliasi.classify.ClassifierEvaluator.addCase(String, E) Use `ClassifierEvaluator.handle(Classified)` instead.
com.aliasi.hmm.HmmEvaluation.addLatticeCase(String[], String[], TagWordLattice) See class documentation.
com.aliasi.util.Arrays.arrayToCSV(Object[]) Use a proper CSV parser.
com.aliasi.util.Arrays.arrayToCSV(String[][]) Use a proper CSV parser.
com.aliasi.medline.MedlineCitation.article() See class documentation.
com.aliasi.medline.Article.articleDate() See class documentation.
com.aliasi.util.Math.assertFiniteNonNegative(String, double) Use `Exceptions.finiteNonNegative(String,double)` instead.
com.aliasi.medline.Article.authorList() See class documentation.
com.aliasi.medline.AuthorList.authors() See class documentation.
com.aliasi.util.Strings.byteToHex(byte) Use `Integer.toHexString(b)` instead.
com.aliasi.dict.Dictionary.categoryEntries(C) Use `Dictionary.categoryEntryList(Object)` instead.
com.aliasi.dict.AbstractDictionary.categoryEntries(C) Use `AbstractDictionary.categoryEntryList(Object)` instead.
com.aliasi.classify.DynamicLMClassifier.categoryEstimator() As of 3.0, use general method `LMClassifier.categoryDistribution()`.
com.aliasi.medline.MedlineCitation.chemicals() See class documentation.
com.aliasi.classify.ClassifierEvaluator.classifier() See class documentation.
com.aliasi.lm.TokenizedLM.collocations(int, int, int) Use `TokenizedLM.collocationSet(int,int,int)` instead.
com.aliasi.medline.MedlineCitation.commentOrCorrections() See class documentation.
com.aliasi.util.Collections.compare(E, E, Comparator) Implement directly using the comparator or objects.
com.aliasi.symbol.SymbolTableCompiler.compileTo(DataOutputStream) As of LingPipe 2.3, use `SymbolTableCompiler.compileTo(ObjectOutput)`.
com.aliasi.symbol.MapSymbolTable.compileTo(ObjectOutput) As of LingPipe 3.1, use `objOut.writeObject(this)`.
com.aliasi.tokenizer.RegExTokenizerFactory.compileTo(ObjectOutput) Use the `Serializable` interface instead.
com.aliasi.tokenizer.NGramTokenizerFactory.compileTo(ObjectOutput) Use the `Serializable` interface instead.
com.aliasi.tokenizer.IndoEuropeanTokenizerFactory.compileTo(ObjectOutput) Use the `Serializable` interface instead.
com.aliasi.tokenizer.CharacterTokenizerFactory.compileTo(ObjectOutput) Use `Serializable` interface instead.
com.aliasi.hmm.HmmEvaluation.confidenceEvaluation() See class documentation.
com.aliasi.corpus.parsers.Reuters21578Parser.corpus(String, File) See class documentation.
com.aliasi.util.Files.createTempFile(String) Use `java.io.File.createTempFile(String,String)` instead.
com.aliasi.util.Arrays.csvToArray(String) Use a propert CSV parser.
com.aliasi.util.Arrays.csvToArray2D(String) Use a proper CSV parser.
com.aliasi.medline.Article.dataBankList() See class documentation.
com.aliasi.medline.DataBankList.dataBanks() See class documentation.
com.aliasi.util.Strings.decimalFormat(double, String, int) Use `DecimalFormat` directly with a pattern, or use the newer `Formatter` class or `String.format(String,Object[])` utility method instead.
com.aliasi.medline.MeshHeading.descriptor() See class documentation.
com.aliasi.util.Collections.elementsToStringBuilder(StringBuilder, Collection) Use `sb.append(c.toString())` instead.
com.aliasi.medline.Article.eLocationIds() See class documentation.
com.aliasi.classify.TradNaiveBayesClassifier.em(TradNaiveBayesClassifier, Factory, Corpus>, Corpus, double) Use `TradNaiveBayesClassifier.emIterator(TradNaiveBayesClassifier,Factory,Corpus,Corpus,double)` instead.
com.aliasi.classify.TradNaiveBayesClassifier.em(TradNaiveBayesClassifier, Factory, Corpus>, Corpus, double, int, double, Reporter) Use `TradNaiveBayesClassifier.emTrain(TradNaiveBayesClassifier,Factory,Corpus,Corpus,double,int,double,Reporter)` instead.
com.aliasi.dict.Dictionary.entries() Use `Dictionary.entryList()` instead.
com.aliasi.dict.AbstractDictionary.entries() Use `AbstractDictionary.entryList()` instead.
com.aliasi.stats.LogisticRegression.estimate(Vector[], int[], RegressionPrior, AnnealingSchedule, double, int, int, PrintWriter) Use `LogisticRegression.estimate(Vector[],int[],RegressionPrior,AnnealingSchedule,Reporter,double,int,int)` instead.
com.aliasi.hmm.HmmEvaluator.evaluation() See the class doc.
com.aliasi.util.Files.fileToURLName(File) Instead of `Files.fileToURLName(file)` use `file.toURI().toURL().toString()`.
com.aliasi.features.ZScoreFeatureExtractor.filter(String, Number) Use `ZScoreFeatureExtractor.zScore(String,double)` instead; this method no longer overrides the the method of the same name in `ModifiedFeatureExtractor` because this class no longer overrides `ModifiedFeatureExtractor`.
com.aliasi.util.BoundedPriorityQueue.first() Use `BoundedPriorityQueue.remove()` instead.
com.aliasi.hmm.HmmDecoder.firstBest(String[]) Use `HmmDecoder.tag(List)` instead.
com.aliasi.hmm.HmmEvaluation.firstBestEvaluation() See class documentation.
com.aliasi.util.Strings.fit(String, int) Use `java.util.Formatter` instead.
com.aliasi.lm.TokenizedLM.frequentTerms(int, int) Use `TokenizedLM.frequentTermSet(int,int)` instead.
com.aliasi.medline.MedlineCitation.generalNotes() See class documentation.
com.aliasi.corpus.parsers.GeniaSentenceParser.getChunkHandler() Use generic `Parser.getHandler()` instead.
com.aliasi.corpus.parsers.GeniaEntityChunkParser.getChunkHandler() Use generic `Parser.getHandler()` instead.
com.aliasi.corpus.parsers.GeneTagChunkParser.getChunkHandler() Use generic `Parser.getHandler()` instead.
com.aliasi.util.AbstractCommand.getCSV(String) Use `String.split(String)` instead.
com.aliasi.util.Collections.getFirst(List) Use `l.get(0)` instead.
com.aliasi.util.Collections.getFirst(Set) Use `set.iterator().next()` instead.
com.aliasi.corpus.parsers.RegexLineTagParser.getTagHandler() Use generic `Parser.getHandler()`.
com.aliasi.corpus.parsers.GeniaPosParser.getTagHandler() Use generic `Parser.getHandler()` instead.
com.aliasi.corpus.parsers.MedlineTextParser.getTextHandler() Use generic `Parser.getHandler()` instead.
com.aliasi.medline.Article.grantList() See class documentation.
com.aliasi.medline.GrantList.grants() See class documentation.
com.aliasi.lm.TokenizedLM.handle(char[], int, int) Use `TokenizedLM.handle(CharSequence)` instead.
com.aliasi.lm.NGramProcessLM.handle(char[], int, int) Use `NGramProcessLM.handle(CharSequence)` instead.
com.aliasi.lm.NGramBoundaryLM.handle(char[], int, int) Use `NGramBoundaryLM.handle(CharSequence)` instead.
com.aliasi.spell.TrainSpellChecker.handle(char[], int, int) Use `TrainSpellChecker.handle(CharSequence)` instead.
com.aliasi.spell.TfIdfDistance.handle(char[], int, int) Use `TfIdfDistance.handle(CharSequence)` instead.
com.aliasi.classify.TradNaiveBayesClassifier.handle(CharSequence, Classification) Use `TradNaiveBayesClassifier.handle(Classified)` instead.
com.aliasi.classify.DynamicLMClassifier.handle(CharSequence, Classification) Use `DynamicLMClassifier.handle(Classified)` instead.
com.aliasi.classify.TfIdfClassifierTrainer.handle(E, Classification) Use `TfIdfClassifierTrainer.handle(Classified)` instead.
com.aliasi.classify.KnnClassifier.handle(E, Classification) Use `KnnClassifier.handle(Classified)` instead.
com.aliasi.classify.ClassifierEvaluator.handle(E, Classification) Use `ClassifierEvaluator.handle(Classified)` instead.
com.aliasi.classify.BernoulliClassifier.handle(E, Classification) Use `BernoulliClassifier.handle(Classified)` instead.
com.aliasi.medline.MedlineHandler.handle(MedlineCitation) See class documentation.
com.aliasi.chunk.TrainTokenShapeChunker.handle(String[], String[], String[]) Use `TrainTokenShapeChunker.handle(Chunking)` instead.
com.aliasi.chunk.ChunkerEvaluator.handle(String[], String[], String[]) Wrap with `BioTagChunkCodec` instead.
com.aliasi.chunk.CharLmRescoringChunker.handle(String[], String[], String[]) Use `CharLmRescoringChunker.handle(Chunking)` instead.
com.aliasi.chunk.CharLmHmmChunker.handle(String[], String[], String[]) Use `CharLmHmmChunker.handle(Chunking)` instead.
com.aliasi.hmm.AbstractHmmEstimator.handle(String[], String[], String[]) use `AbstractHmmEstimator.handle(Tagging)` instead.
com.aliasi.lm.TokenizedLM.infrequentTerms(int, int) Use `TokenizedLM.infrequentTermSet(int,int)` instead.
com.aliasi.util.Collections.intersects(Set, Set) Use `!java.util.Collections.disjoint(set1,set2)`.
com.aliasi.medline.MedlineCitation.investigators() See class documentation.
com.aliasi.util.Collections.isSingleton(Collection) Use `c.size() == 1` instead.
com.aliasi.medline.KeywordList.iterator() See class documentation.
com.aliasi.medline.GrantList.iterator() See class documentation.
com.aliasi.medline.DataBankList.iterator() See class documentation.
com.aliasi.medline.AuthorList.iterator() See class documentation.
com.aliasi.medline.Article.journal() See class documentation.
com.aliasi.medline.MedlineCitation.journalInfo() See class documentation.
com.aliasi.medline.Journal.journalIssue() See class documentation.
com.aliasi.util.ObjectToDoubleMap.keysOrderedByValue() Use `ObjectToDoubleMap.keysOrderedByValueList()` instead.
com.aliasi.medline.MedlineCitation.keywordLists() See class documentation.
com.aliasi.medline.KeywordList.keywords() See class documentation.
com.aliasi.hmm.HmmDecoder.lattice(String[]) Use `HmmDecoder.tagMarginal(List)` instead.
com.aliasi.util.Collections.listToString(List) Use `List.toString()` instead.
com.aliasi.util.Collections.listToStringBuilder(StringBuilder, List) Use `sb.append(ls.toString())`.
com.aliasi.classify.DynamicLMClassifier.lmForCategory(String) As of 3.0, use general `LMClassifier.languageModel(String)`.
com.aliasi.hmm.TagWordLattice.log2ConditionalTags(int) Use `TagWordLattice.log2ConditionalTagList(int)` instead.
com.aliasi.util.Files.makeCleanDir(File) Implement with compound statements in `java.io.File`.
com.aliasi.util.Files.makeCleanDir(File, String) Implement with compound statements in `java.io.File`.
com.aliasi.cluster.LatentDirichletAllocation.mapTopicEstimate(int[], int, int, int, Random) Use `LatentDirichletAllocation.bayesTopicEstimate(int[],int,int,int,Random)` instead.
com.aliasi.medline.MedlineCitation.meshHeadings() See class documentation.
com.aliasi.util.ReversibleMTFListComparator.moveToFront(Comparator) Do not use this class.
com.aliasi.medline.PersonalNameSubject.name() See class documentation.
com.aliasi.medline.Investigator.name() See class documentation.
com.aliasi.medline.Author.name() See class documentation.
com.aliasi.medline.Name.nameId() See class documentation.
com.aliasi.hmm.HmmDecoder.nBest(String[]) Use `HmmDecoder.tagNBest(List,int)` instead.
com.aliasi.hmm.HmmDecoder.nBest(String[], int) Use `HmmDecoder.tagNBest(List,int)` instead.
com.aliasi.hmm.HmmDecoder.nBestConditional(String[]) Use `HmmDecoder.tagNBestConditional(List,int)` instead.
com.aliasi.util.Reflection.newInstance(String) Use `Class.forName(className).getConstructor(new Class[0]).newInstance(new Object[0])` instead.
com.aliasi.util.Reflection.newInstance(String, Object[]) Convert `args` to `argClasses` using `args[i].getClass()`, then call `Class.forName(className).getConstructor(argClasses).newInstace(args)` instead.
com.aliasi.util.Reflection.newInstance(String, Object[], Class[]) Use `Class.forName(className).getConstructor(argClasses).newInstance(args)` instead.
com.aliasi.util.Reflection.newInstance(String, Object[], String[]) Convert `argClassNames` to `argClasses` classes using `Class.forName(argClassNames[i])`, then use `Class.forName(className).getConstructor(argClasses).newInstace(args)` instead.
com.aliasi.lm.TokenizedLM.newTerms(int, int, int, LanguageModel.Tokenized) Use `TokenizedLM.newTermSet(int,int,int,LanguageModel.Tokenized)` instead.
com.aliasi.lm.TokenizedLM.oldTerms(int, int, int, LanguageModel.Tokenized) Use `TokenizedLM.oldTermSet(int,int,int,LanguageModel.Tokenized)` instead.
com.aliasi.medline.MedlineCitation.otherAbstracts() See class documentation.
com.aliasi.medline.MedlineCitation.otherIDs() See class documentation.
com.aliasi.medline.MedlineParser.parse(InputSource, MedlineHandler) Use `setHandler(MedlineHandler)` followed by `parse(InputSource)`.
com.aliasi.corpus.parsers.GigawordTextParser.parseString(char[], int, int) See class documentation.
com.aliasi.matrix.SvdMatrix.partialSvd(int[][], double[][], int, double, double, double, double, double, int, int, PrintWriter) Use `SvdMatrix.partialSvd(int[][],double[][],int,double,double,double,double,Reporter,double,int,int)` instead.
com.aliasi.matrix.SvdMatrix.partialSvd(int[][], double[][], int, double, double, double, double, Random, double, int, int, PrintWriter) Use `SvdMatrix.partialSvd(int[][],double[][],int,double,double,double,double,Random,Reporter,double,int,int)` instead.
com.aliasi.matrix.SvdMatrix.partialSvd(int[][], double[][], int, double, double, double, double, Random, Reporter, double, int, int) Use `SvdMatrix.partialSvd(int[][],double[][],int,double,double,double,double,Random,Reporter,double,int,int)` instead.
com.aliasi.medline.MedlineCitation.personalNameSubjects() See class documentation.
com.aliasi.tag.MarginalTaggerEvaluator.perTokenEvaluation() Use `MarginalTaggerEvaluator.perTokenEval()` instead.
com.aliasi.dict.TrieDictionary.phraseEntries(String)
com.aliasi.dict.Dictionary.phraseEntries(String) Use `Dictionary.phraseEntryList(String)` instead.
com.aliasi.dict.AbstractDictionary.phraseEntries(String) Use `AbstractDictionary.phraseEntryList(String)` instead.
com.aliasi.util.BoundedPriorityQueue.pop() Use `BoundedPriorityQueue.poll()` instead.
com.aliasi.util.Files.prefix(String) Only used as part of `Files.baseName(File)`.
com.aliasi.medline.JournalIssue.pubDate() See class documentation.
com.aliasi.medline.MeshHeading.qualifiers() See class documentation.
com.aliasi.symbol.SymbolTableCompiler.read(DataInputStream) As of LingPipe 2.3, use `SymbolTableCompiler.compileTo(ObjectOutput)` to write and then read in generally from an object input stream.
com.aliasi.util.Strings.readArrayFrom(DataInput) Build this yourself using `DataInput.readUTF()`.
com.aliasi.util.Files.readCharsFromFile(File) Use `readCharsFromFile(file,Strings.UTF8)` instead.
com.aliasi.util.Files.readFromFile(File) Use `readFromFile(file,Strings.UTF8)` instead.
com.aliasi.util.Files.readLinesFromFile(File, String) Use `FileLineReader.readLineArray(File,String)` instead.
com.aliasi.util.Files.readObjectFrom(File) Use `com.aliasi.util.AbstractExteranlizable.readObject(File)` instead.
com.aliasi.cluster.KMeansClusterer.recluster(Set>, int) Use `KMeansClusterer.recluster(Set,Set,Reporter)` with an empty set as second argument, and null reporter instead.
com.aliasi.util.Strings.save(String) Use `new String(s)` instead.
com.aliasi.util.ObjectToDoubleMap.scoredObjectsOrderedByValue() Use `ObjectToDoubleMap.scoredObjectsOrderedByValueList()` instead.
com.aliasi.util.Files.serializeDeserialize(Serializable) Use `com.aliasi.util.AbstractExteranlizable.serializeDeserialize(Serializable)` instead.
com.aliasi.classify.ClassifierEvaluator.setClassifier(Classifier) See class documentation.
com.aliasi.corpus.ChunkHandlerAdapter.setTagHandler(TagHandler) See class documentation.
com.aliasi.tokenizer.FilterTokenizer.setTokenizer(Tokenizer) Create a new immutable instance of `FilterTokenizer` instead.
com.aliasi.util.Collections.setToString(Set) Use `Set.toString()` instead.
com.aliasi.util.Collections.setToStringBuilder(StringBuilder, Set) Use `sb.append(c.toString())` instead.
com.aliasi.tokenizer.SoundexFilterTokenizer.soundexEncoding(String) Use `SoundexTokenizerFactory.soundexEncoding(String)` instead.
com.aliasi.tokenizer.PorterStemmer.stem(String) Use `PorterStemmerTokenizerFactory.stem(String)` instead.
com.aliasi.util.Files.suffix(String) Only used as part of `Files.extension(File)`.
com.aliasi.util.Arrays.sum(int[]) Use `Math.sum(int[])` instead.
com.aliasi.matrix.SvdMatrix.svd(double[][], int, double, double, double, double, double, int, int, PrintWriter) Use `SvdMatrix.svd(double[][],int,double,double,double,double,Reporter,double,int,int)` instead.
com.aliasi.corpus.parsers.BrownPosParser.tagHandler() Moving to demos in 4.0.
com.aliasi.corpus.parsers.AbstractMedTagParser.tagHandler() Use generic `Parser.getHandler()` instead.
com.aliasi.util.Collections.toIntArray(Collection) Implement directly using `Number.intValue()`.
com.aliasi.tag.TaggerEvaluator.tokenEvaluation() Use `TaggerEvaluator.tokenEval()` instead.
com.aliasi.medline.MeshHeading.topics() See class documentation.
com.aliasi.tokenizer.PorterStemmer.toString() Use `PorterStemmerTokenizerFactory.stem(String)` instead.
com.aliasi.util.Collections.toStringArray(Collection) Use `Collection.toArray(Object[])` instead.
com.aliasi.util.Collections.toStringArray(Collection, String[]) Use `Collection.toArray(Object[])` instead.
com.aliasi.lm.TokenizedLM.train(char[], int, int) Use `TokenizedLM.handle(CharSequence)` instead.
com.aliasi.lm.TokenizedLM.train(char[], int, int, int) Use `TokenizedLM.train(CharSequence,int)` instead.
com.aliasi.lm.TokenizedLM.train(CharSequence) Use `TokenizedLM.handle(CharSequence)` instead.
com.aliasi.spell.TrainSpellChecker.train(CharSequence) Use `TrainSpellChecker.handle(CharSequence)` instead.
com.aliasi.classify.LogisticRegressionClassifier.train(FeatureExtractor, Corpus>, int, boolean, RegressionPrior, AnnealingSchedule, double, int, int, PrintWriter) Use `LogisticRegressionClassifier.train(FeatureExtractor,Corpus,int,boolean,RegressionPrior,AnnealingSchedule,Reporter,double,int,int)` instead.
com.aliasi.classify.LogisticRegressionClassifier.train(FeatureExtractor, Corpus>, int, boolean, RegressionPrior, AnnealingSchedule, Reporter, double, int, int) Use `LogisticRegressionClassifier.train(Corpus,FeatureExtractor,int,boolean,RegressionPrior,AnnealingSchedule,double,int,int,Reporter)` instead.
com.aliasi.classify.DynamicLMClassifier.train(String, char[], int, int) Use `DynamicLMClassifier.handle(Classified)` instead.
com.aliasi.classify.BinaryLMClassifier.train(String, char[], int, int) Use `BinaryLMClassifier.handle(Classified)` instead.
com.aliasi.classify.DynamicLMClassifier.train(String, CharSequence) Use `DynamicLMClassifier.handle(Classified)` instead.
com.aliasi.classify.BinaryLMClassifier.train(String, CharSequence) Use `BinaryLMClassifier.handle(Classified)` instead.
com.aliasi.spell.TfIdfDistance.trainIdf(CharSequence) Use `TfIdfDistance.handle(CharSequence)` instead.
com.aliasi.lm.TokenizedLM.trainSequence(char[], int, int, int) Use `TokenizedLM.trainSequence(CharSequence,int)` instead.
com.aliasi.tag.TaggerEvaluator.unknownTokenEvaluation(Set) Use `TaggerEvaluator.unknownTokenEval(Set)` instead.
com.aliasi.classify.XValidatingClassificationCorpus.visitTest(ClassificationHandler) See clas documentation
com.aliasi.classify.XValidatingClassificationCorpus.visitTrain(ClassificationHandler) See clas documentation
com.aliasi.util.Strings.writeArrayTo(DataOutput, String[]) Write your own with `DataOutput.writeUTF(String)` instead.
com.aliasi.util.Files.writeCharsToFile(char[], File) Use `writeCharsToFile(chars,file,Strings.UTF8)` instead.
com.aliasi.util.Files.writeObjectTo(Serializable, File) Use `AbstractExternalizable.serializeTo(Serializable,File)` instead.
com.aliasi.util.Files.writeStringToFile(String, File) Use `writeStringToFile(s,file,Strings.UTF8)` instead.
com.aliasi.symbol.MapSymbolTable.writeTo(ObjectOutput) As of LingPipe 3.1, use `objOut.writeObject(this)`.

Deprecated Constructors
com.aliasi.corpus.parsers.AbstractMedTagParser(TagHandler) Moving in 4.0.
com.aliasi.corpus.parsers.BrownPosParser(TagHandler) Moving to demos in 4.0.
com.aliasi.corpus.parsers.BrownTextParser(TextHandler) See class documentation.
com.aliasi.tokenizer.CharacterTokenCategorizer() Use singleton instance `CharacterTokenCategorizer.INSTANCE` instead.
com.aliasi.tokenizer.CharacterTokenizerFactory() Use singleton instance `CharacterTokenizerFactory.INSTANCE` instead.
com.aliasi.corpus.ChunkHandlerAdapter(TagHandler, TokenizerFactory, boolean) See class documentation.
com.aliasi.classify.ClassifierEvaluator(Classifier, String[]) See class documentation.
com.aliasi.classify.ClassifierEvaluator(Classifier, String[], boolean) See class documentation.
com.aliasi.tokenizer.EnglishStopListFilterTokenizer(Tokenizer) Use `EnglishStopTokenizerFactory` or `ModifyTokenTokenizerFactory.modify(Tokenizer)` instead.
com.aliasi.corpus.parsers.GeneTagParser(TagHandler) Moving to demos in 4.0
com.aliasi.corpus.parsers.GeniaPosParser(TagHandler) Moving to demos in 4.0.
com.aliasi.corpus.parsers.GigawordTextParser(TextHandler) See class documentation.
com.aliasi.hmm.HmmEvaluator(HiddenMarkovModel, String[], int)
com.aliasi.hmm.HmmEvaluator(HmmDecoder, HmmEvaluation) See the class documentation.
com.aliasi.tokenizer.IndoEuropeanTokenCategorizer() Use singleton `IndoEuropeanTokenCategorizer.CATEGORIZER` object instead.
com.aliasi.tokenizer.IndoEuropeanTokenizerFactory() Use singleton instance `IndoEuropeanTokenizerFactory.INSTANCE` instead.
com.aliasi.util.Iterators.Array(E[]) Use the static factory method `Iterators.array(Object[])` instead.
com.aliasi.util.Iterators.ArraySlice(E[], int, int) Use the static factory method `Iterators.arraySlice(Object[],int,int)` instead.
com.aliasi.util.Iterators.Empty() Use the static factory method `Iterators.empty()` instead.
com.aliasi.util.Iterators.Pair(E, E) Use the static factory method `Iterators.pair(Object,Object)` instead.
com.aliasi.util.Iterators.Sequence(Iterator[]) Use the static factory method `Iterators.sequence(List)` instead.
com.aliasi.util.Iterators.Sequence(Iterator, Iterator) Use the static factory method `Iterators.sequence(Iterator,Iterator)` instead.
com.aliasi.util.Iterators.Sequence(Iterator>) Use the static factory method `Iterators.sequence(Iterator)` instead.
com.aliasi.util.Iterators.Singleton(E) Use the static factory method `Iterators.singleton(Object)` instead.
com.aliasi.cluster.KMeansClusterer(FeatureExtractor, int, int)
com.aliasi.tokenizer.LengthStopFilterTokenizer(Tokenizer, int) Use `ModifyTokenTokenizerFactory.modify(Tokenizer)` instead.
com.aliasi.tokenizer.LineTokenizerFactory() Use singleton instance `LineTokenizerFactory.INSTANCE` instead.
com.aliasi.tokenizer.LowerCaseFilterTokenizer(Tokenizer) Use `LowerCaseTokenizerFactory` or `ModifyTokenTokenizerFactory.modify(Tokenizer)` instead.
com.aliasi.tokenizer.LowerCaseFilterTokenizer(Tokenizer, Locale) Use `LowerCaseTokenizerFactory` or `ModifyTokenTokenizerFactory.modify(Tokenizer)` instead.
com.aliasi.corpus.parsers.MedlineTextParser(TextHandler) See class documentation.
com.aliasi.corpus.parsers.MedPostPosParser(TagHandler) Moving to demos in 4.0.
com.aliasi.tokenizer.NormalizeWhiteSpaceFilterTokenizer(Tokenizer) Use `WhitespaceNormTokenizerFactory` or `ModifyTokenTokenizerFactory.modify(Tokenizer)` instead.
com.aliasi.classify.PerceptronClassifier(FeatureExtractor, KernelFunction, Corpus>, String, int) Use constructor `PerceptronClassifier.PerceptronClassifier(Corpus,FeatureExtractor,KernelFunction,String,int,String,String)` instead.
com.aliasi.classify.PerceptronClassifier(FeatureExtractor, KernelFunction, Corpus>, String, int, String, String) Use constructor `PerceptronClassifier.PerceptronClassifier(Corpus,FeatureExtractor,KernelFunction,String,int,String,String)` instead.
com.aliasi.tokenizer.PorterStemmerFilterTokenizer(Tokenizer)
com.aliasi.tokenizer.PunctuationStopListTokenizer(Tokenizer) Use `RegExFilteredTokenizerFactory.RegExFilteredTokenizerFactory(TokenizerFactory,java.util.regex.Pattern)` instead.
com.aliasi.corpus.parsers.RegexLineTagParser(TagHandler, String, int, int, String, String) Being rewritten for new types in 4.0.
com.aliasi.util.ReversibleMTFListComparator(Comparator[]) This class is going away in LingPipe 4.0.
com.aliasi.tokenizer.SoundexFilterTokenizer(Tokenizer) Use `SoundexTokenizerFactory` instead.
com.aliasi.tokenizer.StopListFilterTokenizer(Tokenizer, Set) Use `StopTokenizerFactory` instead.
com.aliasi.corpus.parsers.SvmLightClassificationParser(ClassificationHandler, boolean, int) See the class doc.
com.aliasi.classify.XValidatingClassificationCorpus(Parser>, File[], int) See class documentation
com.aliasi.features.ZScoreFeatureExtractor(FeatureExtractor, Corpus>) Use constructor `ZScoreFeatureExtractor.ZScoreFeatureExtractor(FeatureExtractor,Corpus)` instead.

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