Deprecated API


Contents
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.