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## Deprecated API

Contents

- Deprecated Interfaces
- Deprecated Classes
- Deprecated Exceptions
- Deprecated Fields
- Deprecated Methods
- Deprecated Constructors

Deprecated Interfaces
org.biojava.bio.seq.io.SeqFileFormer Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.SequenceFactory use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilder
org.biojava.bio.taxa.Taxon replaced by classes in `org.biojavax.bio.taxa`
org.biojava.bio.taxa.TaxonFactory replaced by classes in `org.biojavax.bio.taxa`
org.biojava.bio.taxa.TaxonParser replaced by classes in `org.biojavax.bio.taxa`

Deprecated Classes
org.biojava.bio.taxa.AbstractTaxon replaced by classes in `org.biojavax.bio.taxa`
org.biojava.bio.Annotatable.AnnotationForwarder use `new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)` instead
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB Use hibernate and org.biojavax.bio.db.*
org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider Use hibernate and org.biojavax.bio.db.*
org.biojava.bio.seq.db.biosql.DBHelper Use hibernate and org.biojavax.bio.db.*
org.biojava.bio.dist.Distribution.NullModelForwarder use `new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)` instead
org.biojava.bio.taxa.EbiFormat replaced by classes in `org.biojavax.bio.taxa`
org.biojava.bio.seq.io.EmblFileFormer Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.EmblLikeFormat Use org.biojavax.bio.seq.io.EMBLFormat instead
org.biojava.bio.seq.io.EmblLikeLocationParser Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.EmblProcessor Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.FastaDescriptionLineParser Use org.biojavax.bio.seq.io.FastaFormat
org.biojava.bio.seq.io.FastaFormat Use org.biojavax.bio.seq.io.FastaFormat
org.biojava.bio.seq.io.FeatureTableParser Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.GenbankFileFormer Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.GenbankFormat Use org.biojavax.bio.seq.io.GenbankFormat
org.biojava.bio.seq.io.GenbankProcessor Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.GenbankXmlFormat Use org.biojavax.bio.seq.io.INSDseqFormat
org.biojava.bio.seq.io.GenEmblFeatureComparator Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.GenEmblPropertyComparator Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.GenpeptFormat Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.db.biosql.HypersonicDBHelper Use hibernate and org.biojavax.bio.db.*
org.biojava.stats.svm.LinearKernel Just use SparseVector.kernel instead...
org.biojava.bio.seq.db.biosql.MySQLDBHelper Use hibernate and org.biojavax.bio.db.*
org.biojava.bio.seq.db.biosql.OracleDBHelper Use hibernate and org.biojavax.bio.db.*
org.biojava.bio.seq.io.OrganismParser Use org.biojavax.bio.taxa framework instead
org.biojava.utils.ProcessTools preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package.
org.biojava.bio.seq.io.ProteinRefSeqFileFormer Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.ProteinRefSeqProcessor Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.ReferenceAnnotation Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.SeqIOEventEmitter Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.SeqIOTools use org.biojavax.bio.seq.RichSequence.IOTools
org.biojava.bio.search.SequenceDBSearchHit SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
org.biojava.bio.search.SequenceDBSearchResult SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
org.biojava.bio.search.SequenceDBSearchSubHit SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
org.biojava.bio.gui.sequence.SequencePoster This doesn't handle loads of stuff. Use SequencePoster.
org.biojava.bio.dist.SimpleDistributionTrainer Distribution impls should be providing custom trainers.
org.biojava.bio.taxa.SimpleTaxon replaced by classes in `org.biojavax.bio.taxa`
org.biojava.bio.taxa.SimpleTaxonFactory replaced by classes in `org.biojavax.bio.taxa`
org.biojava.bio.seq.io.SwissprotFileFormer Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.io.SwissprotProcessor Use org.biojavax.bio.seq.io framework instead
org.biojava.bio.seq.db.biosql.TaxonSQL Use hibernate and org.biojavax.bio.db.*
org.biojava.bio.seq.db.biosql.UnknownDBHelper Use hibernate and org.biojavax.bio.db.*
org.biojava.bio.taxa.WeakTaxon replaced by classes in `org.biojavax.bio.taxa`
org.biojava.bio.taxa.WeakTaxonFactory replaced by classes in `org.biojavax.bio.taxa`

Deprecated Exceptions
org.biojava.bio.taxa.CircularReferenceException replaced by classes in `org.biojavax.bio.taxa`

Deprecated Fields
org.biojava.bio.program.gff.GFFRecord.NO_FRAME Use GFFTools.NO_FRAME instead
org.biojava.bio.program.gff.GFFRecord.NO_SCORE Use GFFTools.NO_SCORE instead

Deprecated Methods
org.biojava.utils.Changeable.addChangeListener(ChangeListener) use addChangeListener(cl, ChangeType.UNKNOWN)
org.biojavax.SimpleRichAnnotation.containsProperty(Object)
org.biojava.bio.seq.impl.SimpleSequence.createFeature(FeatureHolder, Feature.Template) Please use new 1-arg createFeature instead.
org.biojava.bio.symbol.AlphabetManager.createSymbol(char, Annotation, List, Alphabet) use the new version, without the token argument
org.biojava.bio.symbol.AlphabetManager.createSymbol(char, Annotation, Set, Alphabet) use the three-arg version of this method instead.
org.biojava.bio.symbol.AlphabetManager.createSymbol(char, String, Annotation) Use the two-arg version of this method instead.
org.biojava.bio.seq.io.SeqIOTools.formatToFactory(SequenceFormat, Alphabet) as this essentially duplicates the operation available in the method `identifyBuilderFactory`.
org.biojava.bio.dist.DistributionTools.generateOrderNSequence(String, OrderNDistribution, int) use generateSequence() or generateSymbolList() instead.
org.biojava.bio.program.phred.PhredFormat.getDefaultFormat()
org.biojava.bio.seq.io.SequenceFormat.getDefaultFormat() new implementations should only write a single format.
org.biojava.bio.seq.io.GenbankFormat.getDefaultFormat()
org.biojava.bio.seq.io.GAMEFormat.getDefaultFormat()
org.biojava.bio.seq.io.FastaFormat.getDefaultFormat()
org.biojava.bio.seq.io.EmblLikeFormat.getDefaultFormat()
org.biojava.bio.structure.ChainImpl.getGroup(int) use getAtomGroup or getSeqResGroup instead
org.biojava.bio.structure.Chain.getGroup(int) use getAtomGroup or getSeqResGroup instead
org.biojava.bio.structure.ChainImpl.getGroups() use getAtomGroups instead
org.biojava.bio.structure.Chain.getGroups() use getAtomGroups or getSeqResGroups instead
org.biojava.bio.structure.ChainImpl.getGroups(String) use getAtomGroups instead
org.biojava.bio.structure.Chain.getGroups(String) use getAtomGroups or getSeqResGroups instead
org.biojava.bio.structure.Structure.getHeader() use getPDBHeader instead
org.biojava.bio.structure.ChainImpl.getLength() use getAtomLength instead
org.biojava.bio.structure.Chain.getLength() please use getAtomLength or getLengthSeqRes instead
org.biojava.bio.structure.Chain.getLengthAminos() use getAtomGroups("amino").size() instead.
org.biojavax.SimpleRichAnnotation.getProperties(Object)
org.biojavax.SimpleRichAnnotation.getProperty(Object)
org.biojava.bio.structure.ChainImpl.getSequence() use getAtomSequence instead
org.biojava.bio.structure.Chain.getSequence() use getAtomSequence instead
org.biojava.bio.seq.io.SeqIOTools.guessFileType(File) because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.
org.biojava.utils.AbstractChangeable.hasListeners() use hasListeners(ChangeType) if at all possible
org.biojava.bio.dp.MarkovModel.heads() use `advance().length`
org.biojava.bio.symbol.AlphabetManager.instance() all AlphabetManager methods have become static
org.biojava.bio.program.gff.GFFTools.readGFF(String) use: readGff(File)
org.biojava.bio.program.gff.GFFTools.readGFF(String, GFFRecordFilter) use: readGff(File,GFFRecordFilter)
org.biojava.utils.Changeable.removeChangeListener(ChangeListener) use removeChangeListener(cl, ChangeType.UNKNOWN)
org.biojavax.SimpleRichAnnotation.removeProperty(Object)
org.biojavax.SimpleRichAnnotation.setProperty(Object, Object)
org.biojava.bio.program.sax.FastaSearchSAXParser.setQuerySeq(String) use `setQueryID` instead.
org.biojava.bio.program.sax.FastaSearchSAXParser.setSubjectDB(String) use `setDatabaseID` instead.
org.biojavax.bio.seq.io.RichSeqIOListener.setURI(String) There is no clear mapping between URI and BioSQL. This method is no longer used or supported in biojavax. Don't use it. Calling it may result in exceptions. Use instead setName(String name), setAccession(String accession), setVersion(int version) etc as appropriate.
org.biojava.bio.symbol.AlphabetManager.symbolForName(String) use symbolForLifeScienceID() instead
org.biojava.bio.seq.RNATools.transcribe(SymbolList) The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
org.biojava.bio.program.phred.PhredFormat.writeSequence(Sequence, String, PrintStream) use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.seq.io.SequenceFormat.writeSequence(Sequence, String, PrintStream) use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.seq.io.GenbankFormat.writeSequence(Sequence, String, PrintStream) use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.seq.io.FastaFormat.writeSequence(Sequence, String, PrintStream) use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(Sequence, String, PrintStream) use writeSequence(Sequence seq, PrintStream os)

Deprecated Constructors
org.biojava.bio.BioError(Throwable, String) Use BioError(message, ex) instead.
org.biojava.bio.BioException(Throwable, String) use new BioException(message, ex) instead
org.biojava.bio.BioRuntimeException(Throwable, String) use new BioRuntimeException(message, ex) instead
org.biojava.utils.ChangeVetoException(Throwable, String) use new ChangeVetoException(reason, ex);
org.biojava.bio.symbol.PackedSymbolListFactory(boolean) the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.
org.biojava.utils.ParserException(Throwable, String) use new ParserException(detail, t)
org.biojava.bio.structure.io.PDBParseException(Throwable, String) use new BioException(message, ex) instead
org.biojava.bio.dp.ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory)
org.biojava.bio.proteomics.Protease(String, boolean) Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
org.biojava.bio.proteomics.Protease(String, boolean, String) Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
org.biojava.bio.proteomics.Protease(SymbolList, boolean, SymbolList) Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
org.biojava.directory.RegistryException(Throwable, String) use new RegistryException(message, cause)
org.biojava.bio.dp.SimpleDotState(char, String, Annotation) token is ignored since 1.2. Use the 2-arg constructor instead.
org.biojava.bio.dp.SimpleMarkovModel(int, Alphabet)
org.biojava.bio.structure.StructureException(Throwable, String) use new StructureException(message, ex) instead

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