Deprecated API
Contents
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Deprecated InterfacesInterfaceDescriptionUse org.biojavax.bio.seq.io framework insteaduse org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilderreplaced by classes in
org.biojavax.bio.taxa
replaced by classes inorg.biojavax.bio.taxa
replaced by classes inorg.biojavax.bio.taxa
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Deprecated ClassesClassDescriptionuse
new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)
insteadusenew ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)
insteadDistribution impls should be providing custom trainers.This doesn't handle loads of stuff. Use SequencePoster.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.Use hibernate and org.biojavax.bio.db.*Use hibernate and org.biojavax.bio.db.*Use hibernate and org.biojavax.bio.db.*Use hibernate and org.biojavax.bio.db.*Use hibernate and org.biojavax.bio.db.*Use hibernate and org.biojavax.bio.db.*Use hibernate and org.biojavax.bio.db.*Use hibernate and org.biojavax.bio.db.*Use org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io.EMBLFormat insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io.FastaFormatUse org.biojavax.bio.seq.io.FastaFormatUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io.GenbankFormatUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io.INSDseqFormatUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.taxa framework insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteaduse org.biojavax.bio.seq.RichSequence.IOToolsUse org.biojavax.bio.seq.io framework insteadUse org.biojavax.bio.seq.io framework insteadreplaced by classes inorg.biojavax.bio.taxa
replaced by classes inorg.biojavax.bio.taxa
replaced by classes inorg.biojavax.bio.taxa
replaced by classes inorg.biojavax.bio.taxa
replaced by classes inorg.biojavax.bio.taxa
replaced by classes inorg.biojavax.bio.taxa
Just use SparseVector.kernel instead...preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package.
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Deprecated Exception Classes
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Deprecated FieldsFieldDescriptionUse GFFTools.NO_FRAME insteadUse GFFTools.NO_SCORE instead
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Deprecated MethodsMethodDescriptionuse generateSequence() or generateSymbolList() instead.use
advance().length
use: readGff(File)use: readGff(File,GFFRecordFilter)use writeSequence(Sequence seq, PrintStream os)usesetQueryID
instead.usesetDatabaseID
instead.Please use new 1-arg createFeature instead.use writeSequence(Sequence seq, PrintStream os)use writeSequence(Sequence seq, PrintStream os)use writeSequence(Sequence seq, PrintStream os)as this essentially duplicates the operation available in the methodidentifyBuilderFactory
.because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.new implementations should only write a single format.use writeSequence(Sequence seq, PrintStream os)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.Use the two-arg version of this method instead.use the new version, without the token argumentuse the three-arg version of this method instead.all AlphabetManager methods have become staticuse symbolForLifeScienceID() insteaduse hasListeners(ChangeType) if at all possibleuse addChangeListener(cl, ChangeType.UNKNOWN)use removeChangeListener(cl, ChangeType.UNKNOWN)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.
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Deprecated ConstructorsConstructorDescriptionUse BioError(message, ex) instead.use new BioException(message, ex) insteaduse new BioRuntimeException(message, ex) insteadtoken is ignored since 1.2. Use the 2-arg constructor instead.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.use new RegistryException(message, cause)use new ChangeVetoException(reason, ex);use new ParserException(detail, t)