Deprecated API

Contents

• Interfaces
• Classes
• Exceptions
• Fields
• Methods
• Constructors

Interfaces

Interface	Description
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

Classes

Class	Description
org.biojava.bio.Annotatable.AnnotationForwarder	use new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY) instead
org.biojava.bio.dist.Distribution.NullModelForwarder	use new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY) instead
org.biojava.bio.dist.SimpleDistributionTrainer	Distribution impls should be providing custom trainers.
org.biojava.bio.gui.sequence.SequencePoster	This doesn't handle loads of stuff. Use SequencePoster.
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.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.seq.db.biosql.HypersonicDBHelper	Use hibernate and org.biojavax.bio.db.*
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.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.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.io.OrganismParser	Use org.biojavax.bio.taxa framework instead
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.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.taxa.AbstractTaxon	replaced by classes in org.biojavax.bio.taxa
org.biojava.bio.taxa.EbiFormat	replaced by classes in org.biojavax.bio.taxa
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.taxa.WeakTaxon	replaced by classes in org.biojavax.bio.taxa
org.biojava.bio.taxa.WeakTaxonFactory	replaced by classes in org.biojavax.bio.taxa
org.biojava.stats.svm.LinearKernel	Just use SparseVector.kernel instead...
org.biojava.utils.ProcessTools	preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package.

Exceptions

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

Fields

Field	Description
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

Methods

Method	Description
org.biojava.bio.dist.DistributionTools.generateOrderNSequence(String, OrderNDistribution, int)	use generateSequence() or generateSymbolList() instead.
org.biojava.bio.dp.MarkovModel.heads()	use advance().length
org.biojava.bio.program.gff.GFFTools.readGFF(String)	use: readGff(File)
org.biojava.bio.program.phred.PhredFormat.getDefaultFormat()
org.biojava.bio.program.phred.PhredFormat.writeSequence(Sequence, String, PrintStream)	use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.program.sax.FastaSearchSAXParser.setQuerySeq(String)	use setQueryID instead.
org.biojava.bio.program.sax.FastaSearchSAXParser.setSubjectDB(String)	use setDatabaseID instead.
org.biojava.bio.seq.impl.SimpleSequence.createFeature(FeatureHolder, Feature.Template)	Please use new 1-arg createFeature instead.
org.biojava.bio.seq.io.EmblLikeFormat.getDefaultFormat()
org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(Sequence, String, PrintStream)	use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.seq.io.FastaFormat.getDefaultFormat()
org.biojava.bio.seq.io.FastaFormat.writeSequence(Sequence, String, PrintStream)	use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.seq.io.GAMEFormat.getDefaultFormat()
org.biojava.bio.seq.io.GenbankFormat.getDefaultFormat()
org.biojava.bio.seq.io.GenbankFormat.writeSequence(Sequence, String, PrintStream)	use writeSequence(Sequence seq, PrintStream os)
org.biojava.bio.seq.io.SeqIOTools.formatToFactory(SequenceFormat, Alphabet)	as this essentially duplicates the operation available in the method identifyBuilderFactory.
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.bio.seq.io.SequenceFormat.getDefaultFormat()	new implementations should only write a single format.
org.biojava.bio.seq.io.SequenceFormat.writeSequence(Sequence, String, PrintStream)	use writeSequence(Sequence seq, PrintStream os)
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.symbol.AlphabetManager.createSymbol(char, String, Annotation)	Use the two-arg version of this method instead.
org.biojava.bio.symbol.AlphabetManager.instance()	all AlphabetManager methods have become static
org.biojava.bio.symbol.AlphabetManager.symbolForName(String)	use symbolForLifeScienceID() instead
org.biojava.utils.Changeable.addChangeListener(ChangeListener)	use addChangeListener(cl, ChangeType.UNKNOWN)
org.biojava.utils.Changeable.removeChangeListener(ChangeListener)	use removeChangeListener(cl, ChangeType.UNKNOWN)
org.biojavax.bio.phylo.io.nexus.TreesBlock.addTree(String, WeightedGraph<String, DefaultWeightedEdge>)
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.biojavax.SimpleRichAnnotation.containsProperty(Object)
org.biojavax.SimpleRichAnnotation.getProperties(Object)
org.biojavax.SimpleRichAnnotation.getProperty(Object)
org.biojavax.SimpleRichAnnotation.removeProperty(Object)
org.biojavax.SimpleRichAnnotation.setProperty(Object, Object)

Constructors

Constructor	Description
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.bio.dp.ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory)
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.proteomics.Protease(SymbolList, boolean, SymbolList)	Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
org.biojava.bio.symbol.PackedSymbolListFactory(boolean)	the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.
org.biojava.directory.RegistryException(Throwable, String)	use new RegistryException(message, cause)
org.biojava.utils.ChangeVetoException(Throwable, String)	use new ChangeVetoException(reason, ex);
org.biojava.utils.ParserException(Throwable, String)	use new ParserException(detail, t)