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)