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