Deprecated API

Deprecated Classes

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.stats.svm.LinearKernel
Just use SparseVector.kernel instead...

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.

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.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.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.biojava.bio.program.sax.FastaSearchSAXParser.setQuerySeq(String)
use setQueryID instead.

org.biojava.bio.program.sax.FastaSearchSAXParser.setSubjectDB(String)
use setDatabaseID instead.

org.biojava.bio.symbol.AlphabetManager.symbolForName(String)
use symbolForLifeScienceID() instead

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.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)