## Deprecated API

Deprecated Classes
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.

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.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.program.phred.PhredFormat.getDefaultFormat()
org.biojava.bio.seq.io.GenbankFormat.getDefaultFormat()
org.biojava.bio.seq.io.SequenceFormat.getDefaultFormat() new implementations should only write a single format.
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.bio.symbol.AlphabetManager.instance() all AlphabetManager methods have become static
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.program.phred.PhredFormat.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.SequenceFormat.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.symbol.PackedSymbolListFactory(boolean) the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.
org.biojava.bio.dp.ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory)
org.biojava.bio.seq.ProjectedFeatureHolder(FeatureHolder, FeatureFilter, FeatureHolder, int, boolean) Now just wraps up a LazyFilterFeatureHolder
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.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)