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Deprecated Classes | |
org.biojava.stats.svm.LinearKernel
Just use SparseVector.kernel instead... |
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org.biojava.bio.search.SequenceDBSearchHit
SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical. |
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org.biojava.bio.search.SequenceDBSearchResult
SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical. |
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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 |
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org.biojava.bio.program.gff.GFFRecord.NO_SCORE
Use GFFTools.NO_SCORE instead |
Deprecated Constructors | |
org.biojava.bio.symbol.PackedSymbolListFactory(boolean)
the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately. |
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org.biojava.bio.dp.ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory)
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org.biojava.bio.seq.ProjectedFeatureHolder(FeatureHolder, FeatureFilter, FeatureHolder, int, boolean)
Now just wraps up a LazyFilterFeatureHolder |
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org.biojava.bio.proteomics.Protease(String, boolean)
Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
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org.biojava.bio.proteomics.Protease(String, boolean, String)
Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
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org.biojava.bio.proteomics.Protease(SymbolList, boolean, SymbolList)
Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
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org.biojava.bio.dp.SimpleDotState(char, String, Annotation)
token is ignored since 1.2. Use the 2-arg constructor instead. |
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org.biojava.bio.dp.SimpleMarkovModel(int, Alphabet)
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