Deprecated API


Contents
Deprecated Fields
jebl.evolution.sequences.AminoAcids.CANONICAL_STATES
           
jebl.evolution.sequences.Nucleotides.CANONICAL_STATES
           
jebl.evolution.sequences.Nucleotides.COMPLEMENTARY_STATES
           
jebl.evolution.sequences.GeneticCode.GENETIC_CODES
          use GeneticCode.getGeneticCodes() instead 
jebl.evolution.sequences.AminoAcids.STATES
           
jebl.evolution.sequences.Nucleotides.STATES
           
 

Deprecated Methods
jebl.evolution.io.MEGAExporter.exportAlignment(Alignment)
          Files created by this export method won't be importable by MEGA (because they don't have titles). Use MEGAExporter.exportAlignment(jebl.evolution.alignments.Alignment, String) instead. 
jebl.evolution.io.ImportHelper.getLastMetaComment()
          use ImportHelper.getMetaComments() instead 
jebl.evolution.sequences.State.getName()
          you probably want to use State.getFullName() or State.getCode(). 
jebl.evolution.sequences.GeneticCode.isStartCodon(CodonState)
           
jebl.evolution.sequences.GeneticCode.isStopCodon(CodonState)
           
 

Deprecated Constructors
jebl.evolution.io.NexusImporter(Reader, boolean)
          Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength) 
 



http://code.google.com/p/jebl2/