Deprecated API

Contents

• Fields
• Methods
• Constructors

• Deprecated Fields

  Field

  Description

  jebl.evolution.sequences.AminoAcids.CANONICAL_STATES

  jebl.evolution.sequences.AminoAcids.STATES

  jebl.evolution.sequences.GeneticCode.GENETIC_CODES

  use GeneticCode.getGeneticCodes() instead

  jebl.evolution.sequences.Nucleotides.CANONICAL_STATES

  jebl.evolution.sequences.Nucleotides.COMPLEMENTARY_STATES

  jebl.evolution.sequences.Nucleotides.STATES

• Deprecated Methods

  Method

  Description

  jebl.evolution.io.ImportHelper.getLastMetaComment()

  use ImportHelper.getMetaComments() instead

  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.sequences.GeneticCode.isStartCodon(CodonState)

  jebl.evolution.sequences.GeneticCode.isStopCodon(CodonState)

  jebl.evolution.sequences.State.getName()

  you probably want to use State.getFullName() or State.getCode().

• Deprecated Constructors

  Constructor

  Description

  jebl.evolution.io.NexusImporter(Reader, boolean)

  Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)