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Methods Method Description jebl.evolution.io.ImportHelper.getLastMetaComment() useImportHelper.getMetaComments()
insteadjebl.evolution.io.MEGAExporter.exportAlignment(Alignment) Files created by this export method won't be importable by MEGA (because they don't have titles). UseMEGAExporter.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 useState.getFullName()
orState.getCode()
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Constructors Constructor Description jebl.evolution.io.NexusImporter(Reader, boolean) Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)