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| Deprecated Methods | |
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| 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. |
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| jebl.evolution.io.ImportHelper.getLastMetaComment()
use ImportHelper.getMetaComments() instead |
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| jebl.evolution.sequences.State.getName()
you probably want to use State.getFullName() or State.getCode(). |
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| jebl.evolution.sequences.GeneticCode.isStartCodon(CodonState)
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| jebl.evolution.sequences.GeneticCode.isStopCodon(CodonState)
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| Deprecated Constructors | |
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| jebl.evolution.io.NexusImporter(Reader, boolean)
Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength) |
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