Package jebl.evolution.io
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Interface Summary Interface Description AlignmentExporter AlignmentImporter DistanceMatrixImporter ImmediateSequenceImporter A sequence importer sending the sequences back one by one, which makes it possible to import larger documents if handled wisely on the other side.ImmediateSequenceImporter.Callback SequenceExporter SequenceImporter Interface for importers that do sequencesTreeExporter TreeImporter Interface for importers that do trees -
Class Summary Class Description ByteBuilder Similar to a StringBuilder, but its internal buffer is a byte[] with one entry for each character, so it can only correctly append single-byte characters.FastaExporter Class for exporting a fasta file format.FastaImporter Class for importing Fasta sequential file format.ImportHelper A helper class for phylogenetic file format importersMEGAExporter * Export to MEGA.NewickExporter NewickImporter NexusExporter Export sequences and trees to Nexus format.NexusImporter Class for importing NEXUS file format.PHYLIPExporter Export alignment to Phylip format.PhylipSequentialImporter Class for importing PHYLIP sequential file formatTabDelimitedImporter -
Enum Summary Enum Description DistanceMatrixImporter.Triangle IllegalCharacterPolicy What to do when an imported document contains illegal charactersNexusImporter.NexusBlock Represents the block types used in the nexus format -
Exception Summary Exception Description ImportException ImportException.BadFormatException ImportException.DuplicateFieldException ImportException.DuplicateTaxaException ImportException.MissingFieldException ImportException.ShortSequenceException ImportException.TooFewTaxaException ImportException.UnknownTaxonException ImportException.UnparsableDataException NexusImporter.MissingBlockException Thrown when a block is missing that is required for importing a particular type of data from the nexus input.