Package jebl.evolution.io

Interface Summary

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 sequences
TreeExporter
TreeImporter	Interface for importers that do trees

Class Summary

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 importers
MEGAExporter	* 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 format
TabDelimitedImporter

Enum Summary

DistanceMatrixImporter.Triangle
IllegalCharacterPolicy	What to do when an imported document contains illegal characters
NexusImporter.NexusBlock	Represents the block types used in the nexus format

Exception Summary

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.