# Package jebl.evolution.io

package jebl.evolution.io

Class
Description
AlignmentExporter
AlignmentImporter
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.
DistanceMatrixImporter
DistanceMatrixImporter.Triangle
FastaExporter
Class for exporting a fasta file format.
FastaImporter
Class for importing Fasta sequential file format.
IllegalCharacterPolicy
What to do when an imported document contains illegal characters
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
ImportException
ImportException.BadFormatException
ImportException.DuplicateFieldException
ImportException.DuplicateTaxaException
ImportException.MissingFieldException
ImportException.ShortSequenceException
ImportException.TooFewTaxaException
ImportException.UnknownTaxonException
ImportException.UnparsableDataException
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.
NexusImporter.MissingBlockException
Thrown when a block is missing that is required for importing a particular type of data from the nexus input.
NexusImporter.NexusBlock
Represents the block types used in the nexus format
PHYLIPExporter
Export alignment to Phylip format.
PhylipSequentialImporter
Class for importing PHYLIP sequential file format
SequenceExporter
SequenceImporter
Interface for importers that do sequences
TabDelimitedImporter
TreeExporter
TreeImporter
Interface for importers that do trees