| 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 sequences
|
| TreeExporter | |
| TreeImporter |
Interface for importers that do trees
|
| 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 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 | Description |
|---|---|
| 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 | 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.
|
http://code.google.com/p/jebl2/