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/