| Class | Description |
|---|---|
| BufferedReaderBytesRead |
Need to keep track of actual bytes read and take advantage of buffered reader
performance.
|
| CasePreservingProteinSequenceCreator |
A sequence creator which preserves the case of its input string in
the user collection of the returned ProteinSequence.
|
| DNASequenceCreator |
A helper class that allows different ways to read a string and create a DNA sequence.
|
| FastaGeneWriter |
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
|
| FastaReader<S extends Sequence<?>,C extends Compound> |
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the
primary class used to read Fasta files
|
| FastaReaderHelper | |
| FastaSequenceParser |
Used to parse a stream of a fasta file to get the sequence
|
| FastaWriter<S extends Sequence<?>,C extends Compound> |
The FastaWriter writes a collection of sequences to an outputStream.
|
| FastaWriterHelper |
The class that should be used to write out fasta file of a sequence collection
|
| FileProxyDNASequenceCreator |
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream
the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
|
| FileProxyProteinSequenceCreator |
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream
the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
|
| GenbankReader<S extends AbstractSequence<C>,C extends Compound> |
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the
primary class used to read Genbank files
|
| GenbankReaderHelper | |
| GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> | |
| GenbankWriter<S extends Sequence<?>,C extends Compound> | |
| GenbankWriterHelper |
The class that should be used to write out genbank file of a sequence
collection
|
| GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> |
We store the original header if the sequence is parsed from a fasta file and will use that exact
sequence if we write out the sequences to a fasta file.
|
| GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> |
The default fasta header parser where some headers are well defined based on the source
database which allows us to set the source of the protein sequence and the identifier
that can be used in future implementations to load features from external sources
If the user has a custom header with local data then they can create their own implementation
of a FastaHeaderParserInterface
|
| GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound> | |
| GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound> | |
| GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound> | |
| IUPACParser |
Available translations
1 - UNIVERSAL
2 - VERTEBRATE_MITOCHONDRIAL
3 - YEAST_MITOCHONDRIAL
4 - MOLD_MITOCHONDRIAL
5 - INVERTEBRATE_MITOCHONDRIAL
6 - CILIATE_NUCLEAR
9 - ECHINODERM_MITOCHONDRIAL
10 - EUPLOTID_NUCLEAR
11 - BACTERIAL
12 - ALTERNATIVE_YEAST_NUCLEAR
13 - ASCIDIAN_MITOCHONDRIAL
14 - FLATWORM_MITOCHONDRIAL
15 - BLEPHARISMA_MACRONUCLEAR
16 - 2CHLOROPHYCEAN_MITOCHONDRIAL
21 - TREMATODE_MITOCHONDRIAL
23 - SCENEDESMUS_MITOCHONDRIAL
Taken from NCBI with slight modification and put into the classpath resource.
|
| IUPACParser.IUPACTable |
Holds the concept of a codon table from the IUPAC format
|
| PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> |
The plain fasta header takes everything in the header as a single entity.
|
| ProteinSequenceCreator |
Used to create a ProteinSequence from a String to allow for details
about the location of the sequence etc.
|
| RNASequenceCreator |
Used to create a RNA sequence
|
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