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Packages that use RichSequenceFormat | |
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org.biojavax.bio.seq.io | Classes to support the I/O of RichSequence and Bioentry objects. |
Uses of RichSequenceFormat in org.biojavax.bio.seq.io |
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Classes in org.biojavax.bio.seq.io that implement RichSequenceFormat | |
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class |
EMBLFormat
Format reader for EMBL files. |
class |
EMBLxmlFormat
Format reader for EMBLxml files. |
class |
FastaFormat
Format object representing FASTA files. |
class |
GenbankFormat
Format reader for GenBank files. |
class |
INSDseqFormat
Format reader for INSDseq files. |
static class |
RichSequenceFormat.BasicFormat
Provides a basic format with simple things like line-widths precoded. |
static class |
RichSequenceFormat.HeaderlessFormat
Provides the basic implementation required for simple header/footer-less files such as Genbank. |
class |
UniProtFormat
Format reader for UniProt files. |
class |
UniProtXMLFormat
Format reader for UniProtXML files. |
Constructors in org.biojavax.bio.seq.io with parameters of type RichSequenceFormat | |
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RichStreamReader(BufferedReader reader,
RichSequenceFormat format,
SymbolTokenization symParser,
RichSequenceBuilderFactory sf,
Namespace ns)
Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace. |
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RichStreamReader(InputStream is,
RichSequenceFormat format,
SymbolTokenization symParser,
RichSequenceBuilderFactory sf,
Namespace ns)
Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace. |
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RichStreamWriter(OutputStream os,
RichSequenceFormat format)
Generate a new RichStreamWriter to the stream os and using format. |
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