Uses of Interface
org.biojavax.bio.seq.RichSequenceIterator
Packages that use RichSequenceIterator
Package
Description
Interactions between biojavax objects and a DB.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of RichSequenceIterator in org.biojavax.bio.db
Methods in org.biojavax.bio.db that return RichSequenceIteratorModifier and TypeMethodDescriptionAbstractRichSequenceDB.getRichSequenceIterator()RichSequenceDB.getRichSequenceIterator()Returns a RichSequenceIterator over all sequences in the database. -
Uses of RichSequenceIterator in org.biojavax.bio.seq
Classes in org.biojavax.bio.seq that implement RichSequenceIteratorModifier and TypeClassDescriptionstatic final classUsed to iterate over a single rich sequenceMethods in org.biojavax.bio.seq that return RichSequenceIteratorModifier and TypeMethodDescriptionstatic RichSequenceIteratorRichSequence.IOTools.readEMBL(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBL file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readEMBLDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLxml(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBLxml file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readEMBLxmlDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLxmlProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readEMBLxmlRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readFasta(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a fasta file building a custom type ofRichSequence.static RichSequenceIteratorRichSequence.IOTools.readFasta(BufferedReader br, SymbolTokenization sTok, Namespace ns) Read a fasta file.static RichSequenceIteratorRichSequence.IOTools.readFastaDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readFastaProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readFastaRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readFile(File file, RichSequenceBuilderFactory seqFactory, Namespace ns) Guess which format a file is then attempt to read it.static RichSequenceIteratorGuess which format a file is then attempt to read it.static RichSequenceIteratorRichSequence.IOTools.readGenbank(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a GenBank file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readGenbankDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readGenbankProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readGenbankRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readHashedFastaDNA(BufferedInputStream is, Namespace ns) Iterate over the sequences in an FASTA-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readINSDseq(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a INSDseq file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readINSDseqDNA(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of DNA sequences.static RichSequenceIteratorRichSequence.IOTools.readINSDseqProtein(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of Protein sequences.static RichSequenceIteratorRichSequence.IOTools.readINSDseqRNA(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readStream(BufferedInputStream stream, RichSequenceBuilderFactory seqFactory, Namespace ns) Guess which format a stream is then attempt to read it.static RichSequenceIteratorRichSequence.IOTools.readStream(BufferedInputStream stream, Namespace ns) Guess which format a stream is then attempt to read it.static RichSequenceIteratorRichSequence.IOTools.readUniProt(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readUniProt(BufferedReader br, Namespace ns) Iterate over the sequences in an UniProt-format stream of RNA sequences.static RichSequenceIteratorRichSequence.IOTools.readUniProtXML(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt XML file using a custom type of SymbolList.static RichSequenceIteratorRichSequence.IOTools.readUniProtXML(BufferedReader br, Namespace ns) Iterate over the sequences in an UniProt XML-format stream of RNA sequences. -
Uses of RichSequenceIterator in org.biojavax.bio.seq.io
Classes in org.biojavax.bio.seq.io that implement RichSequenceIteratorModifier and TypeClassDescriptionclassIterates over a Fasta file that is kept in memory for optimized access.classParses a stream into sequences.