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 class
Used to iterate over a single rich sequenceMethods in org.biojavax.bio.seq that return RichSequenceIteratorModifier and TypeMethodDescriptionstatic RichSequenceIterator
RichSequence.IOTools.readEMBL
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBL file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readEMBLDNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of DNA sequences.static RichSequenceIterator
RichSequence.IOTools.readEMBLProtein
(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of Protein sequences.static RichSequenceIterator
RichSequence.IOTools.readEMBLRNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBL-format stream of RNA sequences.static RichSequenceIterator
RichSequence.IOTools.readEMBLxml
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a EMBLxml file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readEMBLxmlDNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of DNA sequences.static RichSequenceIterator
RichSequence.IOTools.readEMBLxmlProtein
(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of Protein sequences.static RichSequenceIterator
RichSequence.IOTools.readEMBLxmlRNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an EMBLxml-format stream of RNA sequences.static RichSequenceIterator
RichSequence.IOTools.readFasta
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a fasta file building a custom type ofRichSequence
.static RichSequenceIterator
RichSequence.IOTools.readFasta
(BufferedReader br, SymbolTokenization sTok, Namespace ns) Read a fasta file.static RichSequenceIterator
RichSequence.IOTools.readFastaDNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of DNA sequences.static RichSequenceIterator
RichSequence.IOTools.readFastaProtein
(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of Protein sequences.static RichSequenceIterator
RichSequence.IOTools.readFastaRNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an FASTA-format stream of RNA sequences.static RichSequenceIterator
RichSequence.IOTools.readFile
(File file, RichSequenceBuilderFactory seqFactory, Namespace ns) Guess which format a file is then attempt to read it.static RichSequenceIterator
Guess which format a file is then attempt to read it.static RichSequenceIterator
RichSequence.IOTools.readGenbank
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a GenBank file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readGenbankDNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of DNA sequences.static RichSequenceIterator
RichSequence.IOTools.readGenbankProtein
(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of Protein sequences.static RichSequenceIterator
RichSequence.IOTools.readGenbankRNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an GenBank-format stream of RNA sequences.static RichSequenceIterator
RichSequence.IOTools.readHashedFastaDNA
(BufferedInputStream is, Namespace ns) Iterate over the sequences in an FASTA-format stream of DNA sequences.static RichSequenceIterator
RichSequence.IOTools.readINSDseq
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a INSDseq file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readINSDseqDNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of DNA sequences.static RichSequenceIterator
RichSequence.IOTools.readINSDseqProtein
(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of Protein sequences.static RichSequenceIterator
RichSequence.IOTools.readINSDseqRNA
(BufferedReader br, Namespace ns) Iterate over the sequences in an INSDseq-format stream of RNA sequences.static RichSequenceIterator
RichSequence.IOTools.readStream
(BufferedInputStream stream, RichSequenceBuilderFactory seqFactory, Namespace ns) Guess which format a stream is then attempt to read it.static RichSequenceIterator
RichSequence.IOTools.readStream
(BufferedInputStream stream, Namespace ns) Guess which format a stream is then attempt to read it.static RichSequenceIterator
RichSequence.IOTools.readUniProt
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.IOTools.readUniProt
(BufferedReader br, Namespace ns) Iterate over the sequences in an UniProt-format stream of RNA sequences.static RichSequenceIterator
RichSequence.IOTools.readUniProtXML
(BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns) Read a UniProt XML file using a custom type of SymbolList.static RichSequenceIterator
RichSequence.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 TypeClassDescriptionclass
Iterates over a Fasta file that is kept in memory for optimized access.class
Parses a stream into sequences.