Uses of Interface
org.biojava.bio.seq.SequenceIterator
Packages that use SequenceIterator
Package
Description
Classes to generate and describe sequence alignments.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
Classes and interfaces for processing and producing flat-file representations
of sequences.
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.
-
Uses of SequenceIterator in org.biojava.bio.alignment
Methods in org.biojava.bio.alignment with parameters of type SequenceIteratorModifier and TypeMethodDescriptionAlignmentAlgorithm.alignAll
(SequenceIterator source, SequenceDB subjectDB) -
Uses of SequenceIterator in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db that return SequenceIteratorModifier and TypeMethodDescriptionAbstractSequenceDB.sequenceIterator()
AnnotatedSequenceDB.sequenceIterator()
DummySequenceDB.sequenceIterator()
HashSequenceDB.sequenceIterator()
IndexedSequenceDB.sequenceIterator()
SequenceDB.sequenceIterator()
Returns a SequenceIterator over all sequences in the database. -
Uses of SequenceIterator in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql that return SequenceIterator -
Uses of SequenceIterator in org.biojava.bio.seq.io
Classes in org.biojava.bio.seq.io that implement SequenceIteratorMethods in org.biojava.bio.seq.io that return SequenceIteratorModifier and TypeMethodDescriptionstatic SequenceIterator
SeqIOTools.readEmbl
(BufferedReader br) Deprecated.Iterate over the sequences in an EMBL-format stream.static SequenceIterator
SeqIOTools.readEmblNucleotide
(BufferedReader br) Deprecated.Iterate over the sequences in an EMBL-format stream.static SequenceIterator
SeqIOTools.readEmblRNA
(BufferedReader br) Deprecated.Iterate over the sequences in an EMBL-format stream, but for RNA.static SequenceIterator
SeqIOTools.readFasta
(BufferedReader br, SymbolTokenization sTok) Deprecated.Read a fasta file.static SequenceIterator
SeqIOTools.readFasta
(BufferedReader br, SymbolTokenization sTok, SequenceBuilderFactory seqFactory) Deprecated.Read a fasta file using a custom type of SymbolList.static SequenceIterator
SeqIOTools.readFastaDNA
(BufferedReader br) Deprecated.Iterate over the sequences in an FASTA-format stream of DNA sequences.static SequenceIterator
SeqIOTools.readFastaProtein
(BufferedReader br) Deprecated.Iterate over the sequences in an FASTA-format stream of Protein sequences.static SequenceIterator
SeqIOTools.readFastaRNA
(BufferedReader br) Deprecated.Iterate over the sequences in an FASTA-format stream of RNA sequences.static SequenceIterator
SeqIOTools.readGenbank
(BufferedReader br) Deprecated.Iterate over the sequences in an Genbank-format stream.static SequenceIterator
SeqIOTools.readGenbankXml
(BufferedReader br) Deprecated.Iterate over the sequences in an GenbankXML-format stream.static SequenceIterator
SeqIOTools.readGenpept
(BufferedReader br) Deprecated.Iterate over the sequences in an Genpept-format stream.static SequenceIterator
SeqIOTools.readSwissprot
(BufferedReader br) Deprecated.Iterate over the sequences in an Swissprot-format stream.Methods in org.biojava.bio.seq.io with parameters of type SequenceIteratorModifier and TypeMethodDescriptionstatic void
SeqIOTools.writeEmbl
(OutputStream os, SequenceIterator in) Deprecated.Writes a stream of Sequences to an OutputStream in EMBL format.static void
SeqIOTools.writeFasta
(OutputStream os, SequenceIterator in) Deprecated.Writes sequences from a SequenceIterator to an OutputStream in Fasta Format.static void
SeqIOTools.writeGenbank
(OutputStream os, SequenceIterator in) Deprecated.Writes a stream of Sequences to an OutputStream in Genbank format.static void
SeqIOTools.writeGenpept
(OutputStream os, SequenceIterator in) Deprecated.Writes a stream of Sequences to an OutputStream in Genpept format.void
StreamWriter.writeStream
(SequenceIterator ss) Write each of the sequences in ss to the stream in the given format.static void
SeqIOTools.writeSwissprot
(OutputStream os, SequenceIterator in) Deprecated.Writes a stream of Sequences to an OutputStream in SwissProt format. -
Uses of SequenceIterator in org.biojavax.bio.db
Methods in org.biojavax.bio.db that return SequenceIteratorModifier and TypeMethodDescriptionAbstractRichSequenceDB.sequenceIterator()
RichSequenceDB.sequenceIterator()
Returns a SequenceIterator over all sequences in the database. -
Uses of SequenceIterator in org.biojavax.bio.seq
Subinterfaces of SequenceIterator in org.biojavax.bio.seqModifier and TypeInterfaceDescriptioninterface
Essentially the same as SequenceIterator.Classes in org.biojavax.bio.seq that implement SequenceIteratorModifier and TypeClassDescriptionstatic final class
Used to iterate over a single rich sequenceMethods in org.biojavax.bio.seq with parameters of type SequenceIteratorModifier and TypeMethodDescriptionstatic void
RichSequence.IOTools.writeEMBL
(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIterator
to anOutputStream
in EMBL Format.static void
RichSequence.IOTools.writeEMBLxml
(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIterator
to anOutputStream
in EMBLxml Format.static void
RichSequence.IOTools.writeFasta
(OutputStream os, SequenceIterator in, Namespace ns) WritesSequence
s from aSequenceIterator
to anOutputStream
in Fasta Format.static void
RichSequence.IOTools.writeFasta
(OutputStream os, SequenceIterator in, Namespace ns, FastaHeader header) WritesSequence
s from aSequenceIterator
to anOutputStream
in Fasta Format.static void
RichSequence.IOTools.writeGenbank
(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIterator
to anOutputStream
in GenBank Format.static void
RichSequence.IOTools.writeINSDseq
(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIterator
to anOutputStream
in INSDseq Format.static void
RichSequence.IOTools.writeUniProt
(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIterator
to anOutputStream
in UniProt Format.static void
RichSequence.IOTools.writeUniProtXML
(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from aSequenceIterator
to anOutputStream
in UniProt XML Format. -
Uses of SequenceIterator in org.biojavax.bio.seq.io
Classes in org.biojavax.bio.seq.io that implement SequenceIteratorModifier and TypeClassDescriptionclass
Iterates over a Fasta file that is kept in memory for optimized access.class
Parses a stream into sequences.Methods in org.biojavax.bio.seq.io with parameters of type SequenceIteratorModifier and TypeMethodDescriptionvoid
RichStreamWriter.writeStream
(SequenceIterator ss, Namespace ns) Write each of the sequences in ss to the stream in the given format.