Uses of Interface
org.biojava.bio.seq.SequenceIterator

Packages that use SequenceIterator

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	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 SequenceIterator

Modifier and Type	Method and Description
List<AlignmentPair>	AlignmentAlgorithm.alignAll(SequenceIterator source, SequenceDB subjectDB)

Uses of SequenceIterator in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db that return SequenceIterator

Modifier and Type	Method and Description
SequenceIterator	SequenceDB.sequenceIterator() Returns a SequenceIterator over all sequences in the database.
SequenceIterator	IndexedSequenceDB.sequenceIterator()
SequenceIterator	HashSequenceDB.sequenceIterator()
SequenceIterator	DummySequenceDB.sequenceIterator()
SequenceIterator	AnnotatedSequenceDB.sequenceIterator()
SequenceIterator	AbstractSequenceDB.sequenceIterator()

Uses of SequenceIterator in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that return SequenceIterator

Modifier and Type	Method and Description
SequenceIterator	BioSQLSequenceDB.sequenceIterator() Deprecated.

Uses of SequenceIterator in org.biojava.bio.seq.io

Classes in org.biojava.bio.seq.io that implement SequenceIterator

Modifier and Type	Class and Description
class	StreamReader Parses a stream into sequences.

Methods in org.biojava.bio.seq.io that return SequenceIterator

Modifier and Type	Method and Description
static 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 SequenceIterator

Modifier and Type	Method and Description
static 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 SequenceIterator

Modifier and Type	Method and Description
SequenceIterator	RichSequenceDB.sequenceIterator() Returns a SequenceIterator over all sequences in the database.
SequenceIterator	AbstractRichSequenceDB.sequenceIterator()

Uses of SequenceIterator in org.biojavax.bio.seq

Subinterfaces of SequenceIterator in org.biojavax.bio.seq

Modifier and Type	Interface and Description
interface	RichSequenceIterator Essentially the same as SequenceIterator.

Classes in org.biojavax.bio.seq that implement SequenceIterator

Modifier and Type	Class and Description
static class	RichSequence.IOTools.SingleRichSeqIterator Used to iterate over a single rich sequence

Methods in org.biojavax.bio.seq with parameters of type SequenceIterator

Modifier and Type	Method and Description
static void	RichSequence.IOTools.writeEMBL(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from a SequenceIterator to an OutputStream in EMBL Format.
static void	RichSequence.IOTools.writeEMBLxml(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from a SequenceIterator to an OutputStream in EMBLxml Format.
static void	RichSequence.IOTools.writeFasta(OutputStream os, SequenceIterator in, Namespace ns) Writes Sequences from a SequenceIterator to an OutputStream in Fasta Format.
static void	RichSequence.IOTools.writeFasta(OutputStream os, SequenceIterator in, Namespace ns, FastaHeader header) Writes Sequences from a SequenceIterator to an OutputStream in Fasta Format.
static void	RichSequence.IOTools.writeGenbank(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from a SequenceIterator to an OutputStream in GenBank Format.
static void	RichSequence.IOTools.writeINSDseq(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from a SequenceIterator to an OutputStream in INSDseq Format.
static void	RichSequence.IOTools.writeUniProt(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from a SequenceIterator to an OutputStream in UniProt Format.
static void	RichSequence.IOTools.writeUniProtXML(OutputStream os, SequenceIterator in, Namespace ns) Writes sequences from a SequenceIterator to an OutputStream in UniProt XML Format.

Uses of SequenceIterator in org.biojavax.bio.seq.io

Classes in org.biojavax.bio.seq.io that implement SequenceIterator

Modifier and Type	Class and Description
class	HashedFastaIterator Iterates over a Fasta file that is kept in memory for optimized access.
class	RichStreamReader Parses a stream into sequences.

Methods in org.biojavax.bio.seq.io with parameters of type SequenceIterator

Modifier and Type	Method and Description
void	RichStreamWriter.writeStream(SequenceIterator ss, Namespace ns) Write each of the sequences in ss to the stream in the given format.