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

Packages that use SequenceIterator
org.biojava.bio.alignment: Classes to generate and describe sequence alignments.
org.biojava.bio.program.das: Development client for the Distributed Annotation System.
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
`abstract List` `SequenceAlignment.alignAll(SequenceIterator source, SequenceDB subjectDB)`
`List<Alignment>` `NeedlemanWunsch.alignAll(SequenceIterator source, SequenceDB subjectDB)`

Uses of SequenceIterator in org.biojava.bio.program.das

Methods in org.biojava.bio.program.das that return SequenceIterator
`SequenceIterator` `DASSequenceDB.sequenceIterator()`

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

Methods in org.biojava.bio.seq.db that return SequenceIterator
`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
`SequenceIterator` `BioSQLSequenceDB.sequenceIterator()` Deprecated.

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

Classes in org.biojava.bio.seq.io that implement SequenceIterator
`class` `StreamReader` Parses a stream into sequences.

Methods in org.biojava.bio.seq.io that return SequenceIterator
`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
`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
`SequenceIterator` `RichSequenceDB.sequenceIterator()` Returns a SequenceIterator over all sequences in the database. Will always return an instance of RichSequenceIterator.
`SequenceIterator` `AbstractRichSequenceDB.sequenceIterator()`

Uses of SequenceIterator in org.biojavax.bio.seq

Subinterfaces of SequenceIterator in org.biojavax.bio.seq
`interface` `RichSequenceIterator` Essentially the same as SequenceIterator.

Classes in org.biojavax.bio.seq that implement SequenceIterator
`static class` `RichSequence.IOTools.SingleRichSeqIterator` Used to iterate over a single rich sequence

Methods in org.biojavax.bio.seq with parameters of type SequenceIterator
`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 `Sequence`s from a `SequenceIterator` to an `OutputStream` in Fasta Format.
`static void` `RichSequence.IOTools.writeFasta(OutputStream os, SequenceIterator in, Namespace ns, FastaHeader header)` Writes `Sequence`s 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
`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
`void` `RichStreamWriter.writeStream(SequenceIterator ss, Namespace ns)` Write each of the sequences in ss to the stream in the given format.