Uses of Interface
org.biojavax.bio.seq.RichSequenceIterator

Packages that use RichSequenceIterator

Package	Description
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 RichSequenceIterator in org.biojavax.bio.db

Methods in org.biojavax.bio.db that return RichSequenceIterator

Modifier and Type	Method	Description
RichSequenceIterator	AbstractRichSequenceDB.getRichSequenceIterator()
RichSequenceIterator	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 RichSequenceIterator

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

Methods in org.biojavax.bio.seq that return RichSequenceIterator

Modifier and Type	Method	Description
static 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 of RichSequence .
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	RichSequence.IOTools.readFile(File file, Namespace ns)	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 RichSequenceIterator

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