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 and Description
RichSequenceIterator	RichSequenceDB.getRichSequenceIterator() Returns a RichSequenceIterator over all sequences in the database.
RichSequenceIterator	AbstractRichSequenceDB.getRichSequenceIterator()

Uses of RichSequenceIterator in org.biojavax.bio.seq

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

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 that return RichSequenceIterator

Modifier and Type	Method and 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, Namespace ns) Read a fasta file.
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.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, Namespace ns) Guess which format a file is then attempt to read it.
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.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, Namespace ns) Guess which format a stream is then attempt to read it.
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.readUniProt(BufferedReader br, Namespace ns) Iterate over the sequences in an UniProt-format stream of RNA sequences.
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.readUniProtXML(BufferedReader br, Namespace ns) Iterate over the sequences in an UniProt XML-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.

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

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

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.