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

Packages that use RichSequenceIterator
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
 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
static class RichSequence.IOTools.SingleRichSeqIterator
          Used to iterate over a single rich sequence
 

Methods in org.biojavax.bio.seq that return RichSequenceIterator
static RichSequenceIterator RichSequence.IOTools.readEMBL(java.io.BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Read a EMBL file using a custom type of SymbolList.
static RichSequenceIterator RichSequence.IOTools.readEMBLDNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an EMBL-format stream of DNA sequences.
static RichSequenceIterator RichSequence.IOTools.readEMBLProtein(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an EMBL-format stream of Protein sequences.
static RichSequenceIterator RichSequence.IOTools.readEMBLRNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an EMBL-format stream of RNA sequences.
static RichSequenceIterator RichSequence.IOTools.readEMBLxml(java.io.BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Read a EMBLxml file using a custom type of SymbolList.
static RichSequenceIterator RichSequence.IOTools.readEMBLxmlDNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an EMBLxml-format stream of DNA sequences.
static RichSequenceIterator RichSequence.IOTools.readEMBLxmlProtein(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an EMBLxml-format stream of Protein sequences.
static RichSequenceIterator RichSequence.IOTools.readEMBLxmlRNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an EMBLxml-format stream of RNA sequences.
static RichSequenceIterator RichSequence.IOTools.readFasta(java.io.BufferedReader br, SymbolTokenization sTok, Namespace ns)
          Read a fasta file.
static RichSequenceIterator RichSequence.IOTools.readFasta(java.io.BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Read a fasta file building a custom type of RichSequence .
static RichSequenceIterator RichSequence.IOTools.readFastaDNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an FASTA-format stream of DNA sequences.
static RichSequenceIterator RichSequence.IOTools.readFastaProtein(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an FASTA-format stream of Protein sequences.
static RichSequenceIterator RichSequence.IOTools.readFastaRNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an FASTA-format stream of RNA sequences.
static RichSequenceIterator RichSequence.IOTools.readFile(java.io.File file, Namespace ns)
          Guess which format a file is then attempt to read it.
static RichSequenceIterator RichSequence.IOTools.readFile(java.io.File file, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Guess which format a file is then attempt to read it.
static RichSequenceIterator RichSequence.IOTools.readGenbank(java.io.BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Read a GenBank file using a custom type of SymbolList.
static RichSequenceIterator RichSequence.IOTools.readGenbankDNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an GenBank-format stream of DNA sequences.
static RichSequenceIterator RichSequence.IOTools.readGenbankProtein(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an GenBank-format stream of Protein sequences.
static RichSequenceIterator RichSequence.IOTools.readGenbankRNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an GenBank-format stream of RNA sequences.
static RichSequenceIterator RichSequence.IOTools.readHashedFastaDNA(java.io.BufferedInputStream is, Namespace ns)
          Iterate over the sequences in an FASTA-format stream of DNA sequences.
static RichSequenceIterator RichSequence.IOTools.readINSDseq(java.io.BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Read a INSDseq file using a custom type of SymbolList.
static RichSequenceIterator RichSequence.IOTools.readINSDseqDNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an INSDseq-format stream of DNA sequences.
static RichSequenceIterator RichSequence.IOTools.readINSDseqProtein(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an INSDseq-format stream of Protein sequences.
static RichSequenceIterator RichSequence.IOTools.readINSDseqRNA(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an INSDseq-format stream of RNA sequences.
static RichSequenceIterator RichSequence.IOTools.readStream(java.io.BufferedInputStream stream, Namespace ns)
          Guess which format a stream is then attempt to read it.
static RichSequenceIterator RichSequence.IOTools.readStream(java.io.BufferedInputStream stream, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Guess which format a stream is then attempt to read it.
static RichSequenceIterator RichSequence.IOTools.readUniProt(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an UniProt-format stream of RNA sequences.
static RichSequenceIterator RichSequence.IOTools.readUniProt(java.io.BufferedReader br, SymbolTokenization sTok, RichSequenceBuilderFactory seqFactory, Namespace ns)
          Read a UniProt file using a custom type of SymbolList.
static RichSequenceIterator RichSequence.IOTools.readUniProtXML(java.io.BufferedReader br, Namespace ns)
          Iterate over the sequences in an UniProt XML-format stream of RNA sequences.
static RichSequenceIterator RichSequence.IOTools.readUniProtXML(java.io.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
 class HashedFastaIterator
          Iterates over a Fasta file that is kept in memory for optimized access.
 class RichStreamReader
          Parses a stream into sequences.