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

Packages that use SequenceIterator
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. 
 

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 AnnotatedSequenceDB.sequenceIterator()
           
 SequenceIterator DummySequenceDB.sequenceIterator()
           
 SequenceIterator IndexedSequenceDB.sequenceIterator()
           
 SequenceIterator AbstractSequenceDB.sequenceIterator()
           
 SequenceIterator HashSequenceDB.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()
           
 

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(java.io.BufferedReader br)
          Iterate over the sequences in an EMBL-format stream.
static SequenceIterator SeqIOTools.readEmblRNA(java.io.BufferedReader br)
          Iterate over the sequences in an EMBL-format stream, but for RNA.
static SequenceIterator SeqIOTools.readEmblNucleotide(java.io.BufferedReader br)
          Iterate over the sequences in an EMBL-format stream.
static SequenceIterator SeqIOTools.readGenbank(java.io.BufferedReader br)
          Iterate over the sequences in an GenBank-format stream.
static SequenceIterator SeqIOTools.readGenpept(java.io.BufferedReader br)
          Iterate over the sequences in an Genpept-format stream.
static SequenceIterator SeqIOTools.readSwissprot(java.io.BufferedReader br)
          Iterate over the sequences in an Swissprot-format stream.
static SequenceIterator SeqIOTools.readFastaDNA(java.io.BufferedReader br)
          Iterate over the sequences in an FASTA-format stream of DNA sequences.
static SequenceIterator SeqIOTools.readFastaRNA(java.io.BufferedReader br)
          Iterate over the sequences in an FASTA-format stream of RNA sequences.
static SequenceIterator SeqIOTools.readFastaProtein(java.io.BufferedReader br)
          Iterate over the sequences in an FASTA-format stream of Protein sequences.
 

Methods in org.biojava.bio.seq.io with parameters of type SequenceIterator
 void StreamWriter.writeStream(SequenceIterator ss)
          Write each of the sequences in ss to the stream in the given format.
static void SeqIOTools.writeFasta(java.io.OutputStream os, SequenceIterator in)
          Writes sequences from a SequenceIterator to an OutputStream in Fasta Format.
static void SeqIOTools.writeEmbl(java.io.OutputStream os, SequenceIterator in)
          Writes a stream of Sequences to an OutputStream in EMBL format.
static void SeqIOTools.writeSwissprot(java.io.OutputStream os, SequenceIterator in)
          Writes a stream of Sequences to an OutputStream in SwissProt format.
static void SeqIOTools.writeGenpept(java.io.OutputStream os, SequenceIterator in)
          Writes a stream of Sequences to an OutputStream in Genpept format.
static void SeqIOTools.writeGenbank(java.io.OutputStream os, SequenceIterator in)
          Writes a stream of Sequences to an OutputStream in Genbank format.