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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()
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Uses of SequenceIterator in org.biojava.bio.seq.db |
Methods in org.biojava.bio.seq.db that return SequenceIterator | |
SequenceIterator |
AbstractSequenceDB.sequenceIterator()
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SequenceIterator |
DummySequenceDB.sequenceIterator()
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SequenceIterator |
AnnotatedSequenceDB.sequenceIterator()
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SequenceIterator |
HashSequenceDB.sequenceIterator()
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SequenceIterator |
SequenceDB.sequenceIterator()
Returns a SequenceIterator over all sequences in the database. |
SequenceIterator |
IndexedSequenceDB.sequenceIterator()
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Uses of SequenceIterator in org.biojava.bio.seq.db.biosql |
Methods in org.biojava.bio.seq.db.biosql that return SequenceIterator | |
SequenceIterator |
BioSQLSequenceDB.sequenceIterator()
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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. |
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