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Packages that use SequenceIterator | |
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org.biojava.bio.alignment | Classes to generate and describe sequence alignments. |
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. |
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 SequenceIterator in org.biojava.bio.alignment |
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Methods in org.biojava.bio.alignment with parameters of type SequenceIterator | |
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List |
NeedlemanWunsch.alignAll(SequenceIterator source,
SequenceDB subjectDB)
|
abstract List |
SequenceAlignment.alignAll(SequenceIterator source,
SequenceDB subjectDB)
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Uses of SequenceIterator in org.biojava.bio.program.das |
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Methods in org.biojava.bio.program.das that return SequenceIterator | |
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SequenceIterator |
DASSequenceDB.sequenceIterator()
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Uses of SequenceIterator in org.biojava.bio.seq.db |
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Methods in org.biojava.bio.seq.db that return SequenceIterator | |
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SequenceIterator |
HashSequenceDB.sequenceIterator()
|
SequenceIterator |
SequenceDB.sequenceIterator()
Returns a SequenceIterator over all sequences in the database. |
SequenceIterator |
IndexedSequenceDB.sequenceIterator()
|
SequenceIterator |
AbstractSequenceDB.sequenceIterator()
|
SequenceIterator |
AnnotatedSequenceDB.sequenceIterator()
|
SequenceIterator |
DummySequenceDB.sequenceIterator()
|
Uses of SequenceIterator in org.biojava.bio.seq.db.biosql |
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Methods in org.biojava.bio.seq.db.biosql that return SequenceIterator | |
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SequenceIterator |
BioSQLSequenceDB.sequenceIterator()
Deprecated. |
Uses of SequenceIterator in org.biojava.bio.seq.io |
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Classes in org.biojava.bio.seq.io that implement SequenceIterator | |
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class |
StreamReader
Parses a stream into sequences. |
Methods in org.biojava.bio.seq.io that return SequenceIterator | |
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static SequenceIterator |
SeqIOTools.readEmbl(BufferedReader br)
Deprecated. Iterate over the sequences in an EMBL-format stream. |
static SequenceIterator |
SeqIOTools.readEmblNucleotide(BufferedReader br)
Deprecated. Iterate over the sequences in an EMBL-format stream. |
static SequenceIterator |
SeqIOTools.readEmblRNA(BufferedReader br)
Deprecated. Iterate over the sequences in an EMBL-format stream, but for RNA. |
static SequenceIterator |
SeqIOTools.readFasta(BufferedReader br,
SymbolTokenization sTok)
Deprecated. Read a fasta file. |
static SequenceIterator |
SeqIOTools.readFasta(BufferedReader br,
SymbolTokenization sTok,
SequenceBuilderFactory seqFactory)
Deprecated. Read a fasta file using a custom type of SymbolList. |
static SequenceIterator |
SeqIOTools.readFastaDNA(BufferedReader br)
Deprecated. Iterate over the sequences in an FASTA-format stream of DNA sequences. |
static SequenceIterator |
SeqIOTools.readFastaProtein(BufferedReader br)
Deprecated. Iterate over the sequences in an FASTA-format stream of Protein sequences. |
static SequenceIterator |
SeqIOTools.readFastaRNA(BufferedReader br)
Deprecated. Iterate over the sequences in an FASTA-format stream of RNA sequences. |
static SequenceIterator |
SeqIOTools.readGenbank(BufferedReader br)
Deprecated. Iterate over the sequences in an Genbank-format stream. |
static SequenceIterator |
SeqIOTools.readGenbankXml(BufferedReader br)
Deprecated. Iterate over the sequences in an GenbankXML-format stream. |
static SequenceIterator |
SeqIOTools.readGenpept(BufferedReader br)
Deprecated. Iterate over the sequences in an Genpept-format stream. |
static SequenceIterator |
SeqIOTools.readSwissprot(BufferedReader br)
Deprecated. Iterate over the sequences in an Swissprot-format stream. |
Methods in org.biojava.bio.seq.io with parameters of type SequenceIterator | |
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static void |
SeqIOTools.writeEmbl(OutputStream os,
SequenceIterator in)
Deprecated. Writes a stream of Sequences to an OutputStream in EMBL format. |
static void |
SeqIOTools.writeFasta(OutputStream os,
SequenceIterator in)
Deprecated. Writes sequences from a SequenceIterator to an OutputStream in Fasta Format. |
static void |
SeqIOTools.writeGenbank(OutputStream os,
SequenceIterator in)
Deprecated. Writes a stream of Sequences to an OutputStream in Genbank format. |
static void |
SeqIOTools.writeGenpept(OutputStream os,
SequenceIterator in)
Deprecated. Writes a stream of Sequences to an OutputStream in Genpept format. |
void |
StreamWriter.writeStream(SequenceIterator ss)
Write each of the sequences in ss to the stream in the given format. |
static void |
SeqIOTools.writeSwissprot(OutputStream os,
SequenceIterator in)
Deprecated. Writes a stream of Sequences to an OutputStream in SwissProt format. |
Uses of SequenceIterator in org.biojavax.bio.db |
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Methods in org.biojavax.bio.db that return SequenceIterator | |
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SequenceIterator |
RichSequenceDB.sequenceIterator()
Returns a SequenceIterator over all sequences in the database. Will always return an instance of RichSequenceIterator. |
SequenceIterator |
AbstractRichSequenceDB.sequenceIterator()
|
Uses of SequenceIterator in org.biojavax.bio.seq |
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Subinterfaces of SequenceIterator in org.biojavax.bio.seq | |
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interface |
RichSequenceIterator
Essentially the same as SequenceIterator. |
Classes in org.biojavax.bio.seq that implement SequenceIterator | |
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static class |
RichSequence.IOTools.SingleRichSeqIterator
Used to iterate over a single rich sequence |
Methods in org.biojavax.bio.seq with parameters of type SequenceIterator | |
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static void |
RichSequence.IOTools.writeEMBL(OutputStream os,
SequenceIterator in,
Namespace ns)
Writes sequences from a SequenceIterator to an OutputStream in
EMBL Format. |
static void |
RichSequence.IOTools.writeEMBLxml(OutputStream os,
SequenceIterator in,
Namespace ns)
Writes sequences from a SequenceIterator to an OutputStream in
EMBLxml Format. |
static void |
RichSequence.IOTools.writeFasta(OutputStream os,
SequenceIterator in,
Namespace ns)
Writes Sequence s from a SequenceIterator to an OutputStream in
Fasta Format. |
static void |
RichSequence.IOTools.writeGenbank(OutputStream os,
SequenceIterator in,
Namespace ns)
Writes sequences from a SequenceIterator to an OutputStream in
GenBank Format. |
static void |
RichSequence.IOTools.writeINSDseq(OutputStream os,
SequenceIterator in,
Namespace ns)
Writes sequences from a SequenceIterator to an OutputStream in
INSDseq Format. |
static void |
RichSequence.IOTools.writeUniProt(OutputStream os,
SequenceIterator in,
Namespace ns)
Writes sequences from a SequenceIterator to an OutputStream in
UniProt Format. |
static void |
RichSequence.IOTools.writeUniProtXML(OutputStream os,
SequenceIterator in,
Namespace ns)
Writes sequences from a SequenceIterator to an OutputStream in
UniProt XML Format. |
Uses of SequenceIterator in org.biojavax.bio.seq.io |
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Classes in org.biojavax.bio.seq.io that implement SequenceIterator | |
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class |
RichStreamReader
Parses a stream into sequences. |
Methods in org.biojavax.bio.seq.io with parameters of type SequenceIterator | |
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void |
RichStreamWriter.writeStream(SequenceIterator ss,
Namespace ns)
Write each of the sequences in ss to the stream in the given format. |
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