|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
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(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 | |
---|---|
class |
HashedFastaIterator
Iterates over a Fasta file that is kept in memory for optimized access. |
class |
RichStreamReader
Parses a stream into sequences. |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |