Utilitary class for creating sequence readers and writers.
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#include <Bpp/Seq/Io/IoSequenceFactory.h>
Utilitary class for creating sequence readers and writers.
Definition at line 53 of file IoSequenceFactory.h.
◆ IoSequenceFactory()
bpp::IoSequenceFactory::IoSequenceFactory |
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Creates a new factory object.
Example:
Alphabet* alphabet = new DNA();
SequenceContainer* sequences = seqReader->read("file.fasta", alphabet);
delete seqReader;
Definition at line 80 of file IoSequenceFactory.h.
◆ ~IoSequenceFactory()
virtual bpp::IoSequenceFactory::~IoSequenceFactory |
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◆ createAlignmentReader()
IAlignment * IoSequenceFactory::createAlignmentReader |
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const std::string & |
format | ) |
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throw | ( | Exception |
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Get a new dynamically created IAlignment object.
- Parameters
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format | The input file format. |
- Returns
- A pointer toward a new IAlignment object.
- Exceptions
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Exception | If the format name do not match any available format. |
Definition at line 78 of file IoSequenceFactory.cpp.
◆ createAlignmentWriter()
OAlignment * IoSequenceFactory::createAlignmentWriter |
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const std::string & |
format | ) |
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throw | ( | Exception |
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virtual |
Get a new dynamically created OAlignment object.
- Parameters
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format | The output file format. |
- Returns
- A pointer toward a new OAlignment object.
- Exceptions
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Exception | If the format name do not match any available format. |
Definition at line 99 of file IoSequenceFactory.cpp.
◆ createReader()
ISequence * IoSequenceFactory::createReader |
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const std::string & |
format | ) |
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throw | ( | Exception |
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virtual |
Get a new dynamically created ISequence object.
- Parameters
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format | The input file format. |
- Returns
- A pointer toward a new ISequence object.
- Exceptions
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Exception | If the format name do not match any available format. |
Definition at line 63 of file IoSequenceFactory.cpp.
◆ createWriter()
OSequence * IoSequenceFactory::createWriter |
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const std::string & |
format | ) |
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throw | ( | Exception |
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virtual |
Get a new dynamically created OSequence object.
- Parameters
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format | The output file format. |
- Returns
- A pointer toward a new OSequence object.
- Exceptions
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Exception | If the format name do not match any available format. |
Definition at line 92 of file IoSequenceFactory.cpp.
◆ CLUSTAL_FORMAT
const string IoSequenceFactory::CLUSTAL_FORMAT = "Clustal" |
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◆ DCSE_FORMAT
const string IoSequenceFactory::DCSE_FORMAT = "DCSE" |
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◆ FASTA_FORMAT
const string IoSequenceFactory::FASTA_FORMAT = "Fasta" |
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◆ GENBANK_FORMAT
const string IoSequenceFactory::GENBANK_FORMAT = "GenBank" |
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◆ MASE_FORMAT
const string IoSequenceFactory::MASE_FORMAT = "Mase" |
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◆ NEXUS_FORMAT
const string IoSequenceFactory::NEXUS_FORMAT = "Nexus" |
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◆ PAML_FORMAT_INTERLEAVED
const string IoSequenceFactory::PAML_FORMAT_INTERLEAVED = "PAML I" |
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◆ PAML_FORMAT_SEQUENTIAL
const string IoSequenceFactory::PAML_FORMAT_SEQUENTIAL = "PAML S" |
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◆ PHYLIP_FORMAT_INTERLEAVED
const string IoSequenceFactory::PHYLIP_FORMAT_INTERLEAVED = "Phylip I" |
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◆ PHYLIP_FORMAT_SEQUENTIAL
const string IoSequenceFactory::PHYLIP_FORMAT_SEQUENTIAL = "Phylip S" |
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The documentation for this class was generated from the following files: