65 if(format == FASTA_FORMAT)
return new Fasta();
66 else if(format == MASE_FORMAT)
return new Mase();
67 else if(format == CLUSTAL_FORMAT)
return new Clustal();
68 else if(format == DCSE_FORMAT)
return new DCSE();
69 else if(format == PHYLIP_FORMAT_INTERLEAVED)
return new Phylip(
false,
false);
70 else if(format == PHYLIP_FORMAT_SEQUENTIAL)
return new Phylip(
false,
true);
71 else if(format == PAML_FORMAT_INTERLEAVED)
return new Phylip(
true,
false);
72 else if(format == PAML_FORMAT_SEQUENTIAL)
return new Phylip(
true,
true);
73 else if(format == GENBANK_FORMAT)
return new GenBank();
75 else throw Exception(
"Format " + format +
" is not supported for sequences input.");
80 if(format == FASTA_FORMAT)
return new Fasta();
81 else if(format == MASE_FORMAT)
return new Mase();
82 else if(format == CLUSTAL_FORMAT)
return new Clustal();
83 else if(format == DCSE_FORMAT)
return new DCSE();
84 else if(format == PHYLIP_FORMAT_INTERLEAVED)
return new Phylip(
false,
false);
85 else if(format == PHYLIP_FORMAT_SEQUENTIAL)
return new Phylip(
false,
true);
86 else if(format == PAML_FORMAT_INTERLEAVED)
return new Phylip(
true,
false);
87 else if(format == PAML_FORMAT_SEQUENTIAL)
return new Phylip(
true,
true);
89 else throw Exception(
"Format " + format +
" is not supported for alignment input.");
94 if(format == FASTA_FORMAT)
return new Fasta();
95 else if(format == MASE_FORMAT)
return new Mase();
96 else throw Exception(
"Format " + format +
" is not supported for output.");
101 if (format == FASTA_FORMAT)
return new Fasta();
102 else if (format == MASE_FORMAT)
return new Mase();
103 else if (format == PHYLIP_FORMAT_INTERLEAVED)
return new Phylip(
false,
false);
104 else if (format == PHYLIP_FORMAT_SEQUENTIAL)
return new Phylip(
false,
true);
105 else if (format == PAML_FORMAT_INTERLEAVED)
return new Phylip(
true,
false);
106 else if (format == PAML_FORMAT_SEQUENTIAL)
return new Phylip(
true,
true);
107 else throw Exception(
"Format " + format +
" is not supported for output.");
virtual IAlignment * createAlignmentReader(const std::string &format)
Get a new dynamically created IAlignment object.
The OAlignment interface.
virtual OSequence * createWriter(const std::string &format)
Get a new dynamically created OSequence object.
The fasta sequence file format.
static const std::string PAML_FORMAT_INTERLEAVED
static const std::string FASTA_FORMAT
This alphabet is used to deal NumericAlphabet.
static const std::string MASE_FORMAT
The clustal sequence file format.
The mase sequence file format.
The Nexus format reader for sequences.
static const std::string PAML_FORMAT_SEQUENTIAL
static const std::string PHYLIP_FORMAT_SEQUENTIAL
Support for the Dedicated Comparative Sequence Editor format.
static const std::string GENBANK_FORMAT
virtual OAlignment * createAlignmentWriter(const std::string &format)
Get a new dynamically created OAlignment object.
static const std::string NEXUS_FORMAT
static const std::string PHYLIP_FORMAT_INTERLEAVED
The GenBank sequence file format.
virtual ISequence * createReader(const std::string &format)
Get a new dynamically created ISequence object.
The IAlignment interface.
static const std::string CLUSTAL_FORMAT
static const std::string DCSE_FORMAT