Package Bio :: Package Align :: Module FormatConvert :: Class FormatConverter
[hide private]
[frames] | no frames]

Class FormatConverter

source code

Convert between different alignment representation formats.

The basic idea behind the converter is that it takes a given format, converts it into the base Alignment class, and then can return an object in any other supported format with the info from the basal alignment.

Supported formats are: o Clustal format (*.aln) o Fasta format (*.fasta)

Instance Methods [hide private]
 
__init__(self, to_convert)
Initialize a converter with a given object.
source code
 
_get_base_info(self)
Retrieve all of the basal (ie Generic.Alignment) info.
source code
 
to_fasta(self)
Convert the current info into a FastaAlignment object.
source code
 
to_clustal(self)
Convert the current info into a ClustalAlignment object.
source code
Method Details [hide private]

__init__(self, to_convert)
(Constructor)

source code 

Initialize a converter with a given object.

Arguments: o to_convert - The class which we are going to be converting.

_get_base_info(self)

source code 

Retrieve all of the basal (ie Generic.Alignment) info.

The idea is that this info is present in all of the classes and this is the information that will be retained in a conversion. Format specific information will be lost.