Package Bio :: Package Application :: Class AbstractCommandline
[show private | hide private]
[frames | no frames]

Class AbstractCommandline

Known Subclasses:
AlignAceCommandline, BlastallCommandline, CompareAceCommandline, EConsenseCommandline, EInvertedCommandline, ENeighborCommandline, EProtDistCommandline, EProtParsCommandline, ESeqBootCommandline, Est2GenomeCommandline, ETandemCommandline, FastacmdCommandline, FuzznucCommandline, PalindromeCommandline, Primer3Commandline, PrimerSearchCommandline, TranalignCommandline, WaterCommandline

Generic interface for running applications from biopython.

This class shouldn't be called directly; it should be subclassed to provide an implementation for a specific application.
Method Summary
  __init__(self)
  __str__(self)
Make the commandline with the currently set options.
  set_parameter(self, name, value)
Set a commandline option for a program.
  _check_value(self, value, name, check_function)
Check whether the given value is valid.

Method Details

__str__(self)
(Informal representation operator)

Make the commandline with the currently set options.

set_parameter(self, name, value=None)

Set a commandline option for a program.

_check_value(self, value, name, check_function)

Check whether the given value is valid.

This uses the passed function 'check_function', which can either return a [0, 1] (bad, good) value or raise an error. Either way this function will raise an error if the value is not valid, or finish silently otherwise.

Generated by Epydoc 2.1 on Mon Aug 27 16:13:11 2007 http://epydoc.sf.net