Author: bugman
Date: Fri Aug 21 17:25:00 2009
New Revision: 9354
URL: http://svn.gna.org/viewcvs/relax?rev=9354&view=rev
Log:
Simplified the sequence user function class by using the check and base_class
modules.
Modified:
1.3/prompt/sequence.py
Modified: 1.3/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/sequence.py?rev=9354&r1=9353&r2=9354&view=diff
==============================================================================
--- 1.3/prompt/sequence.py (original)
+++ 1.3/prompt/sequence.py Fri Aug 21 17:25:00 2009
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003, 2004, 2007-2008 Edward d'Auvergne
#
+# Copyright (C) 2003, 2004, 2007-2009 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -28,23 +28,14 @@
import sys
# relax module imports.
-import help
+from base_class import User_fn_class
+import check
from generic_fns import sequence
from relax_errors import RelaxError, RelaxBoolError, RelaxNoneIntError,
RelaxNoneStrError, RelaxStrError
-class Sequence:
- def __init__(self, relax):
- # Help.
- self.__relax_help__ = \
- """Class for manipulating sequence data."""
-
- # Add the generic help string.
- self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
-
- # Place relax in the class namespace.
- self.__relax__ = relax
-
+class Sequence(User_fn_class):
+ """Class for manipulating sequence data."""
def copy(self, pipe_from=None, pipe_to=None):
"""Copy the molecule, residue, and spin sequence data from one data
pipe to another.
@@ -93,13 +84,9 @@
text = text + ", pipe_to=" + repr(pipe_to) + ")"
print(text)
- # The pipe_from argument.
- if pipe_from != None and not isinstance(pipe_from, str):
- raise RelaxNoneStrError('pipe from', pipe_from)
-
- # The pipe_to argument.
- if pipe_to != None and not isinstance(pipe_to, str):
- raise RelaxNoneStrError('pipe to', pipe_to)
+ # The argument checks.
+ check.is_str(pipe_from, 'pipe from')
+ check.is_str(pipe_to, 'pipe to')
# Both pipe arguments cannot be None.
if pipe_from == None and pipe_to == None:
@@ -140,29 +127,13 @@
text = text + ", spin_name_flag=" + repr(spin_name_flag) + ")"
print(text)
- # Column separator.
- if sep != None and not isinstance(sep, str):
- raise RelaxNoneStrError('column separator', sep)
-
- # Molecule name flag.
- if not isinstance(mol_name_flag, bool):
- raise RelaxBoolError('molecule name flag', mol_name_flag)
-
- # Residue number flag.
- if not isinstance(res_num_flag, bool):
- raise RelaxBoolError('residue number flag', res_num_flag)
-
- # Residue name flag.
- if not isinstance(res_name_flag, bool):
- raise RelaxBoolError('residue name flag', res_name_flag)
-
- # Spin number flag.
- if not isinstance(spin_num_flag, bool):
- raise RelaxBoolError('spin number flag', spin_num_flag)
-
- # Spin name flag.
- if not isinstance(spin_name_flag, bool):
- raise RelaxBoolError('spin name flag', spin_name_flag)
+ # The argument checks.
+ check.is_str(sep, 'column separator')
+ check.is_bool(mol_name_flag, 'molecule name flag')
+ check.is_bool(res_num_flag, 'residue number flag')
+ check.is_bool(res_name_flag, 'residue name flag')
+ check.is_bool(spin_num_flag, 'spin number flag')
+ check.is_bool(spin_name_flag, 'spin name flag')
# Execute the functional code.
sequence.display(sep=sep, mol_name_flag=mol_name_flag,
res_num_flag=res_num_flag, res_name_flag=res_name_flag,
spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
@@ -247,37 +218,15 @@
text = text + ", sep=" + repr(sep) + ")"
print(text)
- # The file name.
- if not isinstance(file, str):
- raise RelaxStrError('file name', file)
-
- # Directory.
- if dir != None and not isinstance(dir, str):
- raise RelaxNoneStrError('directory name', dir)
-
- # Molecule name column.
- if mol_name_col != None and not isinstance(mol_name_col, int):
- raise RelaxNoneIntError('molecule name column', mol_name_col)
-
- # Residue number column.
- if res_name_col != None and not isinstance(res_num_col, int):
- raise RelaxNoneIntError('residue number column', res_num_col)
-
- # Residue name column.
- if res_name_col != None and not isinstance(res_name_col, int):
- raise RelaxNoneIntError('residue name column', res_name_col)
-
- # Spin number column.
- if spin_num_col != None and not isinstance(spin_num_col, int):
- raise RelaxNoneIntError('spin number column', spin_num_col)
-
- # Spin name column.
- if spin_name_col != None and not isinstance(spin_name_col, int):
- raise RelaxNoneIntError('spin name column', spin_name_col)
-
- # Column separator.
- if sep != None and not isinstance(sep, str):
- raise RelaxNoneStrError('column separator', sep)
+ # The argument checks.
+ check.is_str(file, 'file name', False)
+ check.is_str(dir, 'directory name')
+ check.is_int(mol_name_col, 'molecule name column')
+ check.is_int(res_num_col, 'residue number column')
+ check.is_int(res_name_col, 'residue name column')
+ check.is_int(spin_num_col, 'spin number column')
+ check.is_int(spin_name_col, 'spin name column')
+ check.is_str(sep, 'column separator')
# Execute the functional code.
sequence.read(file=file, dir=dir, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep)
@@ -328,41 +277,16 @@
text = text + ", force=" + repr(force) + ")"
print(text)
- # File.
- if not isinstance(file, str):
- raise RelaxStrError('file name', file)
-
- # Directory.
- if dir != None and not isinstance(dir, str):
- raise RelaxNoneStrError('directory name', dir)
-
- # Column separator.
- if sep != None and not isinstance(sep, str):
- raise RelaxNoneStrError('column separator', sep)
-
- # Molecule name flag.
- if not isinstance(mol_name_flag, bool):
- raise RelaxBoolError('molecule name flag', mol_name_flag)
-
- # Residue number flag.
- if not isinstance(res_num_flag, bool):
- raise RelaxBoolError('residue number flag', res_num_flag)
-
- # Residue name flag.
- if not isinstance(res_name_flag, bool):
- raise RelaxBoolError('residue name flag', res_name_flag)
-
- # Spin number flag.
- if not isinstance(spin_num_flag, bool):
- raise RelaxBoolError('spin number flag', spin_num_flag)
-
- # Spin name flag.
- if not isinstance(spin_name_flag, bool):
- raise RelaxBoolError('spin name flag', spin_name_flag)
-
- # The force flag.
- if not isinstance(force, bool):
- raise RelaxBoolError('force flag', force)
+ # The argument checks.
+ check.is_str(file, 'file name', False)
+ check.is_str(dir, 'directory name')
+ check.is_str(sep, 'column separator')
+ check.is_bool(mol_name_flag, 'molecule name flag')
+ check.is_bool(res_num_flag, 'residue number flag')
+ check.is_bool(res_name_flag, 'residue name flag')
+ check.is_bool(spin_num_flag, 'spin number flag')
+ check.is_bool(spin_name_flag, 'spin name flag')
+ check.is_bool(force, 'force flag')
# Execute the functional code.
sequence.write(file=file, dir=dir, sep=sep,
mol_name_flag=mol_name_flag, res_num_flag=res_num_flag,
res_name_flag=res_name_flag, spin_num_flag=spin_num_flag,
spin_name_flag=spin_name_flag, force=force)
r9354 - /1.3/prompt/sequence.py