Author: bugman
Date: Mon Mar 19 06:25:03 2007
New Revision: 3230
URL: http://svn.gna.org/viewcvs/relax?rev=3230&view=rev
Log:
Wrote the generic_fns.selection.parse_token() function and 13 unit tests
covering the function!
The unit tests attempt to cover all proper and improper combinations of the
supplied token including
numbers (integers), names, and number ranges.
Modified:
1.3/generic_fns/selection.py
1.3/test_suite/unit_tests/generic_fns/test_residue.py
1.3/test_suite/unit_tests/generic_fns/test_selection.py
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=3230&r1=3229&r2=3230&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Mon Mar 19 06:25:03 2007
@@ -23,6 +23,7 @@
# Python module imports.
from os import F_OK, access
from re import compile, match, split
+from string import strip
# relax module imports.
from data import Data as relax_data_store
@@ -212,7 +213,76 @@
def parse_token(token):
- return []
+ """Parse the token string and return a list of identifying numbers and
names.
+
+ Firstly the token is split by the ',' character into its individual
elements and all whitespace
+ stripped from the elements. Numbers are converted to integers, names
are left as strings, and
+ ranges are converted into the full list of integers.
+
+ @param token: The identification string, the elements of which are
separated by commas. Each
+ element can be either a single number, a range of numbers (two
numbers separated by '-'), or
+ a name.
+ @type token: str
+ @return: A list of identifying numbers and names.
+ @rtype: list of int and str
+ """
+
+ # No token.
+ if token == None:
+ return None
+
+ # Split by the ',' character.
+ elements = split(',', token)
+
+ # Loop over the elements.
+ list = []
+ for element in elements:
+ # Strip all leading and trailing whitespace.
+ element = strip(element)
+
+ # Find all '-' characters (ignoring the first character, i.e. a
negative number).
+ indecies= []
+ for i in xrange(1,len(element)):
+ if element[i] == '-':
+ indecies.append(i)
+
+ # Range.
+ if indecies:
+ # Invalid range element, only one range char '-' and one
negative sign is allowed.
+ if len(indecies) > 2:
+ raise RelaxError, "The range element " + `element` + " is
invalid."
+
+ # Convert the two numbers to integers.
+ try:
+ start = int(element[:indecies[0]])
+ end = int(element[indecies[0]+1:])
+ except ValueError:
+ raise RelaxError, "The range element " + `element` + " is
invalid as either the start or end of the range are not integers."
+
+ # Test that the starting number is less than the end.
+ if start >= end:
+ raise RelaxError, "The starting number of the range element
" + `element` + " needs to be less than the end number."
+
+ # Create the range and append it to the list.
+ for i in range(start, end+1):
+ list.append(i)
+
+ # Number or name.
+ else:
+ # Try converting the element into an integer.
+ try:
+ element = int(element)
+ except ValueError:
+ pass
+
+ # Append the element.
+ list.append(element)
+
+ # Sort the list.
+ list.sort()
+
+ # Return the identifying list.
+ return list
def residue_loop(selection=None):
Modified: 1.3/test_suite/unit_tests/generic_fns/test_residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/generic_fns/test_residue.py?rev=3230&r1=3229&r2=3230&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_residue.py (original)
+++ 1.3/test_suite/unit_tests/generic_fns/test_residue.py Mon Mar 19 06:25:03
2007
@@ -182,7 +182,7 @@
relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
- # Delete the first and third residues.
+ # Delete all residues.
residue.delete(res_id=':1-4')
# Test that the first residue defaults back to the empty residue.
Modified: 1.3/test_suite/unit_tests/generic_fns/test_selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/generic_fns/test_selection.py?rev=3230&r1=3229&r2=3230&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_selection.py (original)
+++ 1.3/test_suite/unit_tests/generic_fns/test_selection.py Mon Mar 19
06:25:03 2007
@@ -105,6 +105,159 @@
i = i + 1
+ def test_parse_token_single_element_num(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '1'."""
+
+ # Parse the token.
+ list = selection.parse_token('1')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 1)
+ self.assertEqual(list[0], 1)
+
+
+ def test_parse_token_single_element_neg_num(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '-4'."""
+
+ # Parse the token.
+ list = selection.parse_token('-4')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 1)
+ self.assertEqual(list[0], -4)
+
+
+ def test_parse_token_single_element_name(self):
+ """Test the generic_fns.selection.parse_token() function on the
string 'G'."""
+
+ # Parse the token.
+ list = selection.parse_token('G')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 1)
+ self.assertEqual(list[0], 'G')
+
+
+ def test_parse_token_single_element_range(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '1-10'."""
+
+ # Parse the token.
+ list = selection.parse_token('1-10')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 10)
+ for i in range(1, 11):
+ self.assertEqual(list[i-1], i)
+
+
+ def test_parse_token_single_element_neg_range(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '-10--1'."""
+
+ # Parse the token.
+ list = selection.parse_token('-10--1')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 10)
+ j = 0
+ for i in range(-10, -2):
+ self.assertEqual(list[j], i)
+ j = j + 1
+
+
+ def test_parse_token_multi_element_num(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '-2, 1'."""
+
+ # Parse the token.
+ list = selection.parse_token('-2, 1')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 2)
+ self.assertEqual(list[0], -2)
+ self.assertEqual(list[1], 1)
+
+
+ def test_parse_token_multi_element_name(self):
+ """Test the generic_fns.selection.parse_token() function on the
string 'N,CA'."""
+
+ # Parse the token.
+ list = selection.parse_token('N,CA')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 2)
+ self.assertEqual(list[0], 'CA')
+ self.assertEqual(list[1], 'N')
+
+
+ def test_parse_token_multi_element_num_name(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '76,Ala'."""
+
+ # Parse the token.
+ list = selection.parse_token('76,Ala')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 2)
+ self.assertEqual(list[0], 76)
+ self.assertEqual(list[1], 'Ala')
+
+
+ def test_parse_token_multi_element_num_range(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '1,3-5'."""
+
+ # Parse the token.
+ list = selection.parse_token('1,3-5')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 4)
+ self.assertEqual(list[0], 1)
+ self.assertEqual(list[1], 3)
+ self.assertEqual(list[2], 4)
+ self.assertEqual(list[3], 5)
+
+
+ def test_parse_token_multi_element_range_name(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '3-5,NH'."""
+
+ # Parse the token.
+ list = selection.parse_token('3-5,NH')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 4)
+ self.assertEqual(list[0], 3)
+ self.assertEqual(list[1], 4)
+ self.assertEqual(list[2], 5)
+ self.assertEqual(list[3], 'NH')
+
+
+ def test_parse_token_multi_element_range_num_name(self):
+ """Test the generic_fns.selection.parse_token() function on the
string '3-6, 8, Gly'."""
+
+ # Parse the token.
+ list = selection.parse_token('3-6, 8, Gly')
+
+ # Check the list elements.
+ self.assertEqual(len(list), 6)
+ self.assertEqual(list[0], 3)
+ self.assertEqual(list[1], 4)
+ self.assertEqual(list[2], 5)
+ self.assertEqual(list[3], 6)
+ self.assertEqual(list[4], 8)
+ self.assertEqual(list[5], 'Gly')
+
+
+ def test_parse_token_range_fail1(self):
+ """Failure of the generic_fns.selection.parse_token() function on
the string '1-5-7'."""
+
+ # Parse the invalid token.
+ self.assertRaises(RelaxError, selection.parse_token, '1-5-7')
+
+
+ def test_parse_token_range_fail2(self):
+ """Failure of the generic_fns.selection.parse_token() function on
the string '1--3'."""
+
+ # Parse the invalid token.
+ self.assertRaises(RelaxError, selection.parse_token, '1--3')
+
+
def test_residue_loop(self):
"""Test the proper operation of the residue loop with residue
selection.
r3230 - in /1.3: generic_fns/ test_suite/unit_tests/generic_fns/