r14072 - in /branches/xyz: ./ generic_fns/sequence.py relax_io.py -- August 02, 2011 - 17:05

Author: bugman
Date: Tue Aug  2 17:05:32 2011
New Revision: 14072

URL: http://svn.gna.org/viewcvs/relax?rev=14072&view=rev
Log:
Merged revisions 14071 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3

........
  r14071 | bugman | 2011-08-02 16:54:53 +0200 (Tue, 02 Aug 2011) | 5 lines
  
  generic_fns.sequence.validate_sequence() now also checks for the spin ID, 
data and error columns.
  
  This is now used by relax_io.read_spin_data().
........

Modified:
    branches/xyz/   (props changed)
    branches/xyz/generic_fns/sequence.py
    branches/xyz/relax_io.py

Propchange: branches/xyz/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Aug  2 17:05:32 2011
@@ -1,1 +1,1 @@
-/1.3:1-14069
+/1.3:1-14071

Modified: branches/xyz/generic_fns/sequence.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/sequence.py?rev=14072&r1=14071&r2=14072&view=diff
==============================================================================
--- branches/xyz/generic_fns/sequence.py (original)
+++ branches/xyz/generic_fns/sequence.py Tue Aug  2 17:05:32 2011
@@ -306,7 +306,7 @@
     write_spin_data(sys.stdout, mol_names=mol_names, res_nums=res_nums, 
res_names=res_names, spin_nums=spin_nums, spin_names=spin_names)
 
 
-def validate_sequence(data, mol_name_col=None, res_num_col=None, 
res_name_col=None, spin_num_col=None, spin_name_col=None):
+def validate_sequence(data, spin_id_col=None, mol_name_col=None, 
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, 
data_col=None, error_col=None):
     """Test if the sequence data is valid.
 
     The only function this performs is to raise a RelaxError if the data is 
invalid.
@@ -314,6 +314,8 @@
 
     @param data:            The sequence data.
     @type data:             list of lists.
+    @keyword spin_id_col:   The column containing the spin ID strings.
+    @type spin_id_col:      int or None
     @param mol_name_col:    The column containing the molecule name 
information.
     @type mol_name_col:     int or None
     @param res_name_col:    The column containing the residue name 
information.
@@ -326,6 +328,13 @@
     @type spin_num_col:     int or None
     """
 
+    # Spin ID.
+    if spin_id_col:
+        try:
+            data[spin_id_col-1]
+        except IndexError:
+            raise RelaxInvalidSeqError(data)
+
     # Molecule name data.
     if mol_name_col:
         try:
@@ -372,6 +381,20 @@
     if spin_name_col:
         try:
             data[spin_name_col-1]
+        except IndexError:
+            raise RelaxInvalidSeqError(data)
+
+    # Data.
+    if data_col:
+        try:
+            data[data_col-1]
+        except IndexError:
+            raise RelaxInvalidSeqError(data)
+
+    # Errors
+    if error_col:
+        try:
+            data[error_col-1]
         except IndexError:
             raise RelaxInvalidSeqError(data)
 

Modified: branches/xyz/relax_io.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/xyz/relax_io.py?rev=14072&r1=14071&r2=14072&view=diff
==============================================================================
--- branches/xyz/relax_io.py (original)
+++ branches/xyz/relax_io.py Tue Aug  2 17:05:32 2011
@@ -536,7 +536,7 @@
     for line in file_data:
         # Validate the sequence.
         try:
-            generic_fns.sequence.validate_sequence(line, 
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)
+            generic_fns.sequence.validate_sequence(line, 
spin_id_col=spin_id_col, 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, data_col=data_col, error_col=error_col)
         except RelaxInvalidSeqError, msg:
             # Extract the message string, without the RelaxError bit.
             string = msg.__str__()[12:-1]