r27802 - /trunk/lib/spectrum/peak_list.py -- March 10, 2015 - 10:15

Author: bugman
Date: Tue Mar 10 10:15:35 2015
New Revision: 27802

URL: http://svn.gna.org/viewcvs/relax?rev=27802&view=rev
Log:
Modified the spectrum.read_intensities user function backend to be more 
robust.

This affects the generic formatted peak lists, via the 
lib.spectrum.peak_list.intensity_generic()
function.  The peak list reading will now continue reading the file after 
corrupted lines have been
encountered.


Modified:
    trunk/lib/spectrum/peak_list.py

Modified: trunk/lib/spectrum/peak_list.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/peak_list.py?rev=27802&r1=27801&r2=27802&view=diff
==============================================================================
--- trunk/lib/spectrum/peak_list.py     (original)
+++ trunk/lib/spectrum/peak_list.py     Tue Mar 10 10:15:35 2015
@@ -1,6 +1,6 @@
 
###############################################################################
 #                                                                            
 #
-# Copyright (C) 2004-2014 Edward d'Auvergne                                  
 #
+# Copyright (C) 2004-2015 Edward d'Auvergne                                  
 #
 # Copyright (C) 2008 Sebastien Morin                                         
 #
 # Copyright (C) 2013 Troels E. Linnet                                        
 #
 #                                                                            
 #
@@ -112,9 +112,13 @@
     for line in file_data:
         # Loop over the intensity columns, storing the data.
         intensity = []
+        data_flag = False
         for i in range(len(data_col)):
             # Extract the data for the single line (loop of a single 
element).
-            for values in read_spin_data(file_data=[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[i], sep=sep, spin_id=spin_id):
+            for values in read_spin_data(file_data=[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[i], sep=sep, spin_id=spin_id, 
raise_flag=False):
+                # The data flag.
+                data_flag = True
+
                 # Check the values.
                 if len(values) != 6 and data_present:
                     raise RelaxError("The molecule name, residue number and 
name, spin number and name, and value columns could not be found in the data 
%s." % repr(values))
@@ -133,7 +137,8 @@
                     mol_name, res_num, res_name, spin_num, spin_name = values
 
         # Add the assignment to the peak list object.
-        peak_list.add(mol_names=[mol_name, mol_name], res_nums=[res_num, 
res_num], res_names=[res_name, res_name], spin_nums=[spin_num, spin_num], 
spin_names=[spin_name, spin_name], intensity=intensity)
+        if data_flag:
+            peak_list.add(mol_names=[mol_name, mol_name], res_nums=[res_num, 
res_num], res_names=[res_name, res_name], spin_nums=[spin_num, spin_num], 
spin_names=[spin_name, spin_name], intensity=intensity)
 
 
 def read_peak_list(file=None, dir=None, int_col=None, spin_id_col=None, 
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, 
spin_name_col=None, sep=None, spin_id=None):