Source Code for Module relax_warnings

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax is free software; you can redistribute it and/or modify               # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation; either version 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax is distributed in the hope that it will be useful,                    # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing all of the RelaxWarning objects.""" 
 25   
 26  # Python module imports. 
 27  import inspect 
 28  import sys 
 29  import warnings 
 30   
 31  # relax module imports. 
 32  import ansi 
 33  from status import Status; status = Status() 
 34   
 35   
 36  # The warning formatting function. 
 37 -def format(message, category, filename, lineno, line=None): 
 38      """ Replacement for warnings.formatwarning to customise output format.""" 
 39   
 40      # Add the text 'RelaxWarning: ' to the start of the warning message. 
 41      message = "RelaxWarning: %s\n" % message 
 42   
 43      # Print stack-trace in pedantic mode. 
 44      if status.pedantic: 
 45          tb = "" 
 46          for frame in inspect.stack()[4:]: 
 47              file = frame[1] 
 48              lineNo = frame[2] 
 49              func = frame[3] 
 50              tb_frame = '  File "%s", line %i, in %s\n' % (file, lineNo, func) 
 51              try: 
 52                  context = frame[4][frame[5]] 
 53              except TypeError: 
 54                  pass 
 55              else: 
 56                  tb_frame = '%s    %s\n' % (tb_frame, context.strip()) 
 57              tb = tb_frame + tb 
 58          tb = "Traceback (most recent call last):\n%s" % tb 
 59          message = tb + message 
 60   
 61      # Text colouring 
 62      if ansi.enable_control_chars(stream=2): 
 63          # Strip the last newline, if it exists. 
 64          if message[-1] == '\n': 
 65              message = message[:-1] 
 66   
 67          # Reformat. 
 68          message = "%s%s%s\n" % (ansi.relax_warning, message, ansi.end) 
 69   
 70      # Return the warning message. 
 71      return message 
 72   
 73   
 74 -def setup(): 
 75      """Set up the warning system.""" 
 76   
 77      # Format warning messages. 
 78      warnings.formatwarning = format 
 79   
 80      # Set warning filters. 
 81      if status.pedantic: 
 82          warnings.filterwarnings('error', category=BaseWarning) 
 83      else: 
 84          warnings.filterwarnings('always', category=BaseWarning) 
 85   
 86   
 87   
 88  # Base class for all warnings. 
 89  ############################## 
 90   
 91 -class BaseWarning(Warning): 
 92 -    def __str__(self): 
 93          return str(self.text) 
 94   
 95   
 96  # Standard warnings. 
 97  #################### 
 98   
 99 -class RelaxWarning(BaseWarning): 
100 -    def __init__(self, text): 
101          self.text = text 
102   
103   
104  # Sequence errors. 
105  ################## 
106   
107  # Cannot find the spin in the sequence. 
108 -class RelaxNoSpinWarning(BaseWarning): 
109 -    def __init__(self, spin_id): 
110          self.text = "Cannot find the spin %s within the sequence." % spin_id 
111   
112   
113  # PDB warnings. 
114  ############### 
115   
116  # Zero length XH bond vector. 
117 -class RelaxZeroVectorWarning(BaseWarning): 
118 -    def __init__(self, res): 
119          self.text = "The XH bond vector for residue " + repr(res) + " is of zero length." 
120   
121   
122  # The atom is missing from the PDB file. 
123 -class RelaxNoAtomWarning(BaseWarning): 
124 -    def __init__(self, atom, res): 
125          self.text = "The atom %s could not be found for residue %i" % (atom, res) 
126   
127   
128  # The PDB file is missing. 
129 -class RelaxNoPDBFileWarning(BaseWarning): 
130 -    def __init__(self, file): 
131          self.text = "The PDB file %s cannot be found, no structures will be loaded." % file 
132   
133   
134  # File warnings. 
135  ################ 
136   
137  # No data in file. 
138 -class RelaxFileEmptyWarning(BaseWarning): 
139 -    def __init__(self, file): 
140          self.text = "The file '%s' contains no data." % file 
141   
142   
143  # Misc. 
144  ####### 
145   
146  # Deselection warnings 
147 -class RelaxDeselectWarning(BaseWarning): 
148 -    def __init__(self, spin_id, reason): 
149          self.text = "The spin '%s' has been deselected because of %s." % (spin_id, reason) 
150