Author: bugman
Date: Mon Sep 26 18:41:49 2011
New Revision: 14761
URL: http://svn.gna.org/viewcvs/relax?rev=14761&view=rev
Log:
Bug fix for the reporting of non-matching lines in the
spectrum.read_intensities user function.
The file data printed did not match the actual intensity data currently being
processed, hence the
wrong data was being printed as non-matching.
Modified:
1.3/generic_fns/spectrum.py
Modified: 1.3/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=14761&r1=14760&r2=14761&view=diff
==============================================================================
--- 1.3/generic_fns/spectrum.py (original)
+++ 1.3/generic_fns/spectrum.py Mon Sep 26 18:41:49 2011
@@ -708,15 +708,11 @@
@keyword file_data: The data extracted from the file converted into a
list of lists.
@type file_data: list of lists of str
- @keyword int_col: The column containing the peak intensity data. The
default is 16 for
- intensities. Setting the int_col argument to 15 will
use the volumes (or
- evolumes). For a non-standard formatted file, use a
different value.
+ @keyword int_col: The column containing the peak intensity data. The
default is 16 for intensities. Setting the int_col argument to 15 will use
the volumes (or evolumes). For a non-standard formatted file, use a different
value.
@type int_col: int
@raises RelaxError: When the expected peak intensity is not a float.
- @return: The extracted data as a list of lists. The first
dimension corresponds to
- the spin. The second dimension consists of the
proton name, heteronucleus
- name, spin ID string, and the intensity value.
- @rtype: list of lists of str, str, str, float
+ @return: The extracted data as a list of lists. The first
dimension corresponds to the spin. The second dimension consists of the
proton name, heteronucleus name, spin ID string, the intensity value, and the
original line of text
+ @rtype: list of lists of str, str, str, float, str
"""
# Assume the NMRView file has six header lines!
@@ -779,7 +775,7 @@
spin_id = generate_spin_id(res_num=res_num, spin_name=x_name)
# Append the data.
- data.append([h_name, x_name, spin_id, intensity])
+ data.append([h_name, x_name, spin_id, intensity, line])
# Return the data.
return data
@@ -793,14 +789,11 @@
@keyword file_data: The data extracted from the file converted into a
list of lists.
@type file_data: list of lists of str
- @keyword int_col: The column containing the peak intensity data (for a
non-standard formatted
- file).
+ @keyword int_col: The column containing the peak intensity data (for a
non-standard formatted file).
@type int_col: int
@raises RelaxError: When the expected peak intensity is not a float.
- @return: The extracted data as a list of lists. The first
dimension corresponds to
- the spin. The second dimension consists of the
proton name, heteronucleus
- name, spin ID string, and the intensity value.
- @rtype: list of lists of str, str, str, float
+ @return: The extracted data as a list of lists. The first
dimension corresponds to the spin. The second dimension consists of the
proton name, heteronucleus name, spin ID string, the intensity value, and the
original line of text.
+ @rtype: list of lists of str, str, str, float, str
"""
# The number of header lines.
@@ -861,7 +854,7 @@
spin_id = generate_spin_id(res_num=res_num, spin_name=x_name)
# Append the data.
- data.append([h_name, x_name, spin_id, intensity])
+ data.append([h_name, x_name, spin_id, intensity, line])
# Return the data.
return data
@@ -879,14 +872,11 @@
@type heteronuc: str
@keyword proton: The name of the proton as specified in the peak
intensity file.
@type proton: str
- @keyword int_col: The column containing the peak intensity data (for a
non-standard formatted
- file).
+ @keyword int_col: The column containing the peak intensity data (for a
non-standard formatted file).
@type int_col: int
@raises RelaxError: When the expected peak intensity is not a float.
- @return: The extracted data as a list of lists. The first
dimension corresponds to
- the spin. The second dimension consists of the
proton name, heteronucleus
- name, spin ID string, and the intensity value.
- @rtype: list of lists of str, str, str, float
+ @return: The extracted data as a list of lists. The first
dimension corresponds to the spin. The second dimension consists of the
proton name, heteronucleus name, spin ID string, the intensity value, and the
original line of text.
+ @rtype: list of lists of str, str, str, float, str
"""
# The columns.
@@ -973,7 +963,7 @@
spin_id = generate_spin_id(res_num=res_num, spin_name=x_name)
# Append the data.
- data.append([h_name, x_name, spin_id, intensity])
+ data.append([h_name, x_name, spin_id, intensity, line])
# Return the data.
return data
@@ -1088,11 +1078,11 @@
data_flag = False
for i in xrange(len(intensity_data)):
# Extract the data.
- H_name, X_name, spin_id, intensity = intensity_data[i]
+ H_name, X_name, spin_id, intensity, line = intensity_data[i]
# Skip data.
if (X_name and X_name != heteronuc) or (H_name and H_name != proton):
- warn(RelaxWarning("Proton and heteronucleus names do not match,
skipping the data %s." % repr(file_data[i])))
+ warn(RelaxWarning("Proton and heteronucleus names do not match,
skipping the data %s." % line))
continue
# Get the spin container.
r14761 - /1.3/generic_fns/spectrum.py