/usr/share/mmass/mspy/parser_xy.py is in mmass 5.5.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Copyright (C) 2005-2013 Martin Strohalm <www.mmass.org>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# Complete text of GNU GPL can be found in the file LICENSE.TXT in the
# main directory of the program.
# -------------------------------------------------------------------------
# load libs
import re
import os.path
# load stopper
from mod_stopper import CHECK_FORCE_QUIT
# load objects
import obj_peak
import obj_peaklist
import obj_scan
# PARSE SIMPLE ASCII XY
# ---------------------
class parseXY():
"""Parse data from ASCII XY."""
def __init__(self, path):
self.path = path
# check path
if not os.path.exists(path):
raise IOError, 'File not found! --> ' + self.path
# ----
def info(self):
"""Get document info."""
data = {
'title': '',
'operator': '',
'contact': '',
'institution': '',
'date': '',
'instrument': '',
'notes': '',
}
return data
# ----
def scan(self, dataType='continuous'):
"""Get spectrum from document."""
# parse file
data = self._parseData()
# check data
if not data:
return False
# return scan
return self._makeScan(data, dataType)
# ----
def _parseData(self):
"""Parse data."""
# open document
try:
document = file(self.path)
rawData = document.readlines()
document.close()
except IOError:
return False
pattern = re.compile('^([-0-9\.eE+]+)[ \t]*(;|,)?[ \t]*([-0-9\.eE+]*)$')
# read lines
data = []
for line in rawData:
line = line.strip()
# discard comment lines
if not line or line[0] == '#' or line[0:3] == 'm/z':
continue
# check pattern
parts = pattern.match(line)
if parts:
try:
mass = float(parts.group(1))
intensity = float(parts.group(3))
except ValueError:
return False
data.append([mass, intensity])
else:
return False
return data
# ----
def _makeScan(self, scanData, dataType):
"""Make scan object from raw data."""
# parse data as peaklist (discrete points)
if dataType == 'discrete':
buff = []
for point in scanData:
buff.append(obj_peak.peak(point[0], point[1]))
scan = obj_scan.scan(peaklist=obj_peaklist.peaklist(buff))
# parse data as spectrum (continuous line)
else:
scan = obj_scan.scan(profile=scanData)
return scan
# ----
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