def __set_time(self, time_list):
"""
@summary: Sets time-related properties of the data
@param time_list: List of retention times
@type time_list: ListType
@author: Vladimir Likic
"""
# calculate the time step, its spreak, and along the way
# check that retention times are increasing
time_diff_list = []
for ii in range(len(time_list)-1):
t1 = time_list[ii]
t2 = time_list[ii+1]
if not t2 > t1:
error("problem with retention times detected")
time_diff = t2 - t1
time_diff_list.append(time_diff)
time_step = mean(time_diff_list)
time_step_std = std(time_diff_list)
self.__time_list = time_list
self.__time_step = time_step
self.__time_step_std = time_step_std
self.__min_rt = min(time_list)
self.__max_rt = max(time_list)
def __set_time(self, time_list):
"""
@summary: Sets time-related properties of the data
@param time_list: List of retention times
@type time_list: ListType
@author: Vladimir Likic
"""
# calculate the time step, its spreak, and along the way
# check that retention times are increasing
time_diff_list = []
for ii in range(len(time_list)-1):
t1 = time_list[ii]
t2 = time_list[ii+1]
if not t2 > t1:
error("problem with retention times detected")
time_diff = t2 - t1
time_diff_list.append(time_diff)
time_step = mean(time_diff_list)
time_step_std = std(time_diff_list)
self.__time_list = time_list
self.__time_step = time_step
self.__time_step_std = time_step_std
self.__min_rt = min(time_list)
self.__max_rt = max(time_list)
def info(self, print_scan_n=False):
"""
@summary: Prints some information about the data
@param print_scan_n: If set to True will print the number
of m/z values in each scan
@type print_scan_n: BooleanType
@author: Vladimir Likic
"""
# print the summary of simply attributes
print " Data retention time range: %.3f min -- %.3f min" % \
(self.__min_rt/60.0, self.__max_rt/60)
print " Time step: %.3f s (std=%.3f s)" % ( self.__time_step, \
self.__time_step_std )
print " Number of scans: %d" % ( len(self.__scan_list) )
print " Minimum m/z measured: %.3f" % ( self.__min_mass )
print " Maximum m/z measured: %.3f" % ( self.__max_mass )
# calculate median number of m/z values measured per scan
n_list = []
for ii in range(len(self.__scan_list)):
scan = self.__scan_list[ii]
n = len(scan)
n_list.append(n)
if print_scan_n: print n
mz_mean = mean(n_list)
mz_median = median(n_list)
print " Mean number of m/z values per scan: %d" % ( mz_mean )
print " Median number of m/z values per scan: %d" % ( mz_median )
def info(self, print_scan_n=False):
"""
@summary: Prints some information about the data
@param print_scan_n: If set to True will print the number
of m/z values in each scan
@type print_scan_n: BooleanType
@author: Vladimir Likic
"""
# print the summary of simply attributes
print " Data retention time range: %.3f min -- %.3f min" % \
(self.__min_rt/60.0, self.__max_rt/60)
print " Time step: %.3f s (std=%.3f s)" % ( self.__time_step, \
self.__time_step_std )
print " Number of scans: %d" % ( len(self.__scan_list) )
print " Minimum m/z measured: %.3f" % ( self.__min_mass )
print " Maximum m/z measured: %.3f" % ( self.__max_mass )
# calculate median number of m/z values measured per scan
n_list = []
for ii in range(len(self.__scan_list)):
scan = self.__scan_list[ii]
n = len(scan)
n_list.append(n)
if print_scan_n: print n
mz_mean = mean(n_list)
mz_median = median(n_list)
print " Mean number of m/z values per scan: %d" % ( mz_mean )
print " Median number of m/z values per scan: %d" % ( mz_median )
