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#!/usr/bin/python3
##
## @file getAllElementsWithNotes.py
## @brief Utility program, demonstrating how to use the element filter
## class to search the model for elements with specific attributes
## in this example, we look for elements with notes
##
## @author Frank T. Bergmann
##
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
## of libSBML. This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2018 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
##
## Permission is hereby granted, free of charge, to any person obtaining a
## copy of this software and associated documentation files (the "Software"),
## to deal in the Software without restriction, including without limitation
## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
## Software is furnished to do so, subject to the following conditions:
##
## The above copyright notice and this permission notice shall be included in
## all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
## DEALINGS IN THE SOFTWARE.
##
## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
## or promote products derived from this software without specific prior
## written permission.
## ------------------------------------------------------------------------ -->
##
##
import sys
import os.path
import time
import libsbml
# This class implements an element filter, that can be used to find elements
# with notes
class NotesFilter(libsbml.ElementFilter):
def __init__(self):
# call the constructor of the base class
libsbml.ElementFilter.__init__(self)
# The function performing the filtering, here we just check
# that we have a valid element, and that it has notes.
def filter(self, element):
# return in case we don't have a valid element
if element is None or element.isSetNotes() == False:
return False
# otherwise we have notes set and want to keep the element
if element.isSetId():
print (" found : {0}".format(element.getId()))
else:
print (" found element without id")
return True
def main (args):
"""Usage: getAllElementsWithNotes filename
"""
if len(args) != 2:
print(main.__doc__)
sys.exit(1)
filename = args[1]
# read the document
start = time.time() * 1000
document = libsbml.readSBMLFromFile(filename)
stop = time.time() * 1000
print ("")
print (" filename: {0}".format( filename))
print (" read time (ms): {0}".format( stop - start))
# stop in case of serious errors
errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR)
if errors > 0:
print (" error(s): {0}".format(errors))
document.printErrors()
sys.exit (errors)
# create the filter we want to use
filter = NotesFilter()
# get a list of all elements with notes
start = time.time() * 1000
print (" searching ......:")
allElements = document.getListOfAllElements(filter)
stop = time.time() * 1000
print (" search time (ms): {0}".format(stop - start))
print (" elements with notes: {0}".format(allElements.getSize()))
# if we got here all went well ...
if __name__ == '__main__':
main(sys.argv)
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