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#!/usr/bin/env ruby
#
# @file printMath.rb
# @brief Prints Rule, Reaction, and Event formulas in a given SBML Document
# @author Alex Gutteridge (Ruby conversion of examples/c/printMath.c)
# @author Ben Bornstein
#
## <!--------------------------------------------------------------------------
## 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.
## ------------------------------------------------------------------------ -->
require 'libSBML'
module LibSBML
class Model
def printMath
getNumFunctionDefinitions.times do |n|
puts "Function #{n}: #{getFunctionDefinition(n)}"
end
getNumRules.times do |n|
puts "Rule #{n}: #{getRule(n)}"
end
getNumReactions.times do |n|
puts "Reaction #{n}: #{getReaction(n)}"
end
getNumEvents.times do |n|
puts "Event #{n} #{getEvent(n)}"
end
end
end
class FunctionDefinition
def to_s
s = ""
if isSetMath
s << "#{getId}("
math = getMath
#Print function args
if math.getNumChildren > 1
s << math.getLeftChild.getName
((math.getNumChildren)-2).times do |n|
s << ", " + math.getChild(n+1).getName
end
end
s << ") := "
#Print function body
if math.getNumChildren == 0
s << "(no body defined)"
else
s << LibSBML::formulaToString(math.getChild(math.getNumChildren-1))
end
return s
end
end
end
class Rule
def to_s
if isSetMath
LibSBML::formulaToString(getMath)
end
end
end
class Reaction
def to_s
if isSetKineticLaw and getKineticLaw.isSetMath
LibSBML::formulaToString(getKineticLaw.getMath)
end
end
end
class EventAssignment
def to_s
if isSetMath
"#{getVariable} = #{LibSBML::formulaToString(getMath)}"
end
end
end
class Event
def to_s
d = ''
t = ''
a = []
if isSetDelay
d = "Delay: #{LibSBML::formulaToString(getDelay.getMath)} "
end
if isSetTrigger
t = "Trigger: #{LibSBML::formulaToString(getTrigger.getMath)} "
end
getNumEventAssignments.times do |n|
a << getEventAssignment(n).to_s
end
d + t + a.join(", ")
end
end
end
if ARGV.size != 1
puts "Usage: printMath filename"
exit(1)
end
d = LibSBML::readSBML(ARGV[0])
d.printErrors
d.getModel.printMath
|
