#!/usr/bin/env perl
# -*-Perl-*-
## 
## @file    unsetNotes.pl
## @brief   unset notes for each element
## @author  Akiya Jouraku
## 
## <!--------------------------------------------------------------------------
## 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.
## ------------------------------------------------------------------------ -->
## 

use LibSBML;
no strict;

if ($#ARGV != 1 ) {
	print "Usage: unsetNotes <input-filename> <output-filename>\n";
	exit 1;
}

$filename = $ARGV[0];

$document = LibSBML::readSBML($filename);

$errors = $document->getNumErrors();

if ($errors > 0) {
    $document->printErrors();
    exit $errors;
}

$m = $document->getModel();
$m->unsetNotes();

for ($i = 0; $i < $m->getNumReactions(); $i++) {
    $re = $m->getReaction($i);
    $re->unsetNotes();

    for ($j = 0; $j < $re->getNumReactants(); $j++) {
        $rt = $re->getReactant($j);
        $rt->unsetNotes();
    }  
    for ($j = 0; $j < $re->getNumProducts(); $j++) {
        $rt = $re->getProduct($j);
        $rt->unsetNotes();
    }
    for ($j =0; $j < $re->getNumModifiers(); $j++) {
        $md = $re->getModifier($j);
        $md->unsetNotes();
    }
    if ($re->isSetKineticLaw()) {
        $kl = $re->getKineticLaw();
        $kl->unsetNotes();

        for ($j =0; $j < $kl->getNumParameters(); $j++) {
            $pa = $kl->getParameter(j);
            $pa->unsetNotes();
        }
     }
}
for ($i = 0; $i < $m->getNumSpecies(); $i++) {
    $sp = $m->getSpecies($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumCompartments(); $i++) {
    $sp = $m->getCompartment($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumFunctionDefinitions(); $i++) {
    $sp = $m->getFunctionDefinition($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumUnitDefinitions(); $i++) {
    $sp = $m->getUnitDefinition($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumParameters(); $i++) {
    $sp = $m->getParameter($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumRules(); $i++) {
    $sp = $m->getRule($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumInitialAssignments(); $i++) {
    $sp = $m->getInitialAssignment($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumEvents(); $i++) {
    $sp = $m->getEvent($i);
    $sp->unsetNotes();

    for ($j =0; $j <$sp->getNumEventAssignments(); $j++) {
        $ea = $sp->getEventAssignment($j);
        $ea->unsetNotes();
    }
}
for ($i = 0; $i <$m->getNumSpeciesTypes(); $i++) {
    $sp = $m->getSpeciesType($i);
    $sp->unsetNotes();
}
for ($i = 0; $i <$m->getNumConstraints(); $i++) {
    $sp = $m->getConstraint($i);
    $sp->unsetNotes();
}
LibSBML::writeSBML($document, $ARGV[1]);

exit $errors;