Changeset - c32457e84c7f
Parent rev.
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0 14 0
Roeland Merks - 15 years ago 2010-10-14 11:56:01
roeland.merks@cwi.nl
Commit changes

user: Roeland Merks <roeland.merks@cwi.nl>
branch merge
branch 'default'
changed src/ChangeLog
changed src/TutorialCode/Tutorial3/ChangeLog
changed src/TutorialCode/Tutorial3/tutorial3.h
changed src/TutorialCode/Tutorial4/ChangeLog
changed src/TutorialCode/Tutorial4/tutorial4.h
changed src/TutorialCode/Tutorial5/ChangeLog
changed src/TutorialCode/Tutorial5/tutorial5.h
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
13 files changed with 39 insertions and 27 deletions:
src/TutorialCode/Tutorial3/ChangeLog
4
src/TutorialCode/Tutorial3/tutorial3.h
3
src/TutorialCode/Tutorial4/ChangeLog
4
src/TutorialCode/Tutorial4/tutorial4.h
3
src/TutorialCode/Tutorial5/ChangeLog
4
src/TutorialCode/Tutorial5/tutorial5.h
3
src/VirtualLeafpar.tmpl
1
1
src/canvas.cpp
9
14
src/canvas.h
2
src/parameter.cpp
5
6
src/parameter.h
1
1
src/pardialog.cpp
1
1
src/pardialog.h
1
2
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src/TutorialCode/Tutorial3/ChangeLog
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2010-10-14    <guravage@caterpie.sen.cwi.nl>
 

			




	
	
	
		
 
	* tutorial3.h (SimPluginInterface): Added default LeafML file.

			




	
	
	
		
 

			




	
	
	
		
 
2010-06-25    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial3.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

			




	
	
	
		
 

			




	
	
	
		
 
2010-06-23    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial3.pro: Corrected windows library path.

			




	
	
	
		
 

			




        

    


    
    

    

        

                

                    src/TutorialCode/Tutorial3/tutorial3.h
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *  $Id$

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  The Virtual Leaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  The Virtual Leaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
#include <QObject>

			




	
	
	
		
 
#include <QtGui>

			




	
	
	
		
 
#include <QString>

			




	
	
	
		
 
#include "simplugin.h"

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
class Tutorial3 : public QObject, SimPluginInterface {

			




	
	
	
		
 
	Q_OBJECT

			




	
	
	
		
 
	Q_INTERFACES(SimPluginInterface);

			




	
	
	
		
 

			




	
	
	
		
 
public:

			




	
	
	
		
 
	virtual QString ModelID(void);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// Executed after the cellular mechanics steps have equillibrized

			




	
	
	
		
 
	virtual void CellHouseKeeping (CellBase *c);

			




	
	
	
		
 
	// Differential equations describing transport of chemicals from cell to cell

			




	
	
	
		
 
	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);

			




	
	
	
		
 
    

			




	
	
	
		
 
	// Differential equations describing chemical reactions taking place at or near the cell walls

			




	
	
	
		
 
	// (e.g. PIN accumulation)

			




	
	
	
		
 
	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// Differential equations describing chemical reactions inside the cells

			




	
	
	
		
 
	virtual void CellDynamics(CellBase *c, double *dchem);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// to be executed after a cell division

			




	
	
	
		
 
	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// to be executed for coloring a cell

			




	
	
	
		
 
	virtual void SetCellColor(CellBase *c, QColor *color);	

			




	
	
	
		
 
	// return number of chemicals

			




	
	
	
		
 
	virtual int NChem(void);

			




	
	
	
		
 

			




	
	
	
		
 
	// default LeafML file

			




	
	
	
		
 
	virtual QString DefaultLeafML(void) { return QString("tutorial3_init.xml"); }

			




	
	
	
		
 
};

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 

			




        

    


    
    

    

        

                

                    src/TutorialCode/Tutorial4/ChangeLog
                

                

                  
                      
                        

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2010-10-14    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial4.h (SimPluginInterface): Added default LeafML file.

			




	
	
	
		
 

			




	
	
	
		
 
2010-06-25    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial4.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

			




	
	
	
		
 

			




	
	
	
		
 
2010-06-23    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial4.pro: Corrected windows library path.

			




	
	
	
		
 

			




        

    


    
    

    

        

                

                    src/TutorialCode/Tutorial4/tutorial4.h
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *  $Id$

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  The Virtual Leaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  The Virtual Leaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
#include <QObject>

			




	
	
	
		
 
#include <QtGui>

			




	
	
	
		
 
#include <QString>

			




	
	
	
		
 
#include "simplugin.h"

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
class Tutorial4 : public QObject, SimPluginInterface {

			




	
	
	
		
 
	Q_OBJECT

			




	
	
	
		
 
	Q_INTERFACES(SimPluginInterface);

			




	
	
	
		
 

			




	
	
	
		
 
public:

			




	
	
	
		
 
	virtual QString ModelID(void);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// Executed after the cellular mechanics steps have equillibrized

			




	
	
	
		
 
	virtual void CellHouseKeeping (CellBase *c);

			




	
	
	
		
 
	// Differential equations describing transport of chemicals from cell to cell

			




	
	
	
		
 
	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);

			




	
	
	
		
 
    

			




	
	
	
		
 
	// Differential equations describing chemical reactions taking place at or near the cell walls

			




	
	
	
		
 
	// (e.g. PIN accumulation)

			




	
	
	
		
 
	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// Differential equations describing chemical reactions inside the cells

			




	
	
	
		
 
	virtual void CellDynamics(CellBase *c, double *dchem);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// to be executed after a cell division

			




	
	
	
		
 
	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// to be executed for coloring a cell

			




	
	
	
		
 
	virtual void SetCellColor(CellBase *c, QColor *color);	

			




	
	
	
		
 
	// return number of chemicals

			




	
	
	
		
 
	virtual int NChem(void);

			




	
	
	
		
 
	

			




	
	
	
		
 
	virtual double PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w); 

			




	
	
	
		
 

			




	
	
	
		
 
	// default LeafML file

			




	
	
	
		
 
	virtual QString DefaultLeafML(void) { return QString("tutorial4_init.xml"); }

			




	
	
	
		
 
};

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 

			




        

    


    
    

    

        

                

                    src/TutorialCode/Tutorial5/ChangeLog
                

                

                  
                      
                        

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2010-10-14    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial5.h (SimPluginInterface): Added default LeafML file.

			




	
	
	
		
 

			




	
	
	
		
 
2010-06-25    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial5.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

			




	
	
	
		
 

			




	
	
	
		
 
2010-06-23    <guravage@caterpie.sen.cwi.nl>

			




	
	
	
		
 

			




	
	
	
		
 
	* tutorial5.pro: Corrected windows library path.

			




	
	
	
		
 

			




        

    


    
    

    

        

                

                    src/TutorialCode/Tutorial5/tutorial5.h
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *  $Id$

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  The Virtual Leaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  The Virtual Leaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
#include <QObject>

			




	
	
	
		
 
#include <QtGui>

			




	
	
	
		
 
#include <QString>

			




	
	
	
		
 
#include "simplugin.h"

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
class Tutorial5 : public QObject, SimPluginInterface {

			




	
	
	
		
 
	Q_OBJECT

			




	
	
	
		
 
	Q_INTERFACES(SimPluginInterface);

			




	
	
	
		
 

			




	
	
	
		
 
public:

			




	
	
	
		
 
	virtual QString ModelID(void);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// Executed after the cellular mechanics steps have equillibrized

			




	
	
	
		
 
	virtual void CellHouseKeeping (CellBase *c);

			




	
	
	
		
 
	// Differential equations describing transport of chemicals from cell to cell

			




	
	
	
		
 
	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);

			




	
	
	
		
 
    

			




	
	
	
		
 
	// Differential equations describing chemical reactions taking place at or near the cell walls

			




	
	
	
		
 
	// (e.g. PIN accumulation)

			




	
	
	
		
 
	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// Differential equations describing chemical reactions inside the cells

			




	
	
	
		
 
	virtual void CellDynamics(CellBase *c, double *dchem);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// to be executed after a cell division

			




	
	
	
		
 
	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);

			




	
	
	
		
 
	

			




	
	
	
		
 
	// to be executed for coloring a cell

			




	
	
	
		
 
	virtual void SetCellColor(CellBase *c, QColor *color);	

			




	
	
	
		
 
	// return number of chemicals

			




	
	
	
		
 
	virtual int NChem(void);

			




	
	
	
		
 
	

			




	
	
	
		
 
	virtual double PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w); 

			




	
	
	
		
 

			




	
	
	
		
 
	// default LeafML file

			




	
	
	
		
 
	virtual QString DefaultLeafML(void) { return QString("tutorial5_init.xml"); }

			




	
	
	
		
 
};

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 

			




        

    


    
    

    

        

                

                    src/VirtualLeafpar.tmpl
                

                

                  
                      
                        

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@@ -32,97 +32,97 @@ morphogen_expansion_threshold = 0.01 / d

			




	
	
	
		
 
copy_wall = true / bool

			




	
	
	
		
 
label = / label

			




	
	
	
		
 
label = <b>Auxin transport and PIN1 dynamics</b> / label

			




	
	
	
		
 
source = 0. / double

			




	
	
	
		
 
D = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist

			




	
	
	
		
 
initval = 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist

			




	
	
	
		
 
k1 = 1. / double

			




	
	
	
		
 
k2 = 0.3 / double

			




	
	
	
		
 
r = 1. / double

			




	
	
	
		
 
kr = 1. / double

			




	
	
	
		
 
#k3 = 1 / double

			




	
	
	
		
 
#k4 = 0.3 / double

			




	
	
	
		
 
km = 1. / double

			




	
	
	
		
 
Pi_tot = 1. / double

			




	
	
	
		
 
transport = 0.036 / double

			




	
	
	
		
 
ka = 1 / double

			




	
	
	
		
 
# d = 1e-06 / double

			




	
	
	
		
 
# e = 0.01 / double

			




	
	
	
		
 
# f = 10 / double

			




	
	
	
		
 
pin_prod = 0.001 / double

			




	
	
	
		
 
pin_prod_in_epidermis = 0.1 / double

			




	
	
	
		
 
pin_breakdown = 0.001 / double

			




	
	
	
		
 
pin_breakdown_internal = 0.001 / double

			




	
	
	
		
 
aux1prod = 0.001 / double

			




	
	
	
		
 
aux1prodmeso = 0. / double

			




	
	
	
		
 
aux1decay = 0.001 / double

			




	
	
	
		
 
aux1decaymeso = 0.1 / double

			




	
	
	
		
 
aux1transport = 0.036 / double

			




	
	
	
		
 
aux_cons = 0. / double

			




	
	
	
		
 
aux_breakdown = 0. / double

			




	
	
	
		
 
kaux1 = 1 / double

			




	
	
	
		
 
kap = 1 / double

			




	
	
	
		
 
leaf_tip_source = 0.001 / double

			




	
	
	
		
 
sam_efflux = 0.0001 / double

			




	
	
	
		
 
sam_auxin = 10. / double

			




	
	
	
		
 
# gf_prod = 1e-3 / double

			




	
	
	
		
 
# gf_decay = 1e-3 / double

			




	
	
	
		
 
sam_auxin_breakdown = 0 / double

			




	
	
	
		
 
#label = / label

			




	
	
	
		
 
#label = <b>miscellaneous</b> / label

			




	
	
	
		
 
van3prod = 0.002 / double

			




	
	
	
		
 
van3autokat = 0.1 / double

			




	
	
	
		
 
van3sat = 10 / double

			




	
	
	
		
 
k2van3 = 0.3 / double

			




	
	
	
		
 
#glvprod = 0.0 / double

			




	
	
	
		
 
#glvbreakdown = 0. / double

			




	
	
	
		
 
label = / label

			




	
	
	
		
 
label = <b>Integration parameters</b> / label

			




	
	
	
		
 
dt = 0.1 / double 

			




	
	
	
		
 
rd_dt = 1.0 / double

			




	
	
	
		
 
datadir = . / directory 

			




	
	
	
		
 
movie = false / bool

			




	
	
	
		
 
nit = 100000 / int

			




	
	
	
		
 
maxt = 1000. / double

			




	
	
	
		
 
storage_stride = 10 / int

			




	
	
	
		
 
xml_storage_stride = 500 / int

			




	
	
	
		
 
rseed = -1 / int

			




	
	
	
		
 
#label = / label

			




	
	
	
		
 
#label = <b>Parameters for new chemical</b> / label

			




	
	
	
		
 
#glvproduction = 0. / double

			




	
	
	
		
 
#glvdecay = 0. / double

			




	
	
	
		
 
#glvdiffthreshold = 0. / double

			




	
	
	
		
 
label = / label

			




	
	
	
		
 
label = <b>Meinhardt leaf venation model</b> / label

			




	
	
	
		
 
constituous_expansion_limit = 16 / int

			




	
	
	
		
 
vessel_inh_level = 1 / double

			




	
	
	
		
 
vessel_expansion_rate = 0.25 / double

			




	
	
	
		
 
d = 0. / double

			




	
	
	
		
 
e = 0. / double

			




	
	
	
		
 
f = 0. / double

			




	
	
	
		
 
c = 0. / double

			




	
	
	
		
 
mu = 0. / double

			




	
	
	
		
 
nu = 0. / double

			




	
	
	
		
 
rho0 = 0. / double

			




	
	
	
		
 
rho1 = 0. / double

			




	
	
	
		
 
c0 = 0. / double

			




	
	
	
		
 
gamma = 0. / double

			




	
	
	
		
 
eps = 0. / double

			




	
	
	
		
 
label = / label

			




	
	
	
		
 
label = <b>User-defined parameters</b> / label

			




	
	
	
		
 
k = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist

			




	
	
	
		
 
i1 = 0 / int

			




	
	
	
		
 
i2 = 0 / int

			




	
	
	
		
 
i3 = 0 / int

			




	
	
	
		
 
i4 = 0 / int

			




	
	
	
		
 
i5 = 0 / int

			




	
	
	
		
 
s1 =  / string

			




	
	
	
		
 
s2 =  / string

			




	
	
	
		
 
s3 =  / string

			




	
	
	
		
 
b1 = false / bool

			




	
	
	
		
 
b2 = false / bool

			




	
	
	
		
 
b3 = false / bool

			




	
	
	
		
 
b4 = false / bool

			




	
	
	
		
 
dir1 = . / directory

			




	
	
	
		
 
dir2 = . / directory

			




	
	
	
		
 
export_interval = 0 / int

			




	
	
	
		
 
export_fn_prefix = CellData_ / string

			




	
	
	
		
 
export_fn_prefix = cell. / string

			




        

    


    
    

    

        

                

                    src/canvas.cpp
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 
#include <time.h>

			




	
	
	
		
 
#include <string>

			




	
	
	
		
 
#include <fstream>

			




	
	
	
		
 
#include <streambuf>

			




	
	
	
		
 
#include <QGraphicsScene>

			




	
	
	
		
 
#include <QGraphicsView>

			




	
	
	
		
 
#include <qdatetime.h>

			




	
	
	
		
 
#include <q3mainwindow.h>

			




	
	
	
		
 
#include <qstatusbar.h>

			




	
	
	
		
 
#include <qmessagebox.h>

			




	
	
	
		
 
#include <qmenubar.h>

			




	
	
	
		
 
#include <qapplication.h>

			




	
	
	
		
 
#include <qpainter.h>

			




	
	
	
		
 
#include <qprinter.h>

			




	
	
	
		
 
#include <qlabel.h>

			




	
	
	
		
 
#include <qimage.h>

			




	
	
	
		
 
#include <q3progressdialog.h>

			




	
	
	
		
 
#include <qtimer.h>

			




	
	
	
		
 
#include <qslider.h>

			




	
	
	
		
 
#include <qpixmap.h>

			




	
	
	
		
 
#include <qfile.h>

			




	
	
	
		
 
#include <qdir.h>

			




	
	
	
		
 
#include <q3filedialog.h>

			




	
	
	
		
 
#include <QGraphicsItem>

			




	
	
	
		
 
#include <QList>

			




	
	
	
		
 
#include <QDir>

			




	
	
	
		
 

			




	
	
	
		
 
#include <QDebug>

			




	
	
	
		
 

			




	
	
	
		
 
#include <set>

			




	
	
	
		
 

			




	
	
	
		
 
//Added by qt3to4:

			




	
	
	
		
 
#include <Q3ValueList>

			




	
	
	
		
 
#include <Q3PopupMenu>

			




	
	
	
		
 
#include <QMouseEvent>

			




	
	
	
		
 
#include <typeinfo>

			




	
	
	
		
 
#include <cstring>

			




	
	
	
		
 
#include <q3process.h>

			




	
	
	
		
 
#include <qlayout.h>

			




	
	
	
		
 
#include <qspinbox.h>

			




	
	
	
		
 
#include <fstream>

			




	
	
	
		
 
#include <sstream>

			




	
	
	
		
 
#include "pardialog.h"

			




	
	
	
		
 
#include "parameter.h"

			




	
	
	
		
 
#include "canvas.h"

			




	
	
	
		
 
#include "node.h"

			




	
	
	
		
 
#include "nodeset.h"

			




	
	
	
		
 
#include "nodeitem.h"

			




	
	
	
		
 
#include "cellitem.h"

			




	
	
	
		
 
#include "wallitem.h"

			




	
	
	
		
 
#include "mesh.h"

			




	
	
	
		
 
#include "xmlwrite.h"

			




	
	
	
		
 
#include "miscq.h"

			




	
	
	
		
 
#include "OptionFileDialog.h"

			




	
	
	
		
 
#include <cstdlib>

			




	
	
	
		
 
#include <cstdio>

			




	
	
	
		
 
#include "modelcatalogue.h"

			




	
	
	
		
 

			




	
	
	
		
 
#include <algorithm>

			




	
	
	
		
 

			




	
	
	
		
 
// Include VIB and PSB logos

			




	
	
	
		
 
#include "psb.xpm"

			




	
	
	
		
 
#include "cwi.xpm"

			




	
	
	
		
 

			




	
	
	
		
 
static const std::string _module_id("$Id$");

			




	
	
	
		
 

			




	
	
	
		
 
using namespace std;

			




	
	
	
		
 

			




	
	
	
		
 
// We use a global variable to save memory - all the brushes and pens in

			




	
	
	
		
 
// the mesh are shared.

			




	
	
	
		
 

			




	
	
	
		
 
#define FNAMESIZE 100

			




	
	
	
		
 
#define QUOTE_ME(s) QUOTE_ME_2NDLEV(s)

			




	
	
	
		
 
#define QUOTE_ME_2NDLEV(s) #s

			




	
	
	
		
 

			




	
	
	
		
 
static QColor dark_red("darkRed");

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
static const int imageRTTI = 984376;

			




	
	
	
		
 
extern Parameter par;

			




	
	
	
		
 
const QString Main::caption("Virtual leaf");

			




	
	
	
		
 
const QString Main::caption_with_file("Virtual leaf: %1");

			




	
	
	
		
 

			




	
	
	
		
 
FigureEditor::FigureEditor(

			




	
	
	
		
 
			   QGraphicsScene& c, Mesh &m, QWidget* parent,

			




	
	
	
		
 
			   const char* name, Qt::WindowFlags f) :

			




	
	
	
		
 
  QGraphicsView(&c,parent), mesh(m)

			




	
	
	
		
 
{

			




	
	
	
		
 
  intersection_line = 0;

			




	
	
	
		
 
  //angle_line = 0;

			




	
	
	
		
 
  setInteractive(true);

			




	
	
	
		
 
  moving = 0;  

			




	
	
	
		
 
  rotation_mode = false;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void FigureEditor::clear()

			




	
	
	
		
 
{

			




	
	
	
		
 
  QList<QGraphicsItem *> list = scene()->items();

			




	
	
	
		
 
  QList<QGraphicsItem *>::Iterator it = list.begin();

			




	
	
	
		
 
  for (; it != list.end(); ++it) {

			




	
	
	
		
 
    delete *it;

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void FigureEditor::wheelEvent(QWheelEvent *event)

			




	
	
	
		
 
{

			




	
	
	
		
 
  scaleView(pow((double)2, -event->delta() / 240.0));

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void FigureEditor::scaleView (qreal scaleFactor)

			




	
	
	
		
 
{

			




	
	
	
		
 
  qreal factor = matrix().scale(scaleFactor, scaleFactor).mapRect(QRectF(0, 0, 1, 1)). width();

			




	
	
	
		
 
  if (factor < 0.07 || factor > 100) return;

			




	
	
	
		
 
  scale (scaleFactor, scaleFactor);

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void FigureEditor::Save(const char *fname, const char *format, int sizex, int sizey)

			




	
	
	
		
 
{

			




	
	
	
		
 

			




	
	
	
		
 
  QImage *image = new QImage(sizex, sizey, QImage::Format_RGB32);

			




	
	
	
		
 
  image->fill(QColor(Qt::white).rgb());

			




	
	
	
		
 
  QPainter *painter=new QPainter(image);

			




	
	
	
		
 

			




	
	
	
		
 
  render(painter);

			




	
	
	
		
 

			




	
	
	
		
 
  image->save(QString(fname),format);

			




	
	
	
		
 
  delete painter;

			




	
	
	
		
 
  delete image;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void FigureEditor::mousePressEvent(QMouseEvent* e)

			




	
	
	
		
 
{

			




	
	
	
		
 
  static QList<Node*> selected;

			




	
	
	
		
 
  emit MousePressed();

			




	
	
	
		
 

			




	
	
	
		
 
  //QPointF p = matrix().inverted().map(e->pos());

			




	
	
	
		
 
  QPointF p = mapToScene(e->pos());

			




	
	
	
		
 

			




	
	
	
		
 
#ifdef QDEBUG  

			




	
	
	
		
 
  qDebug() << endl << "MousePressEvent location: (" << p.x() << "," << p.y() << ")." << endl;

			




	
	
	
		
 
  qDebug() << "Magnification:  " << Cell::Magnification() << endl;

			




	
	
	
		
 
  qDebug() << "Offsets:  " << Cell::Offset() << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
  QList<QGraphicsItem *> l=scene()->items(p);

			




	
	
	
		
 

			




	
	
	
		
 
#ifdef QDEBUG  

			




	
	
	
		
 
  qDebug() << "MousePressEvents, items: " << l.size() << endl;

			




	
	
	
		
 
  qDebug() << "Mouse button modifier: " << e->modifiers() << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




	
	
	
		
 
  if (e->button()==Qt::RightButton || l.size()==0) {

			




	
	
	
		
 

			




	
	
	
		
 
    //cerr << "Drawing an intersection line from " << p.x() << ", " << p.y() << endl;

			




	
	
	
		
 
    intersection_line = new QGraphicsLineItem( 0, scene() );

			




	
	
	
		
 
    intersection_line->setPen( QPen( QColor("red"), 3, Qt::DashLine ) );

			




	
	
	
		
 
    intersection_line->setLine( QLineF(p,p) );

			




	
	
	
		
 
    intersection_line->setZValue( 100 );

			




	
	
	
		
 
    intersection_line->show();

			




	
	
	
		
 
  }

			




	
	
	
		
 

			




	
	
	
		
 
  for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {

			




	
	
	
		
 
#ifdef QDEBUG

			




	
	
	
		
 
    qDebug() << typeid(**it).name() << endl;

			




	
	
	
		
 
#endif

			




	
	
		
 
@@ -387,193 +388,193 @@ void FigureEditor::mouseReleaseEvent(QMo

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
// returns a vector of pointer to cells colliding with intersection line

			




	
	
	
		
 
vector <CellItem *> FigureEditor::getIntersectedCells(void)

			




	
	
	
		
 
{ 

			




	
	
	
		
 
  vector <CellItem *> colliding_cells;

			




	
	
	
		
 

			




	
	
	
		
 
  QList<QGraphicsItem *> l = intersection_line->collidingItems( );

			




	
	
	
		
 

			




	
	
	
		
 
#ifdef QDEBUG

			




	
	
	
		
 
  qDebug() <<  "l.size() = " << l.size() << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




	
	
	
		
 
  for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {

			




	
	
	
		
 

			




	
	
	
		
 
#ifdef QDEBUG

			




	
	
	
		
 
    qDebug() << typeid(**it).name() << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




	
	
	
		
 
    if ( !strcmp(typeid(**it).name(),"8CellItem") ) {

			




	
	
	
		
 
      colliding_cells.push_back(dynamic_cast<CellItem *>(*it));

			




	
	
	
		
 
    }

			




	
	
	
		
 
  }

			




	
	
	
		
 

			




	
	
	
		
 
  delete intersection_line;

			




	
	
	
		
 
  intersection_line = 0;

			




	
	
	
		
 
  return colliding_cells;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void FigureEditor::FullRedraw(void)

			




	
	
	
		
 
{

			




	
	
	
		
 
  QList<QRectF> rl;

			




	
	
	
		
 
  rl << sceneRect();

			




	
	
	
		
 
  updateScene(rl);   

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
NodeItem *FigureEditor::selectedNodeItem(QList<QGraphicsItem *> graphicItems) const

			




	
	
	
		
 
{

			




	
	
	
		
 
  NodeItem *nodeItem = 0;

			




	
	
	
		
 
  // graphicItems is a list of the QgraphicItems under the mouse click event 

			




	
	
	
		
 
  QList<QGraphicsItem *>::Iterator it = graphicItems.begin();

			




	
	
	
		
 
  for (; it != graphicItems.end(); ++it) {

			




	
	
	
		
 
    if ( !strcmp(typeid(**it).name(),"8NodeItem")) {

			




	
	
	
		
 
      // the object under the mouse click is a Nodeitem

			




	
	
	
		
 
      nodeItem = dynamic_cast<NodeItem *>(*it);

			




	
	
	
		
 
      // indicate we've selected it

			




	
	
	
		
 
      nodeItem->setBrush(dark_red);

			




	
	
	
		
 
      break;

			




	
	
	
		
 
    }

			




	
	
	
		
 
  }

			




	
	
	
		
 
  return nodeItem;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void FigureEditor::insertNode(QPointF p)

			




	
	
	
		
 
{

			




	
	
	
		
 
  Node *node = new Node(p.x(), p.y(), 0);

			




	
	
	
		
 
  mesh.AddNode(node);

			




	
	
	
		
 
  scene()->clearSelection();

			




	
	
	
		
 
  dynamic_cast<Main *>(parent())->Plot();

			




	
	
	
		
 
  FullRedraw();

			




	
	
	
		
 
#ifdef QDEBUG  

			




	
	
	
		
 
  qDebug() << "Node: " << p << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
static uint mainCount = 0;

			




	
	
	
		
 

			




	
	
	
		
 
Main::Main(QGraphicsScene& c, Mesh &m, QWidget* parent, const char* name, Qt::WindowFlags f) :

			




	
	
	
		
 
  Q3MainWindow(parent,name,f),

			




	
	
	
		
 
  MainBase(c,m),

			




	
	
	
		
 
  mesh(m)

			




	
	
	
		
 
{

			




	
	
	
		
 
  editor = new FigureEditor(canvas,mesh, this);

			




	
	
	
		
 

			




	
	
	
		
 
#ifdef QDEBUG

			




	
	
	
		
 
  qDebug() << "Interactive = " << editor->isEnabled();

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




	
	
	
		
 
  working_dir = 0;

			




	
	
	
		
 
  QObject::connect( editor, SIGNAL(MousePressed()), this, SLOT(PauseIfRunning()));

			




	
	
	
		
 
  QObject::connect( editor, SIGNAL(MouseReleased()), this, SLOT(ContIfRunning()));

			




	
	
	
		
 
  QMenuBar* menu = menuBar();

			




	
	
	
		
 

			




	
	
	
		
 
  Q3PopupMenu* file = new Q3PopupMenu( menu );

			




	
	
	
		
 

			




	
	
	
		
 
  file->insertItem("&Read leaf", this, SLOT(readStateXML()));

			




	
	
	
		
 
  file->insertItem("&Save leaf", this, SLOT(saveStateXML()));

			




	
	
	
		
 
  file->insertItem("Snapshot", this, SLOT(snapshot()), Qt::CTRL+Qt::SHIFT+Qt::Key_S);

			




	
	
	
		
 

			




	
	
	
		
 
  file->insertSeparator();

			




	
	
	
		
 
  file->insertItem("Read next leaf", this, SLOT(readNextStateXML()), Qt::Key_PageDown);

			




	
	
	
		
 
  file->insertItem("Read previous leaf", this, SLOT(readPrevStateXML()), Qt::Key_PageUp);

			




	
	
	
		
 
  file->insertItem("Read last leaf", this, SLOT(readLastStateXML()), Qt::Key_End);

			




	
	
	
		
 
  file->insertItem("Read first leaf", this, SLOT(readFirstStateXML()), Qt::Key_Home);

			




	
	
	
		
 
  file->insertItem("Export cell areas", this, SLOT(exportCellData()));

			




	
	
	
		
 
  file->insertItem("Export cell data", this, SLOT(exportCellData()));

			




	
	
	
		
 

			




	
	
	
		
 
  file->insertSeparator();

			




	
	
	
		
 
  file->insertItem("&Print...", this, SLOT(print()), Qt::CTRL+Qt::Key_P);

			




	
	
	
		
 
  file->insertSeparator();

			




	
	
	
		
 
  file->insertItem("E&xit", qApp, SLOT(quit()), Qt::CTRL+Qt::Key_Q);

			




	
	
	
		
 
  menu->insertItem("&File", file);

			




	
	
	
		
 

			




	
	
	
		
 
  Q3PopupMenu* edit = new Q3PopupMenu( menu );

			




	
	
	
		
 
  edit->insertItem("Reset Chemicals and Transporters", this, SLOT( CleanMesh()), Qt::CTRL+Qt::Key_R );

			




	
	
	
		
 
  edit->insertItem("Reset Chemicals", this, SLOT( CleanMeshChemicals()) );

			




	
	
	
		
 
  edit->insertItem("Reset Transporters", this, SLOT( CleanMeshTransporters()) );

			




	
	
	
		
 
  edit->insertItem("Randomize PIN1 Transporters", this, SLOT( RandomizeMesh()) );

			




	
	
	
		
 
  edit->insertItem("Cut away SAM", this, SLOT( CutSAM() ));

			




	
	
	
		
 
  menu->insertItem("&Edit", edit);

			




	
	
	
		
 

			




	
	
	
		
 
  run = new Q3PopupMenu( menu );

			




	
	
	
		
 
  running = false;

			




	
	
	
		
 
  paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);

			




	
	
	
		
 
  run->setItemChecked(paused_id, FALSE);

			




	
	
	
		
 

			




	
	
	
		
 
  menu->insertItem("&Run", run);

			




	
	
	
		
 

			




	
	
	
		
 
  view = new Q3PopupMenu( menu );

			




	
	
	
		
 
  view->insertItem("&Zoom in", this, SLOT(zoomIn()), Qt::CTRL+Qt::Key_Equal);

			




	
	
	
		
 
  view->insertItem("Zoom &out", this, SLOT(zoomOut()), Qt::CTRL+Qt::Key_Minus);

			




	
	
	
		
 
  view->insertSeparator();

			




	
	
	
		
 
  com_id = view->insertItem("Show cell &centers", this, SLOT(toggleShowCellCenters()));

			




	
	
	
		
 
  view->setItemChecked(com_id, FALSE);

			




	
	
	
		
 

			




	
	
	
		
 
  mesh_id = view->insertItem("Show &nodes", this, SLOT(toggleShowNodes()), Qt::CTRL+Qt::SHIFT+Qt::Key_N);

			




	
	
	
		
 
  view->setItemChecked(mesh_id, TRUE);

			




	
	
	
		
 
  node_number_id = view->insertItem("Show node numbers", this, SLOT(toggleNodeNumbers()), Qt::CTRL+Qt::SHIFT+Qt::Key_M);

			




	
	
	
		
 
  view->setItemChecked(node_number_id, FALSE);

			




	
	
	
		
 
  cell_number_id = view->insertItem("Show cell numbers", this, SLOT(toggleCellNumbers()));

			




	
	
	
		
 
  view->setItemChecked(cell_number_id, FALSE);

			




	
	
	
		
 
  hide_cells_id = view->insertItem("Hide cells", this, SLOT(toggleHideCells()));

			




	
	
	
		
 
  view->setItemChecked(hide_cells_id, FALSE);

			




	
	
	
		
 
  border_id = view->insertItem("Show &border cells", this, SLOT(toggleShowBorderCells()));

			




	
	
	
		
 
  view->setItemChecked(border_id, FALSE);

			




	
	
	
		
 
  cell_axes_id = view->insertItem("Show cell &axes", this, SLOT(toggleCellAxes()));

			




	
	
	
		
 
  cell_strain_id = view->insertItem("Show cell &strain", this, SLOT(toggleCellStrain()));

			




	
	
	
		
 
  view->setItemChecked(cell_axes_id, FALSE);

			




	
	
	
		
 
  fluxes_id = view->insertItem("Show &fluxes", this, SLOT(toggleShowFluxes()));

			




	
	
	
		
 
  view->setItemChecked(fluxes_id, FALSE);

			




	
	
	
		
 
  cell_walls_id = view->insertItem("Show transporters", this, SLOT(toggleShowWalls()));

			




	
	
	
		
 
  view->setItemChecked(cell_walls_id, FALSE);

			




	
	
	
		
 
 // apoplasts_id = view->insertItem("Show apoplasts", this, SLOT(toggleShowApoplasts()));

			




	
	
	
		
 
 // view->setItemChecked(apoplasts_id, FALSE);

			




	
	
	
		
 
  view->insertSeparator();

			




	
	
	
		
 
  only_boundary_id = view->insertItem("Show only leaf &boundary", this, SLOT(toggleLeafBoundary()));

			




	
	
	
		
 
  view->insertSeparator();

			




	
	
	
		
 
  movie_frames_id = view->insertItem("Start saving movie &frames", this, SLOT(toggleMovieFrames()));

			




	
	
	
		
 
  view->setItemChecked(movie_frames_id, par.movie);

			




	
	
	
		
 

			




	
	
	
		
 
  view->setItemChecked(only_boundary_id, FALSE);

			




	
	
	
		
 
  menu->insertItem("&View", view);

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
  options = new Q3PopupMenu( menu );

			




	
	
	
		
 
  dyn_cells_id = options->insertItem("Cell growth", this, SLOT(toggleDynCells()));

			




	
	
	
		
 
  options->setItemChecked(dyn_cells_id, true);

			




	
	
	
		
 

			




	
	
	
		
 
  options->insertItem("Edit &parameters", this, SLOT(EditParameters()), Qt::CTRL+Qt::Key_E);

			




	
	
	
		
 

			




	
	
	
		
 
  rotation_mode_id = options->insertItem("Rotate leaf", this, SLOT(EnterRotationMode()), Qt::CTRL + Qt::SHIFT + Qt::Key_R);

			




	
	
	
		
 
  options->setItemChecked(rotation_mode_id, false);

			




	
	
	
		
 

			




	
	
	
		
 
  menu->insertItem("&Options",options);

			




	
	
	
		
 

			




	
	
	
		
 
  // Menu of models

			




	
	
	
		
 
  modelmenu = new QMenu( menu );

			




	
	
	
		
 
  menu->insertItem("&Models", modelmenu);

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
  menu->insertSeparator();

			




	
	
	
		
 

			




	
	
	
		
 
  helpmenu = new Q3PopupMenu( menu );

			




	
	
	
		
 
  tooltips_id = helpmenu->insertItem("Show Cell&Info", this, SLOT(Refresh()));

			




	
	
	
		
 
  helpmenu->setItemChecked(tooltips_id, true);

			




	
	
	
		
 
  helpmenu->insertSeparator();

			




	
	
	
		
 
    //helpmenu->insertSeparator();

			




	
	
	
		
 
  helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) );

			




	
	
	
		
 
  helpmenu->insertItem("About", this, SLOT(about()) ); //, Key_F1);

			




	
	
	
		
 
	

			




	
	
	
		
 
	menu->insertItem("&Help",helpmenu);

			




	
	
	
		
 
  statusBar();

			




	
	
	
		
 
  setCentralWidget(editor);

			




	
	
	
		
 
  printer = 0;

			




	
	
	
		
 
  init();

			




	
	
	
		
 

			




	
	
	
		
 
  // Start timer which repetitively invokes

			




	
	
	
		
 
  // a simulation time step

			




	
	
	
		
 
  timer = new QTimer( this );

			




	
	
	
		
 
  connect( timer, SIGNAL(timeout()), SLOT(TimeStepWrap()) );

			




	
	
	
		
 

			




	
	
	
		
 
  stopSimulation();

			




	
	
		
 
@@ -1072,218 +1073,212 @@ void Main::startSimulation(void)

			




	
	
	
		
 
void Main::stopSimulation(void)

			




	
	
	
		
 
{

			




	
	
	
		
 
  timer->stop();

			




	
	
	
		
 
  cerr << "Stopping simulation" << endl;

			




	
	
	
		
 
  statusBar()->message("Simulation paused");

			




	
	
	
		
 
  running = false;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::togglePaused()

			




	
	
	
		
 
{

			




	
	
	
		
 
  bool s = run->isItemChecked(paused_id);

			




	
	
	
		
 
  if (s) {

			




	
	
	
		
 
    cerr << "Calling start simulation" << endl;

			




	
	
	
		
 
    startSimulation();

			




	
	
	
		
 
  } else {

			




	
	
	
		
 
    cerr << "Calling stop simulation" << endl;

			




	
	
	
		
 
    stopSimulation();

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::setFluxArrowSize(int size)

			




	
	
	
		
 
{

			




	
	
	
		
 
  flux_arrow_size = size/100.;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void Main::enlarge()

			




	
	
	
		
 
{

			




	
	
	
		
 
  canvas.setSceneRect( QRectF( 0,0, canvas.width()*4./3., canvas.height()*4./3.) );

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::shrink()

			




	
	
	
		
 
{

			




	
	
	
		
 
  canvas.setSceneRect( QRectF( 0,0, canvas.width()*3/4, canvas.height()*3/4) );

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void Main::scale(double factor)

			




	
	
	
		
 
{

			




	
	
	
		
 
  QMatrix m = editor->matrix();

			




	
	
	
		
 
  m.scale(factor, factor);

			




	
	
	
		
 
  editor->setMatrix( m );

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::zoomIn()

			




	
	
	
		
 
{

			




	
	
	
		
 
  QMatrix m = editor->matrix();

			




	
	
	
		
 
  m.scale( 1.1, 1.1 );

			




	
	
	
		
 
  editor->setMatrix( m );

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::zoomOut()

			




	
	
	
		
 
{

			




	
	
	
		
 
  QMatrix m = editor->matrix();

			




	
	
	
		
 
  m.scale( 0.9, 0.9 );

			




	
	
	
		
 
  editor->setMatrix( m );

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void Main::print()

			




	
	
	
		
 
{

			




	
	
	
		
 
  if ( !printer ) printer = new QPrinter;

			




	
	
	
		
 

			




	
	
	
		
 
  if ( printer->setup(this) ) {

			




	
	
	
		
 

			




	
	
	
		
 
    //    extern Mesh mesh;

			




	
	
	
		
 
    Vector bbll,bbur;

			




	
	
	
		
 
    mesh.BoundingBox(bbll,bbur);

			




	
	
	
		
 

			




	
	
	
		
 
#ifdef QDEBUG

			




	
	
	
		
 
    qDebug() << "bbll = " << bbll << endl;

			




	
	
	
		
 
    qDebug() << "bbur = " << bbur << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 
    double cw = (bbur.x - bbll.x);

			




	
	
	
		
 
    double ch = (bbur.y - bbll.y);

			




	
	
	
		
 
    QPainter pp(printer);

			




	
	
	
		
 
    QRect vp=pp.viewport();

			




	
	
	
		
 
#ifdef QDEBUG

			




	
	
	
		
 
    qDebug() << "Paper width = " << vp.width() << " x " << vp.height() << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




	
	
	
		
 
    // Note that Cell is also translated...

			




	
	
	
		
 
    pp.translate(-bbur.x,-bbur.y);

			




	
	
	
		
 
    if (cw>ch) {

			




	
	
	
		
 
      pp.scale(vp.width()/(2*cw*Cell::Magnification()), vp.width()/(2*cw*Cell::Magnification()));

			




	
	
	
		
 
    } else {

			




	
	
	
		
 
      pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));

			




	
	
	
		
 
    }

			




	
	
	
		
 
    canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void Main::TimeStepWrap(void)

			




	
	
	
		
 
{

			




	
	
	
		
 
  static int t=0;

			




	
	
	
		
 
  stringstream fname;

			




	
	
	
		
 

			




	
	
	
		
 
  TimeStep();

			




	
	
	
		
 
  t++;

			




	
	
	
		
 

			




	
	
	
		
 
  if ((par.export_interval > 0) && ((t % par.export_interval) == 0)){

			




	
	
	
		
 
    this->exportCellData(QString(par.datadir) + QString('/') + QString(par.export_fn_prefix) + this->TimeStamp());

			




	
	
	
		
 
    fname << par.datadir << "/" << par.export_fn_prefix;

			




	
	
	
		
 
    fname.fill('0');

			




	
	
	
		
 
    fname.width(6);

			




	
	
	
		
 
    fname << t << ".csv";

			




	
	
	
		
 
    this->exportCellData(QString(fname.str().c_str()));

			




	
	
	
		
 
  }

			




	
	
	
		
 

			




	
	
	
		
 
  // check number of timesteps

			




	
	
	
		
 
  if (t==par.nit) {

			




	
	
	
		
 
    emit SimulationDone();

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
QString Main::TimeStamp(){

			




	
	
	
		
 
  time_t rawtime;

			




	
	
	
		
 
  struct tm * timeinfo;

			




	
	
	
		
 
  char buffer [15];

			




	
	
	
		
 

			




	
	
	
		
 
  time ( &rawtime );

			




	
	
	
		
 
  timeinfo = localtime ( &rawtime );

			




	
	
	
		
 
  strftime (buffer,15,"%Y%m%d%H%M%S",timeinfo);

			




	
	
	
		
 
  return QString(buffer);

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void Main::RestartSim(void)

			




	
	
	
		
 
{

			




	
	
	
		
 

			




	
	
	
		
 
  stopSimulation();

			




	
	
	
		
 
  if ( QMessageBox::question(

			




	
	
	
		
 
			     this,

			




	
	
	
		
 
			     tr("Restart simulation?"),

			




	
	
	
		
 
			     tr("Restart simulation.\n"

			




	
	
	
		
 
				"Are you sure?"),

			




	
	
	
		
 
			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {

			




	
	
	
		
 

			




	
	
	
		
 
    cerr << "Restarting simulation" << endl;

			




	
	
	
		
 
    //    extern Mesh mesh;

			




	
	
	
		
 
    mesh.Clear();

			




	
	
	
		
 
    Init();

			




	
	
	
		
 
    Plot();

			




	
	
	
		
 
    editor->FullRedraw();

			




	
	
	
		
 
  } 

			




	
	
	
		
 
  //startSimulation();

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void Main::FitCanvasToWindow(void)

			




	
	
	
		
 
{

			




	
	
	
		
 

			




	
	
	
		
 
  double scale_factor_x = (double)editor->width()/(double)canvas.width();

			




	
	
	
		
 
  double scale_factor_y = (double)editor->height()/(double)canvas.height();

			




	
	
	
		
 
  double scale_factor = scale_factor_x > scale_factor_y ? scale_factor_x : scale_factor_y;

			




	
	
	
		
 
  QMatrix m = editor->matrix();

			




	
	
	
		
 

			




	
	
	
		
 
#ifdef QDEBUG  

			




	
	
	
		
 
  qDebug() << "editor->width() = " << editor->width() << endl;

			




	
	
	
		
 
  qDebug() << "editor->height() = " << editor->height() << endl;

			




	
	
	
		
 

			




	
	
	
		
 
  qDebug() << "scale_factor = " << scale_factor << endl;

			




	
	
	
		
 
  qDebug() << "scale_factor_x = " << scale_factor_x << endl;

			




	
	
	
		
 
  qDebug() << "scale_factor_y = " << scale_factor_y << endl;

			




	
	
	
		
 
#endif

			




	
	
	
		
 
  m.scale( scale_factor, scale_factor );

			




	
	
	
		
 
  editor->setMatrix( m );

			




	
	
	
		
 
  editor->show();

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::PauseIfRunning(void)

			




	
	
	
		
 
{

			




	
	
	
		
 
  if (running) {

			




	
	
	
		
 
    timer->stop();

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::ContIfRunning(void)

			




	
	
	
		
 
{

			




	
	
	
		
 
  if (running) {

			




	
	
	
		
 
    timer->start( 0 );

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::FitLeafToCanvas(void) 

			




	
	
	
		
 
{

			




	
	
	
		
 

			




	
	
	
		
 
  Vector ll,ur;

			




	
	
	
		
 
  mesh.BoundingBox(ll, ur);

			




	
	
	
		
 

			




	
	
	
		
 
  ll*=Cell::Magnification(); ur*=Cell::Magnification();

			




	
	
	
		
 

			




	
	
	
		
 
  // give the leaf some space

			




	
	
	
		
 
  Vector border = ((ur-ll)/5.);

			




	
	
	
		
 

			




	
	
	
		
 
  QRectF bb( ll.x - border.x, ll.y - border.y, ur.x-ll.x + 2*border.x, ur.y-ll.y + 2*border.y );

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
  // cerr << ur << ", " << ll << endl;

			




	
	
	
		
 
  // editor->fitInView(bb, Qt::KeepAspectRatio);

			




	
	
	
		
 
  editor->ensureVisible(bb);

			




	
	
	
		
 
  //editor->setTransform(viewport);

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Main::CleanMesh(void) 

			




	
	
	
		
 
{

			




	
	
	
		
 
  vector<double> clean_chem(Cell::NChem());

			




	
	
	
		
 
  vector<double> clean_transporters(Cell::NChem());

			




	
	
	
		
 

			




	
	
	
		
 
  for (int i=0;i<Cell::NChem();i++) {

			




	
	
	
		
 
    clean_chem[i]=par.initval[i];

			




	
	
	
		
 
    clean_transporters[i]=0.;		

			




	
	
	
		
 
  }

			




	
	
	
		
 

			




	
	
	
		
 
  mesh.CleanChemicals(clean_chem);

			




	
	
	
		
 
  mesh.CleanTransporters(clean_transporters);

			




	
	
	
		
 

			




	
	
	
		
 
  mesh.setTime(0);

			




	
	
	
		
 
  Plot();

			




	
	
	
		
 

			




	
	
	
		
 
  editor->FullRedraw();

			




	
	
	
		
 
}

			




	
	
	
		
 

			




        

    


    
    

    

        

                

                    src/canvas.h
                

                

                  
                      
                        

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@@ -134,150 +134,148 @@ class Main : public Q3MainWindow, public

			




	
	
	
		
 
  }

			




	
	
	
		
 

			




	
	
	
		
 
  void FitCanvasToWindow();

			




	
	
	
		
 
  void FitLeafToCanvas(void);

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
  public slots:

			




	
	
	
		
 

			




	
	
	
		
 
  void about();

			




	
	
	
		
 
  void gpl();

			




	
	
	
		
 
  void TimeStepWrap();

			




	
	
	
		
 
  void togglePaused();

			




	
	
	
		
 
  void setFluxArrowSize(int size);

			




	
	
	
		
 
  void RestartSim(void);

			




	
	
	
		
 
  void toggleShowCellCenters(void);

			




	
	
	
		
 
  void toggleShowNodes(void);

			




	
	
	
		
 
  void toggleShowBorderCells(void);

			




	
	
	
		
 
  void toggleShowFluxes(void);

			




	
	
	
		
 
  void toggleNodeNumbers(void);

			




	
	
	
		
 
  void toggleCellNumbers(void);

			




	
	
	
		
 
  void toggleCellAxes(void);

			




	
	
	
		
 
  void toggleCellStrain(void);

			




	
	
	
		
 
  void toggleShowWalls(void);

			




	
	
	
		
 
  void toggleShowApoplasts(void);

			




	
	
	
		
 
  void toggleDynCells(void);

			




	
	
	
		
 
  void toggleMovieFrames(void);

			




	
	
	
		
 
  void toggleLeafBoundary(void);

			




	
	
	
		
 
  void toggleHideCells(void);

			




	
	
	
		
 
  void print();

			




	
	
	
		
 
  void startSimulation(void);

			




	
	
	
		
 
  void stopSimulation(void);

			




	
	
	
		
 
  void RefreshInfoBar(void);

			




	
	
	
		
 

			




	
	
	
		
 
  void EnterRotationMode(void)

			




	
	
	
		
 
  {

			




	
	
	
		
 

			




	
	
	
		
 
    UserMessage("Rotation mode. Click mouse to exit.");

			




	
	
	
		
 
    if (editor) {

			




	
	
	
		
 
      editor->rot_angle = 0. ; 

			




	
	
	
		
 

			




	
	
	
		
 
      // Exit rotation mode if mouse is clicked

			




	
	
	
		
 
      connect(editor, SIGNAL(MousePressed()), this, SLOT(ExitRotationMode()));

			




	
	
	
		
 
      

			




	
	
	
		
 
      editor->setMouseTracking(true);

			




	
	
	
		
 

			




	
	
	
		
 
    }

			




	
	
	
		
 

			




	
	
	
		
 
  }

			




	
	
	
		
 
  void ExitRotationMode(void)

			




	
	
	
		
 
  { 

			




	
	
	
		
 
    UserMessage("Exited rotation mode.",2000);

			




	
	
	
		
 

			




	
	
	
		
 
    options->setItemChecked(rotation_mode_id, false); 

			




	
	
	
		
 
    if (editor)

			




	
	
	
		
 
      disconnect(editor, SIGNAL(MousePressed()), this, SLOT(ExitRotationMode()));

			




	
	
	
		
 
    editor->setMouseTracking(false);

			




	
	
	
		
 
 

			




	
	
	
		
 
  }

			




	
	
	
		
 

			




	
	
	
		
 
  virtual void UserMessage(QString message, int timeout=0);

			




	
	
	
		
 
  void Refresh(void) { Plot(); }

			




	
	
	
		
 
  void PauseIfRunning(void);

			




	
	
	
		
 
  void ContIfRunning(void);

			




	
	
	
		
 
  virtual void XMLReadSettings(xmlNode *settings);

			




	
	
	
		
 

			




	
	
	
		
 
  private slots:

			




	
	
	
		
 
  void aboutQt();

			




	
	
	
		
 
  void newView();

			




	
	
	
		
 
  void EditParameters();

			




	
	
	
		
 
  void readStateXML();

			




	
	
	
		
 
  int readStateXML(const char *filename, bool geometry = true, bool pars=true, bool simtime = true);

			




	
	
	
		
 
  void readNextStateXML();

			




	
	
	
		
 
  void readPrevStateXML();

			




	
	
	
		
 
  void readFirstStateXML();

			




	
	
	
		
 
  void readLastStateXML();

			




	
	
	
		
 
  void exportCellData();

			




	
	
	
		
 
  void exportCellData(QString);

			




	
	
	
		
 
  void saveStateXML();

			




	
	
	
		
 
  void snapshot();

			




	
	
	
		
 
  void savePars();

			




	
	
	
		
 
  void readPars();

			




	
	
	
		
 
  void clear();

			




	
	
	
		
 
  void init();

			




	
	
	
		
 
  virtual void CutSAM() { MainBase::CutSAM(); Refresh();}

			




	
	
	
		
 

			




	
	
	
		
 
  void enlarge();

			




	
	
	
		
 
  void shrink();

			




	
	
	
		
 
  void zoomIn();

			




	
	
	
		
 
  void zoomOut();

			




	
	
	
		
 

			




	
	
	
		
 
  void CleanMesh();

			




	
	
	
		
 
  void CleanMeshChemicals(void);

			




	
	
	
		
 
  void CleanMeshTransporters(void);

			




	
	
	
		
 

			




	
	
	
		
 
  void RandomizeMesh();

			




	
	
	
		
 

			




	
	
	
		
 
  QString TimeStamp();

			




	
	
	
		
 

			




	
	
	
		
 
 signals:

			




	
	
	
		
 
  void SimulationDone(void);

			




	
	
	
		
 
  void ParsChanged(void);

			




	
	
	
		
 

			




	
	
	
		
 
 protected:

			




	
	
	
		
 
  Mesh &mesh;

			




	
	
	
		
 

			




	
	
	
		
 
 private:

			




	
	
	
		
 
  NodeSet *node_set;

			




	
	
	
		
 
  FigureEditor *editor;

			




	
	
	
		
 
  Q3PopupMenu* options;

			




	
	
	
		
 
  Q3PopupMenu *view;

			




	
	
	
		
 
  Q3PopupMenu *run;

			




	
	
	
		
 
  QMenu *modelmenu;

			




	
	
	
		
 
  Q3PopupMenu *helpmenu;

			




	
	
	
		
 

			




	
	
	
		
 
  QPrinter* printer;

			




	
	
	
		
 
  const QDir *working_dir;

			




	
	
	
		
 
  QString currentFile;

			




	
	
	
		
 
  //  toggle item states 

			




	
	
	
		
 
  int dbf_id; // options->Double Buffer

			




	
	
	
		
 
  int com_id; // view->Show centers

			




	
	
	
		
 
  int mesh_id; // view->Show mesh

			




	
	
	
		
 
  int node_number_id; // view->Show Node numbers

			




	
	
	
		
 
  int cell_number_id; // view->Show Cell numbers

			




	
	
	
		
 
  int border_id; // view->Show border cells

			




	
	
	
		
 
  int paused_id; // run->Simulation paused

			




	
	
	
		
 
  int cell_axes_id; // view->Show cell axes

			




	
	
	
		
 
  int cell_strain_id; // view->Show cell strain

			




	
	
	
		
 
  int only_boundary_id; // view ->Show only leaf boundary

			




	
	
	
		
 
  int cell_walls_id; // view -> Show transporters

			




	
	
	
		
 
  //int apoplasts_id; // view -> Show apoplasts

			




	
	
	
		
 
  int tooltips_id; // help -> Show Cell Info

			




	
	
	
		
 
  int hide_cells_id; // view->Hide Cells

			




	
	
	
		
 
  double flux_arrow_size;

			




	
	
	
		
 
  int movie_frames_id;

			




	
	
	
		
 
  int fluxes_id;

			




	
	
	
		
 
  int dyn_cells_id;

			




	
	
	
		
 
  int rotation_mode_id;

			




	
	
	
		
 
  int insert_mode_id;

			




	
	
	
		
 
  QTimer *timer;

			




	
	
	
		
 
  QFile *gifanim;

			




	
	
	
		
 
  bool running;

			




	
	
	
		
 
  virtual xmlNode *XMLSettingsTree(void);

			




	
	
	
		
 
  static const QString caption;

			




	
	
	
		
 
  static const QString caption_with_file;

			




	
	
	
		
 
  InfoBar *infobar;

			




	
	
	
		
 
};

			




	
	
	
		
 

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




	
	
	
		
 
/* finis*/

			




        

    


    
    

    

        

                

                    src/parameter.cpp
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 
// WARNING: This file is automatically generated by make_parameter_source.pl.

			




	
	
	
		
 
// Do not edit. All edits will be discarded.

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
#include "parameter.h"

			




	
	
	
		
 
#include <cstdio>

			




	
	
	
		
 
#include <cstring>

			




	
	
	
		
 
#include <cstdlib>

			




	
	
	
		
 
#include <cerrno>

			




	
	
	
		
 
#include <iostream>

			




	
	
	
		
 
#include <sstream>

			




	
	
	
		
 
#include "output.h"

			




	
	
	
		
 
#include "parse.h"

			




	
	
	
		
 
#include "xmlwrite.h"

			




	
	
	
		
 
#include "warning.h"

			




	
	
	
		
 
#include <QLocale>

			




	
	
	
		
 
#include <QDir>

			




	
	
	
		
 
#include <QStringList>

			




	
	
	
		
 

			




	
	
	
		
 
using namespace std;

			




	
	
	
		
 

			




	
	
	
		
 
static const std::string _module_id("$Id$");

			




	
	
	
		
 

			




	
	
	
		
 
Parameter::Parameter() {

			




	
	
	
		
 
  arrowcolor = strdup("white");

			




	
	
	
		
 
  arrowsize = 100;

			




	
	
	
		
 
  textcolor = strdup("red");

			




	
	
	
		
 
  cellnumsize = 1;

			




	
	
	
		
 
  nodenumsize = 1;

			




	
	
	
		
 
  node_mag = 1.0;

			




	
	
	
		
 
  outlinewidth = 1.0;

			




	
	
	
		
 
  cell_outline_color = strdup("forestgreen");

			




	
	
	
		
 
  resize_stride = 0;

			




	
	
	
		
 
  T = 1.0;

			




	
	
	
		
 
  lambda_length = 100.;

			




	
	
	
		
 
  lambda_celllength = 0.;

			




	
	
	
		
 
  target_length = 60.;

			




	
	
	
		
 
  cell_expansion_rate = 1.;

			




	
	
	
		
 
  cell_div_expansion_rate = 0.;

			




	
	
	
		
 
  auxin_dependent_growth = true;

			




	
	
	
		
 
  ode_accuracy = 1e-4;

			




	
	
	
		
 
  mc_stepsize = 0.4;

			




	
	
	
		
 
  mc_cell_stepsize = 0.2;

			




	
	
	
		
 
  energy_threshold = 1000.;

			




	
	
	
		
 
  bend_lambda = 0.;

			




	
	
	
		
 
  alignment_lambda = 0.;

			




	
	
	
		
 
  rel_cell_div_threshold = 2.;

			




	
	
	
		
 
  rel_perimeter_stiffness = 2;

			




	
	
	
		
 
  collapse_node_threshold = 0.05;

			




	
	
	
		
 
  morphogen_div_threshold = 0.2;

			




	
	
	
		
 
  morphogen_expansion_threshold = 0.01;

			




	
	
	
		
 
  copy_wall = true;

			




	
	
	
		
 
  source = 0.;

			




	
	
	
		
 
  D = new double[15];

			




	
	
	
		
 
  D[0] = 0.;

			




	
	
	
		
 
  D[1] = 0.0;

			




	
	
	
		
 
  D[2] = 0.0;

			




	
	
	
		
 
  D[3] = 0.;

			




	
	
	
		
 
  D[4] = 0.;

			




	
	
	
		
 
  D[5] = 0.;

			




	
	
	
		
 
  D[6] = 0.;

			




	
	
	
		
 
  D[7] = 0.;

			




	
	
	
		
 
  D[8] = 0.;

			




	
	
	
		
 
  D[9] = 0.;

			




	
	
	
		
 
  D[10] = 0.;

			




	
	
	
		
 
  D[11] = 0.;

			




	
	
	
		
 
  D[12] = 0.;

			




	
	
	
		
 
  D[13] = 0.;

			




	
	
	
		
 
  D[14] = 0.;

			




	
	
	
		
 
  initval = new double[15];

			




	
	
	
		
 
  initval[0] = 0.;

			




	
	
	
		
 
  initval[1] = 0.;

			




	
	
	
		
 
  initval[2] = 0.;

			




	
	
	
		
 
  initval[3] = 0.;

			




	
	
	
		
 
  initval[4] = 0.;

			




	
	
	
		
 
  initval[5] = 0.;

			




	
	
	
		
 
  initval[6] = 0.;

			




	
	
	
		
 
  initval[7] = 0.;

			




	
	
	
		
 
  initval[8] = 0.;

			




	
	
	
		
 
  initval[9] = 0.;

			




	
	
	
		
 
  initval[10] = 0.;

			




	
	
	
		
 
  initval[11] = 0.;

			




	
	
	
		
 
  initval[12] = 0.;

			




	
	
	
		
 
  initval[13] = 0.;

			




	
	
	
		
 
  initval[14] = 0.;

			




	
	
	
		
 
  k1 = 1.;

			




	
	
	
		
 
  k2 = 0.3;

			




	
	
	
		
 
  r = 1.;

			




	
	
	
		
 
  kr = 1.;

			




	
	
	
		
 
  km = 1.;

			




	
	
	
		
 
  Pi_tot = 1.;

			




	
	
	
		
 
  transport = 0.036;

			




	
	
	
		
 
  ka = 1;

			




	
	
	
		
 
  pin_prod = 0.001;

			




	
	
	
		
 
  pin_prod_in_epidermis = 0.1;

			




	
	
	
		
 
  pin_breakdown = 0.001;

			




	
	
	
		
 
  pin_breakdown_internal = 0.001;

			




	
	
	
		
 
  aux1prod = 0.001;

			




	
	
	
		
 
  aux1prodmeso = 0.;

			




	
	
	
		
 
  aux1decay = 0.001;

			




	
	
	
		
 
  aux1decaymeso = 0.1;

			




	
	
	
		
 
  aux1transport = 0.036;

			




	
	
	
		
 
  aux_cons = 0.;

			




	
	
	
		
 
  aux_breakdown = 0.;

			




	
	
	
		
 
  kaux1 = 1;

			




	
	
	
		
 
  kap = 1;

			




	
	
	
		
 
  leaf_tip_source = 0.001;

			




	
	
	
		
 
  sam_efflux = 0.0001;

			




	
	
	
		
 
  sam_auxin = 10.;

			




	
	
	
		
 
  sam_auxin_breakdown = 0;

			




	
	
	
		
 
  van3prod = 0.002;

			




	
	
	
		
 
  van3autokat = 0.1;

			




	
	
	
		
 
  van3sat = 10;

			




	
	
	
		
 
  k2van3 = 0.3;

			




	
	
	
		
 
  dt = 0.1;

			




	
	
	
		
 
  rd_dt = 1.0;

			




	
	
	
		
 
  datadir = strdup(".");

			




	
	
	
		
 
  datadir = AppendHomeDirIfPathRelative(datadir);

			




	
	
	
		
 
  movie = false;

			




	
	
	
		
 
  nit = 100000;

			




	
	
	
		
 
  maxt = 1000.;

			




	
	
	
		
 
  storage_stride = 10;

			




	
	
	
		
 
  xml_storage_stride = 500;

			




	
	
	
		
 
  rseed = -1;

			




	
	
	
		
 
  constituous_expansion_limit = 16;

			




	
	
	
		
 
  vessel_inh_level = 1;

			




	
	
	
		
 
  vessel_expansion_rate = 0.25;

			




	
	
	
		
 
  d = 0.;

			




	
	
	
		
 
  e = 0.;

			




	
	
	
		
 
  f = 0.;

			




	
	
	
		
 
  c = 0.;

			




	
	
	
		
 
  mu = 0.;

			




	
	
	
		
 
  nu = 0.;

			




	
	
	
		
 
  rho0 = 0.;

			




	
	
	
		
 
  rho1 = 0.;

			




	
	
	
		
 
  c0 = 0.;

			




	
	
	
		
 
  gamma = 0.;

			




	
	
	
		
 
  eps = 0.;

			




	
	
	
		
 
  k = new double[15];

			




	
	
	
		
 
  k[0] = 0.;

			




	
	
	
		
 
  k[1] = 0.0;

			




	
	
	
		
 
  k[2] = 0.0;

			




	
	
	
		
 
  k[3] = 0.;

			




	
	
	
		
 
  k[4] = 0.;

			




	
	
	
		
 
  k[5] = 0.;

			




	
	
	
		
 
  k[6] = 0.;

			




	
	
	
		
 
  k[7] = 0.;

			




	
	
	
		
 
  k[8] = 0.;

			




	
	
	
		
 
  k[9] = 0.;

			




	
	
	
		
 
  k[10] = 0.;

			




	
	
	
		
 
  k[11] = 0.;

			




	
	
	
		
 
  k[12] = 0.;

			




	
	
	
		
 
  k[13] = 0.;

			




	
	
	
		
 
  k[14] = 0.;

			




	
	
	
		
 
  i1 = 0;

			




	
	
	
		
 
  i2 = 0;

			




	
	
	
		
 
  i3 = 0;

			




	
	
	
		
 
  i4 = 0;

			




	
	
	
		
 
  i5 = 0;

			




	
	
	
		
 
  s1 = strdup("");

			




	
	
	
		
 
  s2 = strdup("");

			




	
	
	
		
 
  s3 = strdup("");

			




	
	
	
		
 
  b1 = false;

			




	
	
	
		
 
  b2 = false;

			




	
	
	
		
 
  b3 = false;

			




	
	
	
		
 
  b4 = false;

			




	
	
	
		
 
  dir1 = strdup(".");

			




	
	
	
		
 
  dir2 = strdup(".");

			




	
	
	
		
 
  export_interval = 100;

			




	
	
	
		
 
  export_fn_prefix = strdup("CELLDATA");

			




	
	
	
		
 
  export_interval = 0;

			




	
	
	
		
 
  export_fn_prefix = strdup("cell.");

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
Parameter::~Parameter() {

			




	
	
	
		
 
    

			




	
	
	
		
 
// destruct parameter object

			




	
	
	
		
 
// free string parameter

			




	
	
	
		
 
CleanUp();

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Parameter::CleanUp(void) {

			




	
	
	
		
 
  if (arrowcolor) 

			




	
	
	
		
 
     free(arrowcolor);

			




	
	
	
		
 
  if (textcolor) 

			




	
	
	
		
 
     free(textcolor);

			




	
	
	
		
 
  if (cell_outline_color) 

			




	
	
	
		
 
     free(cell_outline_color);

			




	
	
	
		
 
  if (D) 

			




	
	
	
		
 
     free(D);

			




	
	
	
		
 
  if (initval) 

			




	
	
	
		
 
     free(initval);

			




	
	
	
		
 
  if (datadir) 

			




	
	
	
		
 
     free(datadir);

			




	
	
	
		
 
  if (k) 

			




	
	
	
		
 
     free(k);

			




	
	
	
		
 
  if (s1) 

			




	
	
	
		
 
     free(s1);

			




	
	
	
		
 
  if (s2) 

			




	
	
	
		
 
     free(s2);

			




	
	
	
		
 
  if (s3) 

			




	
	
	
		
 
     free(s3);

			




	
	
	
		
 
  if (dir1) 

			




	
	
	
		
 
     free(dir1);

			




	
	
	
		
 
  if (dir2) 

			




	
	
	
		
 
     free(dir2);

			




	
	
	
		
 
  if (export_fn_prefix) 

			




	
	
	
		
 
     free(export_fn_prefix);

			




	
	
	
		
 

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Parameter::Read(const char *filename) {

			




	
	
	
		
 
    

			




	
	
	
		
 
  static bool ReadP=false;

			




	
	
	
		
 

			




	
	
	
		
 
  if (ReadP) {

			




	
	
	
		
 

			




	
	
	
		
 
    //throw "Run Time Error in parameter.cpp: Please Read parameter file only once!!";

			




	
	
	
		
 
    CleanUp();

			




	
	
	
		
 
	

			




	
	
	
		
 
  } else

			




	
	
	
		
 
    ReadP=true;

			




	
	
	
		
 

			




	
	
	
		
 
  FILE *fp=OpenReadFile(filename);

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
  arrowcolor = sgetpar(fp, "arrowcolor", "white", true);

			




	
	
	
		
 
  arrowsize = fgetpar(fp, "arrowsize", 100, true);

			




	
	
	
		
 
  textcolor = sgetpar(fp, "textcolor", "red", true);

			




	
	
	
		
 
  cellnumsize = igetpar(fp, "cellnumsize", 1, true);

			




	
	
	
		
 
  nodenumsize = igetpar(fp, "nodenumsize", 1, true);

			




	
	
	
		
 
  node_mag = fgetpar(fp, "node_mag", 1.0, true);

			




	
	
	
		
 
  outlinewidth = fgetpar(fp, "outlinewidth", 1.0, true);

			




	
	
	
		
 
  cell_outline_color = sgetpar(fp, "cell_outline_color", "forestgreen", true);

			




	
	
	
		
 
  resize_stride = igetpar(fp, "resize_stride", 0, true);

			




	
	
	
		
 
  T = fgetpar(fp, "T", 1.0, true);

			




	
	
	
		
 
  lambda_length = fgetpar(fp, "lambda_length", 100., true);

			




	
	
	
		
 
  lambda_celllength = fgetpar(fp, "lambda_celllength", 0., true);

			




	
	
	
		
 
  target_length = fgetpar(fp, "target_length", 60., true);

			




	
	
	
		
 
  cell_expansion_rate = fgetpar(fp, "cell_expansion_rate", 1., true);

			




	
	
	
		
 
  cell_div_expansion_rate = fgetpar(fp, "cell_div_expansion_rate", 0., true);

			




	
	
	
		
 
  auxin_dependent_growth = bgetpar(fp, "auxin_dependent_growth", true, true);

			




	
	
	
		
 
  ode_accuracy = fgetpar(fp, "ode_accuracy", 1e-4, true);

			




	
	
	
		
 
  mc_stepsize = fgetpar(fp, "mc_stepsize", 0.4, true);

			




	
	
	
		
 
  mc_cell_stepsize = fgetpar(fp, "mc_cell_stepsize", 0.2, true);

			




	
	
	
		
 
  energy_threshold = fgetpar(fp, "energy_threshold", 1000., true);

			




	
	
	
		
 
  bend_lambda = fgetpar(fp, "bend_lambda", 0., true);

			




	
	
	
		
 
  alignment_lambda = fgetpar(fp, "alignment_lambda", 0., true);

			




	
	
	
		
 
  rel_cell_div_threshold = fgetpar(fp, "rel_cell_div_threshold", 2., true);

			




	
	
	
		
 
  rel_perimeter_stiffness = fgetpar(fp, "rel_perimeter_stiffness", 2, true);

			




	
	
	
		
 
  collapse_node_threshold = fgetpar(fp, "collapse_node_threshold", 0.05, true);

			




	
	
	
		
 
  morphogen_div_threshold = fgetpar(fp, "morphogen_div_threshold", 0.2, true);

			




	
	
	
		
 
  morphogen_expansion_threshold = fgetpar(fp, "morphogen_expansion_threshold", 0.01, true);

			




	
	
	
		
 
  copy_wall = bgetpar(fp, "copy_wall", true, true);

			




	
	
	
		
 
  source = fgetpar(fp, "source", 0., true);

			




	
	
	
		
 
  D = dgetparlist(fp, "D", 15, true);

			




	
	
	
		
 
  initval = dgetparlist(fp, "initval", 15, true);

			




	
	
	
		
 
  k1 = fgetpar(fp, "k1", 1., true);

			




	
	
	
		
 
  k2 = fgetpar(fp, "k2", 0.3, true);

			




	
	
	
		
 
  r = fgetpar(fp, "r", 1., true);

			




	
	
	
		
 
  kr = fgetpar(fp, "kr", 1., true);

			




	
	
	
		
 
  km = fgetpar(fp, "km", 1., true);

			




	
	
	
		
 
  Pi_tot = fgetpar(fp, "Pi_tot", 1., true);

			




	
	
	
		
 
  transport = fgetpar(fp, "transport", 0.036, true);

			




	
	
	
		
 
  ka = fgetpar(fp, "ka", 1, true);

			




	
	
	
		
 
  pin_prod = fgetpar(fp, "pin_prod", 0.001, true);

			




	
	
	
		
 
  pin_prod_in_epidermis = fgetpar(fp, "pin_prod_in_epidermis", 0.1, true);

			




	
	
	
		
 
  pin_breakdown = fgetpar(fp, "pin_breakdown", 0.001, true);

			




	
	
	
		
 
  pin_breakdown_internal = fgetpar(fp, "pin_breakdown_internal", 0.001, true);

			




	
	
	
		
 
  aux1prod = fgetpar(fp, "aux1prod", 0.001, true);

			




	
	
	
		
 
  aux1prodmeso = fgetpar(fp, "aux1prodmeso", 0., true);

			




	
	
	
		
 
  aux1decay = fgetpar(fp, "aux1decay", 0.001, true);

			




	
	
	
		
 
  aux1decaymeso = fgetpar(fp, "aux1decaymeso", 0.1, true);

			




	
	
	
		
 
  aux1transport = fgetpar(fp, "aux1transport", 0.036, true);

			




	
	
	
		
 
  aux_cons = fgetpar(fp, "aux_cons", 0., true);

			




	
	
	
		
 
  aux_breakdown = fgetpar(fp, "aux_breakdown", 0., true);

			




	
	
	
		
 
  kaux1 = fgetpar(fp, "kaux1", 1, true);

			




	
	
	
		
 
  kap = fgetpar(fp, "kap", 1, true);

			




	
	
	
		
 
  leaf_tip_source = fgetpar(fp, "leaf_tip_source", 0.001, true);

			




	
	
	
		
 
  sam_efflux = fgetpar(fp, "sam_efflux", 0.0001, true);

			




	
	
	
		
 
  sam_auxin = fgetpar(fp, "sam_auxin", 10., true);

			




	
	
	
		
 
  sam_auxin_breakdown = fgetpar(fp, "sam_auxin_breakdown", 0, true);

			




	
	
	
		
 
  van3prod = fgetpar(fp, "van3prod", 0.002, true);

			




	
	
	
		
 
  van3autokat = fgetpar(fp, "van3autokat", 0.1, true);

			




	
	
	
		
 
  van3sat = fgetpar(fp, "van3sat", 10, true);

			




	
	
	
		
 
  k2van3 = fgetpar(fp, "k2van3", 0.3, true);

			




	
	
	
		
 
  dt = fgetpar(fp, "dt", 0.1, true);

			




	
	
	
		
 
  rd_dt = fgetpar(fp, "rd_dt", 1.0, true);

			




	
	
	
		
 
  datadir = sgetpar(fp, "datadir", ".", true);

			




	
	
	
		
 
  datadir = AppendHomeDirIfPathRelative(datadir);

			




	
	
	
		
 
  if (strcmp(datadir, "."))

			




	
	
	
		
 
    MakeDir(datadir);

			




	
	
	
		
 
  movie = bgetpar(fp, "movie", false, true);

			




	
	
	
		
 
  nit = igetpar(fp, "nit", 100000, true);

			




	
	
	
		
 
  maxt = fgetpar(fp, "maxt", 1000., true);

			




	
	
	
		
 
  storage_stride = igetpar(fp, "storage_stride", 10, true);

			




	
	
	
		
 
  xml_storage_stride = igetpar(fp, "xml_storage_stride", 500, true);

			




	
	
	
		
 
  rseed = igetpar(fp, "rseed", -1, true);

			




	
	
	
		
 
  constituous_expansion_limit = igetpar(fp, "constituous_expansion_limit", 16, true);

			




	
	
	
		
 
  vessel_inh_level = fgetpar(fp, "vessel_inh_level", 1, true);

			




	
	
	
		
 
  vessel_expansion_rate = fgetpar(fp, "vessel_expansion_rate", 0.25, true);

			




	
	
	
		
 
  d = fgetpar(fp, "d", 0., true);

			




	
	
	
		
 
  e = fgetpar(fp, "e", 0., true);

			




	
	
	
		
 
  f = fgetpar(fp, "f", 0., true);

			




	
	
	
		
 
  c = fgetpar(fp, "c", 0., true);

			




	
	
	
		
 
  mu = fgetpar(fp, "mu", 0., true);

			




	
	
	
		
 
  nu = fgetpar(fp, "nu", 0., true);

			




	
	
	
		
 
  rho0 = fgetpar(fp, "rho0", 0., true);

			




	
	
	
		
 
  rho1 = fgetpar(fp, "rho1", 0., true);

			




	
	
	
		
 
  c0 = fgetpar(fp, "c0", 0., true);

			




	
	
	
		
 
  gamma = fgetpar(fp, "gamma", 0., true);

			




	
	
	
		
 
  eps = fgetpar(fp, "eps", 0., true);

			




	
	
	
		
 
  k = dgetparlist(fp, "k", 15, true);

			




	
	
	
		
 
  i1 = igetpar(fp, "i1", 0, true);

			




	
	
	
		
 
  i2 = igetpar(fp, "i2", 0, true);

			




	
	
	
		
 
  i3 = igetpar(fp, "i3", 0, true);

			




	
	
	
		
 
  i4 = igetpar(fp, "i4", 0, true);

			




	
	
	
		
 
  i5 = igetpar(fp, "i5", 0, true);

			




	
	
	
		
 
  s1 = sgetpar(fp, "s1", "", true);

			




	
	
	
		
 
  s2 = sgetpar(fp, "s2", "", true);

			




	
	
	
		
 
  s3 = sgetpar(fp, "s3", "", true);

			




	
	
	
		
 
  b1 = bgetpar(fp, "b1", false, true);

			




	
	
	
		
 
  b2 = bgetpar(fp, "b2", false, true);

			




	
	
	
		
 
  b3 = bgetpar(fp, "b3", false, true);

			




	
	
	
		
 
  b4 = bgetpar(fp, "b4", false, true);

			




	
	
	
		
 
  dir1 = sgetpar(fp, "dir1", ".", true);

			




	
	
	
		
 
  if (strcmp(dir1, "."))

			




	
	
	
		
 
    MakeDir(dir1);

			




	
	
	
		
 
  dir2 = sgetpar(fp, "dir2", ".", true);

			




	
	
	
		
 
  if (strcmp(dir2, "."))

			




	
	
	
		
 
    MakeDir(dir2);

			




	
	
	
		
 
  export_interval = igetpar(fp, "export_interval", 100, true);

			




	
	
	
		
 
  export_fn_prefix = sgetpar(fp, "export_fn_prefix", "CELLDATA", true);

			




	
	
	
		
 
  export_interval = igetpar(fp, "export_interval", 0, true);

			




	
	
	
		
 
  export_fn_prefix = sgetpar(fp, "export_fn_prefix", "cell.", true);

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
const char *sbool(const bool &p) {

			




	
	
	
		
 

			




	
	
	
		
 
  const char *true_str="true";

			




	
	
	
		
 
  const char *false_str="false";

			




	
	
	
		
 
  if (p)

			




	
	
	
		
 
    return true_str;

			




	
	
	
		
 
  else

			




	
	
	
		
 
    return false_str;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
void Parameter::Write(ostream &os) const {

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
  if (arrowcolor) 

			




	
	
	
		
 
  os << " arrowcolor = " << arrowcolor << endl;

			




	
	
	
		
 
  os << " arrowsize = " << arrowsize << endl;

			




	
	
	
		
 

			




	
	
	
		
 
  if (textcolor) 

			




	
	
	
		
 
  os << " textcolor = " << textcolor << endl;

			




	
	
	
		
 
  os << " cellnumsize = " << cellnumsize << endl;

			




	
	
	
		
 
  os << " nodenumsize = " << nodenumsize << endl;

			




	
	
	
		
 
  os << " node_mag = " << node_mag << endl;

			




	
	
	
		
 
  os << " outlinewidth = " << outlinewidth << endl;

			




	
	
	
		
 

			




	
	
	
		
 
  if (cell_outline_color) 

			




	
	
	
		
 
  os << " cell_outline_color = " << cell_outline_color << endl;

			




	
	
	
		
 
  os << " resize_stride = " << resize_stride << endl;

			




	
	
	
		
 
  os << " T = " << T << endl;

			




	
	
	
		
 
  os << " lambda_length = " << lambda_length << endl;

			




	
	
	
		
 
  os << " lambda_celllength = " << lambda_celllength << endl;

			




	
	
	
		
 
  os << " target_length = " << target_length << endl;

			




	
	
	
		
 
  os << " cell_expansion_rate = " << cell_expansion_rate << endl;

			




	
	
	
		
 
  os << " cell_div_expansion_rate = " << cell_div_expansion_rate << endl;

			




	
	
	
		
 
  os << " auxin_dependent_growth = " << sbool(auxin_dependent_growth) << endl;

			




	
	
	
		
 
  os << " ode_accuracy = " << ode_accuracy << endl;

			




	
	
	
		
 
  os << " mc_stepsize = " << mc_stepsize << endl;

			




	
	
	
		
 
  os << " mc_cell_stepsize = " << mc_cell_stepsize << endl;

			




	
	
	
		
 
  os << " energy_threshold = " << energy_threshold << endl;

			




	
	
	
		
 
  os << " bend_lambda = " << bend_lambda << endl;

			




	
	
	
		
 
  os << " alignment_lambda = " << alignment_lambda << endl;

			




	
	
	
		
 
  os << " rel_cell_div_threshold = " << rel_cell_div_threshold << endl;

			




	
	
	
		
 
  os << " rel_perimeter_stiffness = " << rel_perimeter_stiffness << endl;

			




	
	
	
		
 
  os << " collapse_node_threshold = " << collapse_node_threshold << endl;

			




	
	
	
		
 
  os << " morphogen_div_threshold = " << morphogen_div_threshold << endl;

			




	
	
	
		
 
  os << " morphogen_expansion_threshold = " << morphogen_expansion_threshold << endl;

			




	
	
	
		
 
  os << " copy_wall = " << sbool(copy_wall) << endl;

			




	
	
	
		
 
  os << " source = " << source << endl;

			




	
	
	
		
 
  os << " D = "<< D[0] << ", " << D[1] << ", " << D[2] << ", " << D[3] << ", " << D[4] << ", " << D[5] << ", " << D[6] << ", " << D[7] << ", " << D[8] << ", " << D[9] << ", " << D[10] << ", " << D[11] << ", " << D[12] << ", " << D[13] << ", " << D[14] << endl;

			




	
	
	
		
 
  os << " initval = "<< initval[0] << ", " << initval[1] << ", " << initval[2] << ", " << initval[3] << ", " << initval[4] << ", " << initval[5] << ", " << initval[6] << ", " << initval[7] << ", " << initval[8] << ", " << initval[9] << ", " << initval[10] << ", " << initval[11] << ", " << initval[12] << ", " << initval[13] << ", " << initval[14] << endl;

			




	
	
	
		
 
  os << " k1 = " << k1 << endl;

			




	
	
	
		
 
  os << " k2 = " << k2 << endl;

			




	
	
	
		
 
  os << " r = " << r << endl;

			




	
	
	
		
 
  os << " kr = " << kr << endl;

			




	
	
	
		
 
  os << " km = " << km << endl;

			




	
	
	
		
 
  os << " Pi_tot = " << Pi_tot << endl;

			




	
	
	
		
 
  os << " transport = " << transport << endl;

			




	
	
	
		
 
  os << " ka = " << ka << endl;

			




	
	
	
		
 
  os << " pin_prod = " << pin_prod << endl;

			




	
	
	
		
 
  os << " pin_prod_in_epidermis = " << pin_prod_in_epidermis << endl;

			




	
	
	
		
 
  os << " pin_breakdown = " << pin_breakdown << endl;

			




	
	
	
		
 
  os << " pin_breakdown_internal = " << pin_breakdown_internal << endl;

			




	
	
	
		
 
  os << " aux1prod = " << aux1prod << endl;

			




	
	
	
		
 
  os << " aux1prodmeso = " << aux1prodmeso << endl;

			




	
	
	
		
 
  os << " aux1decay = " << aux1decay << endl;

			




	
	
	
		
 
  os << " aux1decaymeso = " << aux1decaymeso << endl;

			




	
	
	
		
 
  os << " aux1transport = " << aux1transport << endl;

			




	
	
	
		
 
  os << " aux_cons = " << aux_cons << endl;

			




	
	
	
		
 
  os << " aux_breakdown = " << aux_breakdown << endl;

			




	
	
	
		
 
  os << " kaux1 = " << kaux1 << endl;

			




	
	
	
		
 
  os << " kap = " << kap << endl;

			




	
	
	
		
 
  os << " leaf_tip_source = " << leaf_tip_source << endl;

			




	
	
	
		
 
  os << " sam_efflux = " << sam_efflux << endl;

			




	
	
	
		
 
  os << " sam_auxin = " << sam_auxin << endl;

			




	
	
	
		
 
  os << " sam_auxin_breakdown = " << sam_auxin_breakdown << endl;

			




	
	
	
		
 
  os << " van3prod = " << van3prod << endl;

			




	
	
	
		
 
  os << " van3autokat = " << van3autokat << endl;

			




	
	
	
		
 
  os << " van3sat = " << van3sat << endl;

			




	
	
	
		
 
  os << " k2van3 = " << k2van3 << endl;

			




	
	
	
		
 
  os << " dt = " << dt << endl;

			




	
	
	
		
 
  os << " rd_dt = " << rd_dt << endl;

			




	
	
	
		
 
  if (datadir) {

			




	
	
	
		
 
                                     QDir dataDir = QDir::home().relativeFilePath(datadir);

			




	
	
	
		
 
                                     os << " datadir = " << dataDir.dirName().toStdString() << endl;

			




	
	
	
		
 
                                 }

			




	
	
	
		
 
                                 else {

			




	
	
	
		
 
                                     os << "datadir = ." << endl;

			




	
	
	
		
 
                                 }

			




	
	
	
		
 
  os << " movie = " << sbool(movie) << endl;

			




	
	
	
		
 
  os << " nit = " << nit << endl;

			




	
	
	
		
 
  os << " maxt = " << maxt << endl;

			




	
	
	
		
 
  os << " storage_stride = " << storage_stride << endl;

			




	
	
	
		
 
  os << " xml_storage_stride = " << xml_storage_stride << endl;

			




	
	
	
		
 
  os << " rseed = " << rseed << endl;

			




	
	
	
		
 
  os << " constituous_expansion_limit = " << constituous_expansion_limit << endl;

			




	
	
		
 
@@ -1800,97 +1800,96 @@ if (!strcmp(namec, "gamma")) {

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'gamma' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "eps")) {

			




	
	
	
		
 
  eps = standardlocale.toDouble(valc, &ok);

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'eps' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "i1")) {

			




	
	
	
		
 
  i1 = standardlocale.toInt(valc, &ok);

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i1' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "i2")) {

			




	
	
	
		
 
  i2 = standardlocale.toInt(valc, &ok);

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i2' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "i3")) {

			




	
	
	
		
 
  i3 = standardlocale.toInt(valc, &ok);

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i3' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "i4")) {

			




	
	
	
		
 
  i4 = standardlocale.toInt(valc, &ok);

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i4' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "i5")) {

			




	
	
	
		
 
  i5 = standardlocale.toInt(valc, &ok);

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i5' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "s1")) {

			




	
	
	
		
 
  if (s1) { free(s1); }

			




	
	
	
		
 
  s1=strdup(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "s2")) {

			




	
	
	
		
 
  if (s2) { free(s2); }

			




	
	
	
		
 
  s2=strdup(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "s3")) {

			




	
	
	
		
 
  if (s3) { free(s3); }

			




	
	
	
		
 
  s3=strdup(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "b1")) {

			




	
	
	
		
 
b1 = strtobool(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "b2")) {

			




	
	
	
		
 
b2 = strtobool(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "b3")) {

			




	
	
	
		
 
b3 = strtobool(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "b4")) {

			




	
	
	
		
 
b4 = strtobool(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "dir1")) {

			




	
	
	
		
 
  if (dir1) { free(dir1); }

			




	
	
	
		
 
  dir1=strdup(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "dir2")) {

			




	
	
	
		
 
  if (dir2) { free(dir2); }

			




	
	
	
		
 
  dir2=strdup(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "export_interval")) {

			




	
	
	
		
 
  export_interval = standardlocale.toInt(valc, &ok);

			




	
	
	
		
 
  if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'export_interval' from XML file.",valc); }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "export_fn_prefix")) {

			




	
	
	
		
 
  if (export_fn_prefix) { free(export_fn_prefix); }

			




	
	
	
		
 
  export_fn_prefix=strdup(valc);

			




	
	
	
		
 
}

			




	
	
	
		
 
}

			




	
	
	
		
 
void Parameter::AssignValArrayToPar(const char *namec, vector<double> valarray) {

			




	
	
	
		
 
if (!strcmp(namec, "D")) {

			




	
	
	
		
 
  int i=0;

			




	
	
	
		
 
  vector<double>::const_iterator v=valarray.begin();

			




	
	
	
		
 
  while (v!=valarray.end() && i <= 14 ) {

			




	
	
	
		
 
     D[i++]=*(v++);

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "initval")) {

			




	
	
	
		
 
  int i=0;

			




	
	
	
		
 
  vector<double>::const_iterator v=valarray.begin();

			




	
	
	
		
 
  while (v!=valarray.end() && i <= 14 ) {

			




	
	
	
		
 
     initval[i++]=*(v++);

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 
if (!strcmp(namec, "k")) {

			




	
	
	
		
 
  int i=0;

			




	
	
	
		
 
  vector<double>::const_iterator v=valarray.begin();

			




	
	
	
		
 
  while (v!=valarray.end() && i <= 14 ) {

			




	
	
	
		
 
     k[i++]=*(v++);

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
ostream &operator<<(ostream &os, Parameter &p) {

			




	
	
	
		
 
    p.Write(os);

			




	
	
	
		
 
    return os;

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
/* finis */

			




        

    


    
    

    

        

                

                    src/parameter.h
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  $Id$

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 
// WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.

			




	
	
	
		
 
// All edits will be discarded.

			




	
	
	
		
 
// Do not edit. All edits will be discarded.

			




	
	
	
		
 

			




	
	
	
		
 
#ifndef _PARAMETER_H_

			




	
	
	
		
 
#define _PARAMETER_H_

			




	
	
	
		
 
#include "vector.h"

			




	
	
	
		
 
#include <vector>

			




	
	
	
		
 

			




	
	
	
		
 
#include <libxml/parser.h>

			




	
	
	
		
 
#include <libxml/tree.h>

			




	
	
	
		
 

			




	
	
	
		
 
 class Parameter {

			




	
	
	
		
 
		

			




	
	
	
		
 
 public: 

			




	
	
	
		
 
   Parameter();

			




	
	
	
		
 
   ~Parameter();

			




	
	
	
		
 
   void CleanUp(void);

			




	
	
	
		
 
   void Read(const char *filename);

			




	
	
	
		
 
   void Write(ostream &os) const;

			




	
	
	
		
 
   void XMLAdd(xmlNode *root) const;

			




	
	
	
		
 
   void XMLRead(xmlNode *root);

			




	
	
	
		
 
   void AssignValToPar(const char *namec, const char *valc);

			




	
	
	
		
 
   void AssignValArrayToPar(const char *namec, vector<double> valarray);

			




	
	
	
		
 
  char * arrowcolor;

			




	
	
	
		
 
  double arrowsize;

			




	
	
	
		
 
  char * textcolor;

			




	
	
	
		
 
  int cellnumsize;

			




	
	
	
		
 
  int nodenumsize;

			




	
	
	
		
 
  double node_mag;

			




	
	
	
		
 
  double outlinewidth;

			




	
	
	
		
 
  char * cell_outline_color;

			




	
	
	
		
 
  int resize_stride;

			




	
	
	
		
 
  double T;

			




	
	
	
		
 
  double lambda_length;

			




	
	
	
		
 
  double lambda_celllength;

			




	
	
	
		
 
  double target_length;

			




	
	
	
		
 
  double cell_expansion_rate;

			




	
	
	
		
 
  double cell_div_expansion_rate;

			




	
	
	
		
 
  bool auxin_dependent_growth;

			




	
	
	
		
 
  double ode_accuracy;

			




	
	
	
		
 
  double mc_stepsize;

			




	
	
	
		
 
  double mc_cell_stepsize;

			




	
	
	
		
 
  double energy_threshold;

			




	
	
	
		
 
  double bend_lambda;

			




	
	
	
		
 
  double alignment_lambda;

			




	
	
	
		
 
  double rel_cell_div_threshold;

			




	
	
	
		
 
  double rel_perimeter_stiffness;

			




	
	
	
		
 
  double collapse_node_threshold;

			




	
	
	
		
 
  double morphogen_div_threshold;

			




	
	
	
		
 
  double morphogen_expansion_threshold;

			




	
	
	
		
 
  bool copy_wall;

			




	
	
	
		
 
  double source;

			




	
	
	
		
 
  double * D;

			




	
	
	
		
 
  double * initval;

			




	
	
	
		
 
  double k1;

			




	
	
	
		
 
  double k2;

			




	
	
	
		
 
  double r;

			




	
	
	
		
 
  double kr;

			




	
	
	
		
 
  double km;

			




	
	
	
		
 
  double Pi_tot;

			




	
	
	
		
 
  double transport;

			




	
	
	
		
 
  double ka;

			




	
	
	
		
 
  double pin_prod;

			




	
	
	
		
 
  double pin_prod_in_epidermis;

			




	
	
	
		
 
  double pin_breakdown;

			




	
	
	
		
 
  double pin_breakdown_internal;

			




	
	
	
		
 
  double aux1prod;

			




	
	
	
		
 
  double aux1prodmeso;

			




	
	
	
		
 
  double aux1decay;

			




	
	
	
		
 
  double aux1decaymeso;

			




	
	
	
		
 
  double aux1transport;

			




	
	
	
		
 
  double aux_cons;

			




	
	
	
		
 
  double aux_breakdown;

			




	
	
	
		
 
  double kaux1;

			




	
	
	
		
 
  double kap;

			




	
	
	
		
 
  double leaf_tip_source;

			




	
	
	
		
 
  double sam_efflux;

			




	
	
	
		
 
  double sam_auxin;

			




	
	
	
		
 
  double sam_auxin_breakdown;

			




	
	
	
		
 
  double van3prod;

			




	
	
	
		
 
  double van3autokat;

			




	
	
	
		
 
  double van3sat;

			




	
	
	
		
 
  double k2van3;

			




	
	
	
		
 
  double dt;

			




	
	
	
		
 
  double rd_dt;

			




	
	
	
		
 
  char * datadir;

			




	
	
	
		
 
  bool movie;

			




	
	
	
		
 
  int nit;

			




	
	
	
		
 
  double maxt;

			




	
	
	
		
 
  int storage_stride;

			




	
	
	
		
 
  int xml_storage_stride;

			




	
	
	
		
 
  int rseed;

			




	
	
	
		
 
  int constituous_expansion_limit;

			




	
	
	
		
 
  double vessel_inh_level;

			




	
	
	
		
 
  double vessel_expansion_rate;

			




	
	
	
		
 
  double d;

			




	
	
	
		
 
  double e;

			




	
	
	
		
 
  double f;

			




        

    


    
    

    

        

                

                    src/pardialog.cpp
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 
// WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.

			




	
	
	
		
 
// Do not edit. All edits will be discarded.

			




	
	
	
		
 

			




	
	
	
		
 
#include "pardialog.h"

			




	
	
	
		
 
#include "parameter.h"

			




	
	
	
		
 
#include <cstring>

			




	
	
	
		
 
#include <qdialog.h>

			




	
	
	
		
 
#include <qlabel.h>

			




	
	
	
		
 
#include <qlineedit.h>

			




	
	
	
		
 
#include <qmessagebox.h>

			




	
	
	
		
 

			




	
	
	
		
 
static const std::string _module_id("$Id$");

			




	
	
	
		
 

			




	
	
	
		
 
ParameterDialog::ParameterDialog(QWidget *parent, const char *name, Qt::WindowFlags f) : QDialog(parent,name,false,f) {

			




	
	
	
		
 
    extern Parameter par;

			




	
	
	
		
 
  arrowcolor_edit = new QLineEdit( QString("%1").arg(par.arrowcolor), this, "arrowcolor_edit" );

			




	
	
	
		
 
  arrowsize_edit = new QLineEdit( QString("%1").arg(par.arrowsize), this, "arrowsize_edit" );

			




	
	
	
		
 
  textcolor_edit = new QLineEdit( QString("%1").arg(par.textcolor), this, "textcolor_edit" );

			




	
	
	
		
 
  cellnumsize_edit = new QLineEdit( QString("%1").arg(par.cellnumsize), this, "cellnumsize_edit" );

			




	
	
	
		
 
  nodenumsize_edit = new QLineEdit( QString("%1").arg(par.nodenumsize), this, "nodenumsize_edit" );

			




	
	
	
		
 
  node_mag_edit = new QLineEdit( QString("%1").arg(par.node_mag), this, "node_mag_edit" );

			




	
	
	
		
 
  outlinewidth_edit = new QLineEdit( QString("%1").arg(par.outlinewidth), this, "outlinewidth_edit" );

			




	
	
	
		
 
  cell_outline_color_edit = new QLineEdit( QString("%1").arg(par.cell_outline_color), this, "cell_outline_color_edit" );

			




	
	
	
		
 
  resize_stride_edit = new QLineEdit( QString("%1").arg(par.resize_stride), this, "resize_stride_edit" );

			




	
	
	
		
 
  T_edit = new QLineEdit( QString("%1").arg(par.T), this, "T_edit" );

			




	
	
	
		
 
  lambda_length_edit = new QLineEdit( QString("%1").arg(par.lambda_length), this, "lambda_length_edit" );

			




	
	
	
		
 
  lambda_celllength_edit = new QLineEdit( QString("%1").arg(par.lambda_celllength), this, "lambda_celllength_edit" );

			




	
	
	
		
 
  target_length_edit = new QLineEdit( QString("%1").arg(par.target_length), this, "target_length_edit" );

			




	
	
	
		
 
  cell_expansion_rate_edit = new QLineEdit( QString("%1").arg(par.cell_expansion_rate), this, "cell_expansion_rate_edit" );

			




	
	
	
		
 
  cell_div_expansion_rate_edit = new QLineEdit( QString("%1").arg(par.cell_div_expansion_rate), this, "cell_div_expansion_rate_edit" );

			




	
	
	
		
 
  auxin_dependent_growth_edit = new QLineEdit( QString("%1").arg(sbool(par.auxin_dependent_growth)), this, "auxin_dependent_growth_edit" );

			




	
	
	
		
 
  ode_accuracy_edit = new QLineEdit( QString("%1").arg(par.ode_accuracy), this, "ode_accuracy_edit" );

			




	
	
	
		
 
  mc_stepsize_edit = new QLineEdit( QString("%1").arg(par.mc_stepsize), this, "mc_stepsize_edit" );

			




	
	
	
		
 
  mc_cell_stepsize_edit = new QLineEdit( QString("%1").arg(par.mc_cell_stepsize), this, "mc_cell_stepsize_edit" );

			




	
	
	
		
 
  energy_threshold_edit = new QLineEdit( QString("%1").arg(par.energy_threshold), this, "energy_threshold_edit" );

			




	
	
	
		
 
  bend_lambda_edit = new QLineEdit( QString("%1").arg(par.bend_lambda), this, "bend_lambda_edit" );

			




	
	
	
		
 
  alignment_lambda_edit = new QLineEdit( QString("%1").arg(par.alignment_lambda), this, "alignment_lambda_edit" );

			




	
	
	
		
 
  rel_cell_div_threshold_edit = new QLineEdit( QString("%1").arg(par.rel_cell_div_threshold), this, "rel_cell_div_threshold_edit" );

			




	
	
	
		
 
  rel_perimeter_stiffness_edit = new QLineEdit( QString("%1").arg(par.rel_perimeter_stiffness), this, "rel_perimeter_stiffness_edit" );

			




	
	
	
		
 
  collapse_node_threshold_edit = new QLineEdit( QString("%1").arg(par.collapse_node_threshold), this, "collapse_node_threshold_edit" );

			




	
	
	
		
 
  morphogen_div_threshold_edit = new QLineEdit( QString("%1").arg(par.morphogen_div_threshold), this, "morphogen_div_threshold_edit" );

			




	
	
	
		
 
  morphogen_expansion_threshold_edit = new QLineEdit( QString("%1").arg(par.morphogen_expansion_threshold), this, "morphogen_expansion_threshold_edit" );

			




	
	
	
		
 
  copy_wall_edit = new QLineEdit( QString("%1").arg(sbool(par.copy_wall)), this, "copy_wall_edit" );

			




	
	
	
		
 
  source_edit = new QLineEdit( QString("%1").arg(par.source), this, "source_edit" );

			




	
	
	
		
 
  QString D_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");

			




	
	
	
		
 
  D_string = D_string.arg(par.D[0]).arg(par.D[1]).arg(par.D[2]).arg(par.D[3]).arg(par.D[4]).arg(par.D[5]).arg(par.D[6]).arg(par.D[7]).arg(par.D[8]).arg(par.D[9]).arg(par.D[10]).arg(par.D[11]).arg(par.D[12]).arg(par.D[13]).arg(par.D[14]);

			




	
	
	
		
 
  D_edit = new QLineEdit( D_string, this, "D_edit" );

			




	
	
	
		
 
  QString initval_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");

			




	
	
	
		
 
  initval_string = initval_string.arg(par.initval[0]).arg(par.initval[1]).arg(par.initval[2]).arg(par.initval[3]).arg(par.initval[4]).arg(par.initval[5]).arg(par.initval[6]).arg(par.initval[7]).arg(par.initval[8]).arg(par.initval[9]).arg(par.initval[10]).arg(par.initval[11]).arg(par.initval[12]).arg(par.initval[13]).arg(par.initval[14]);

			




	
	
	
		
 
  initval_edit = new QLineEdit( initval_string, this, "initval_edit" );

			




	
	
	
		
 
  k1_edit = new QLineEdit( QString("%1").arg(par.k1), this, "k1_edit" );

			




	
	
	
		
 
  k2_edit = new QLineEdit( QString("%1").arg(par.k2), this, "k2_edit" );

			




	
	
	
		
 
  r_edit = new QLineEdit( QString("%1").arg(par.r), this, "r_edit" );

			




	
	
	
		
 
  kr_edit = new QLineEdit( QString("%1").arg(par.kr), this, "kr_edit" );

			




	
	
	
		
 
  km_edit = new QLineEdit( QString("%1").arg(par.km), this, "km_edit" );

			




	
	
	
		
 
  Pi_tot_edit = new QLineEdit( QString("%1").arg(par.Pi_tot), this, "Pi_tot_edit" );

			




	
	
	
		
 
  transport_edit = new QLineEdit( QString("%1").arg(par.transport), this, "transport_edit" );

			




	
	
	
		
 
  ka_edit = new QLineEdit( QString("%1").arg(par.ka), this, "ka_edit" );

			




	
	
	
		
 
  pin_prod_edit = new QLineEdit( QString("%1").arg(par.pin_prod), this, "pin_prod_edit" );

			




	
	
	
		
 
  pin_prod_in_epidermis_edit = new QLineEdit( QString("%1").arg(par.pin_prod_in_epidermis), this, "pin_prod_in_epidermis_edit" );

			




	
	
	
		
 
  pin_breakdown_edit = new QLineEdit( QString("%1").arg(par.pin_breakdown), this, "pin_breakdown_edit" );

			




	
	
	
		
 
  pin_breakdown_internal_edit = new QLineEdit( QString("%1").arg(par.pin_breakdown_internal), this, "pin_breakdown_internal_edit" );

			




	
	
	
		
 
  aux1prod_edit = new QLineEdit( QString("%1").arg(par.aux1prod), this, "aux1prod_edit" );

			




	
	
	
		
 
  aux1prodmeso_edit = new QLineEdit( QString("%1").arg(par.aux1prodmeso), this, "aux1prodmeso_edit" );

			




	
	
	
		
 
  aux1decay_edit = new QLineEdit( QString("%1").arg(par.aux1decay), this, "aux1decay_edit" );

			




	
	
	
		
 
  aux1decaymeso_edit = new QLineEdit( QString("%1").arg(par.aux1decaymeso), this, "aux1decaymeso_edit" );

			




	
	
	
		
 
  aux1transport_edit = new QLineEdit( QString("%1").arg(par.aux1transport), this, "aux1transport_edit" );

			




	
	
	
		
 
  aux_cons_edit = new QLineEdit( QString("%1").arg(par.aux_cons), this, "aux_cons_edit" );

			




	
	
	
		
 
  aux_breakdown_edit = new QLineEdit( QString("%1").arg(par.aux_breakdown), this, "aux_breakdown_edit" );

			




	
	
	
		
 
  kaux1_edit = new QLineEdit( QString("%1").arg(par.kaux1), this, "kaux1_edit" );

			




	
	
	
		
 
  kap_edit = new QLineEdit( QString("%1").arg(par.kap), this, "kap_edit" );

			




	
	
	
		
 
  leaf_tip_source_edit = new QLineEdit( QString("%1").arg(par.leaf_tip_source), this, "leaf_tip_source_edit" );

			




	
	
	
		
 
  sam_efflux_edit = new QLineEdit( QString("%1").arg(par.sam_efflux), this, "sam_efflux_edit" );

			




	
	
	
		
 
  sam_auxin_edit = new QLineEdit( QString("%1").arg(par.sam_auxin), this, "sam_auxin_edit" );

			




	
	
	
		
 
  sam_auxin_breakdown_edit = new QLineEdit( QString("%1").arg(par.sam_auxin_breakdown), this, "sam_auxin_breakdown_edit" );

			




	
	
	
		
 
  van3prod_edit = new QLineEdit( QString("%1").arg(par.van3prod), this, "van3prod_edit" );

			




	
	
	
		
 
  van3autokat_edit = new QLineEdit( QString("%1").arg(par.van3autokat), this, "van3autokat_edit" );

			




	
	
	
		
 
  van3sat_edit = new QLineEdit( QString("%1").arg(par.van3sat), this, "van3sat_edit" );

			




	
	
	
		
 
  k2van3_edit = new QLineEdit( QString("%1").arg(par.k2van3), this, "k2van3_edit" );

			




	
	
	
		
 
  dt_edit = new QLineEdit( QString("%1").arg(par.dt), this, "dt_edit" );

			




	
	
	
		
 
  rd_dt_edit = new QLineEdit( QString("%1").arg(par.rd_dt), this, "rd_dt_edit" );

			




	
	
	
		
 
  datadir_edit = new QLineEdit( QString("%1").arg(par.datadir), this, "datadir_edit" );

			




	
	
	
		
 
  movie_edit = new QLineEdit( QString("%1").arg(sbool(par.movie)), this, "movie_edit" );

			




	
	
	
		
 
  nit_edit = new QLineEdit( QString("%1").arg(par.nit), this, "nit_edit" );

			




	
	
	
		
 
  maxt_edit = new QLineEdit( QString("%1").arg(par.maxt), this, "maxt_edit" );

			




	
	
	
		
 
  storage_stride_edit = new QLineEdit( QString("%1").arg(par.storage_stride), this, "storage_stride_edit" );

			




	
	
	
		
 
  xml_storage_stride_edit = new QLineEdit( QString("%1").arg(par.xml_storage_stride), this, "xml_storage_stride_edit" );

			




	
	
	
		
 
  rseed_edit = new QLineEdit( QString("%1").arg(par.rseed), this, "rseed_edit" );

			




	
	
	
		
 
  constituous_expansion_limit_edit = new QLineEdit( QString("%1").arg(par.constituous_expansion_limit), this, "constituous_expansion_limit_edit" );

			




	
	
	
		
 
  vessel_inh_level_edit = new QLineEdit( QString("%1").arg(par.vessel_inh_level), this, "vessel_inh_level_edit" );

			




	
	
	
		
 
  vessel_expansion_rate_edit = new QLineEdit( QString("%1").arg(par.vessel_expansion_rate), this, "vessel_expansion_rate_edit" );

			




	
	
	
		
 
  d_edit = new QLineEdit( QString("%1").arg(par.d), this, "d_edit" );

			




	
	
	
		
 
  e_edit = new QLineEdit( QString("%1").arg(par.e), this, "e_edit" );

			




	
	
	
		
 
  f_edit = new QLineEdit( QString("%1").arg(par.f), this, "f_edit" );

			




	
	
	
		
 
  c_edit = new QLineEdit( QString("%1").arg(par.c), this, "c_edit" );

			




	
	
	
		
 
  mu_edit = new QLineEdit( QString("%1").arg(par.mu), this, "mu_edit" );

			




	
	
	
		
 
  nu_edit = new QLineEdit( QString("%1").arg(par.nu), this, "nu_edit" );

			




	
	
		
 
@@ -725,97 +726,96 @@ void ParameterDialog::Reset(void) {

			




	
	
	
		
 
  target_length_edit->setText( QString("%1").arg(par.target_length) );

			




	
	
	
		
 
  cell_expansion_rate_edit->setText( QString("%1").arg(par.cell_expansion_rate) );

			




	
	
	
		
 
  cell_div_expansion_rate_edit->setText( QString("%1").arg(par.cell_div_expansion_rate) );

			




	
	
	
		
 
  auxin_dependent_growth_edit->setText( QString("%1").arg(sbool(par.auxin_dependent_growth)));

			




	
	
	
		
 
  ode_accuracy_edit->setText( QString("%1").arg(par.ode_accuracy) );

			




	
	
	
		
 
  mc_stepsize_edit->setText( QString("%1").arg(par.mc_stepsize) );

			




	
	
	
		
 
  mc_cell_stepsize_edit->setText( QString("%1").arg(par.mc_cell_stepsize) );

			




	
	
	
		
 
  energy_threshold_edit->setText( QString("%1").arg(par.energy_threshold) );

			




	
	
	
		
 
  bend_lambda_edit->setText( QString("%1").arg(par.bend_lambda) );

			




	
	
	
		
 
  alignment_lambda_edit->setText( QString("%1").arg(par.alignment_lambda) );

			




	
	
	
		
 
  rel_cell_div_threshold_edit->setText( QString("%1").arg(par.rel_cell_div_threshold) );

			




	
	
	
		
 
  rel_perimeter_stiffness_edit->setText( QString("%1").arg(par.rel_perimeter_stiffness) );

			




	
	
	
		
 
  collapse_node_threshold_edit->setText( QString("%1").arg(par.collapse_node_threshold) );

			




	
	
	
		
 
  morphogen_div_threshold_edit->setText( QString("%1").arg(par.morphogen_div_threshold) );

			




	
	
	
		
 
  morphogen_expansion_threshold_edit->setText( QString("%1").arg(par.morphogen_expansion_threshold) );

			




	
	
	
		
 
  copy_wall_edit->setText( QString("%1").arg(sbool(par.copy_wall)));

			




	
	
	
		
 
  source_edit->setText( QString("%1").arg(par.source) );

			




	
	
	
		
 
  QString D_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");

			




	
	
	
		
 
  D_string = D_string.arg(par.D[0]).arg(par.D[1]).arg(par.D[2]).arg(par.D[3]).arg(par.D[4]).arg(par.D[5]).arg(par.D[6]).arg(par.D[7]).arg(par.D[8]).arg(par.D[9]).arg(par.D[10]).arg(par.D[11]).arg(par.D[12]).arg(par.D[13]).arg(par.D[14]);

			




	
	
	
		
 
  D_edit->setText( D_string );

			




	
	
	
		
 
  QString initval_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");

			




	
	
	
		
 
  initval_string = initval_string.arg(par.initval[0]).arg(par.initval[1]).arg(par.initval[2]).arg(par.initval[3]).arg(par.initval[4]).arg(par.initval[5]).arg(par.initval[6]).arg(par.initval[7]).arg(par.initval[8]).arg(par.initval[9]).arg(par.initval[10]).arg(par.initval[11]).arg(par.initval[12]).arg(par.initval[13]).arg(par.initval[14]);

			




	
	
	
		
 
  initval_edit->setText( initval_string );

			




	
	
	
		
 
  k1_edit->setText( QString("%1").arg(par.k1) );

			




	
	
	
		
 
  k2_edit->setText( QString("%1").arg(par.k2) );

			




	
	
	
		
 
  r_edit->setText( QString("%1").arg(par.r) );

			




	
	
	
		
 
  kr_edit->setText( QString("%1").arg(par.kr) );

			




	
	
	
		
 
  km_edit->setText( QString("%1").arg(par.km) );

			




	
	
	
		
 
  Pi_tot_edit->setText( QString("%1").arg(par.Pi_tot) );

			




	
	
	
		
 
  transport_edit->setText( QString("%1").arg(par.transport) );

			




	
	
	
		
 
  ka_edit->setText( QString("%1").arg(par.ka) );

			




	
	
	
		
 
  pin_prod_edit->setText( QString("%1").arg(par.pin_prod) );

			




	
	
	
		
 
  pin_prod_in_epidermis_edit->setText( QString("%1").arg(par.pin_prod_in_epidermis) );

			




	
	
	
		
 
  pin_breakdown_edit->setText( QString("%1").arg(par.pin_breakdown) );

			




	
	
	
		
 
  pin_breakdown_internal_edit->setText( QString("%1").arg(par.pin_breakdown_internal) );

			




	
	
	
		
 
  aux1prod_edit->setText( QString("%1").arg(par.aux1prod) );

			




	
	
	
		
 
  aux1prodmeso_edit->setText( QString("%1").arg(par.aux1prodmeso) );

			




	
	
	
		
 
  aux1decay_edit->setText( QString("%1").arg(par.aux1decay) );

			




	
	
	
		
 
  aux1decaymeso_edit->setText( QString("%1").arg(par.aux1decaymeso) );

			




	
	
	
		
 
  aux1transport_edit->setText( QString("%1").arg(par.aux1transport) );

			




	
	
	
		
 
  aux_cons_edit->setText( QString("%1").arg(par.aux_cons) );

			




	
	
	
		
 
  aux_breakdown_edit->setText( QString("%1").arg(par.aux_breakdown) );

			




	
	
	
		
 
  kaux1_edit->setText( QString("%1").arg(par.kaux1) );

			




	
	
	
		
 
  kap_edit->setText( QString("%1").arg(par.kap) );

			




	
	
	
		
 
  leaf_tip_source_edit->setText( QString("%1").arg(par.leaf_tip_source) );

			




	
	
	
		
 
  sam_efflux_edit->setText( QString("%1").arg(par.sam_efflux) );

			




	
	
	
		
 
  sam_auxin_edit->setText( QString("%1").arg(par.sam_auxin) );

			




	
	
	
		
 
  sam_auxin_breakdown_edit->setText( QString("%1").arg(par.sam_auxin_breakdown) );

			




	
	
	
		
 
  van3prod_edit->setText( QString("%1").arg(par.van3prod) );

			




	
	
	
		
 
  van3autokat_edit->setText( QString("%1").arg(par.van3autokat) );

			




	
	
	
		
 
  van3sat_edit->setText( QString("%1").arg(par.van3sat) );

			




	
	
	
		
 
  k2van3_edit->setText( QString("%1").arg(par.k2van3) );

			




	
	
	
		
 
  dt_edit->setText( QString("%1").arg(par.dt) );

			




	
	
	
		
 
  rd_dt_edit->setText( QString("%1").arg(par.rd_dt) );

			




	
	
	
		
 
  datadir_edit->setText( QString("%1").arg(par.datadir) );

			




	
	
	
		
 
  movie_edit->setText( QString("%1").arg(sbool(par.movie)));

			




	
	
	
		
 
  nit_edit->setText( QString("%1").arg(par.nit) );

			




	
	
	
		
 
  maxt_edit->setText( QString("%1").arg(par.maxt) );

			




	
	
	
		
 
  storage_stride_edit->setText( QString("%1").arg(par.storage_stride) );

			




	
	
	
		
 
  xml_storage_stride_edit->setText( QString("%1").arg(par.xml_storage_stride) );

			




	
	
	
		
 
  rseed_edit->setText( QString("%1").arg(par.rseed) );

			




	
	
	
		
 
  constituous_expansion_limit_edit->setText( QString("%1").arg(par.constituous_expansion_limit) );

			




	
	
	
		
 
  vessel_inh_level_edit->setText( QString("%1").arg(par.vessel_inh_level) );

			




	
	
	
		
 
  vessel_expansion_rate_edit->setText( QString("%1").arg(par.vessel_expansion_rate) );

			




	
	
	
		
 
  d_edit->setText( QString("%1").arg(par.d) );

			




	
	
	
		
 
  e_edit->setText( QString("%1").arg(par.e) );

			




	
	
	
		
 
  f_edit->setText( QString("%1").arg(par.f) );

			




	
	
	
		
 
  c_edit->setText( QString("%1").arg(par.c) );

			




	
	
	
		
 
  mu_edit->setText( QString("%1").arg(par.mu) );

			




	
	
	
		
 
  nu_edit->setText( QString("%1").arg(par.nu) );

			




	
	
	
		
 
  rho0_edit->setText( QString("%1").arg(par.rho0) );

			




	
	
	
		
 
  rho1_edit->setText( QString("%1").arg(par.rho1) );

			




	
	
	
		
 
  c0_edit->setText( QString("%1").arg(par.c0) );

			




	
	
	
		
 
  gamma_edit->setText( QString("%1").arg(par.gamma) );

			




	
	
	
		
 
  eps_edit->setText( QString("%1").arg(par.eps) );

			




	
	
	
		
 
  QString k_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");

			




	
	
	
		
 
  k_string = k_string.arg(par.k[0]).arg(par.k[1]).arg(par.k[2]).arg(par.k[3]).arg(par.k[4]).arg(par.k[5]).arg(par.k[6]).arg(par.k[7]).arg(par.k[8]).arg(par.k[9]).arg(par.k[10]).arg(par.k[11]).arg(par.k[12]).arg(par.k[13]).arg(par.k[14]);

			




	
	
	
		
 
  k_edit->setText( k_string );

			




	
	
	
		
 
  i1_edit->setText( QString("%1").arg(par.i1) );

			




	
	
	
		
 
  i2_edit->setText( QString("%1").arg(par.i2) );

			




	
	
	
		
 
  i3_edit->setText( QString("%1").arg(par.i3) );

			




	
	
	
		
 
  i4_edit->setText( QString("%1").arg(par.i4) );

			




	
	
	
		
 
  i5_edit->setText( QString("%1").arg(par.i5) );

			




	
	
	
		
 
  s1_edit->setText( QString("%1").arg(par.s1) );

			




	
	
	
		
 
  s2_edit->setText( QString("%1").arg(par.s2) );

			




	
	
	
		
 
  s3_edit->setText( QString("%1").arg(par.s3) );

			




	
	
	
		
 
  b1_edit->setText( QString("%1").arg(sbool(par.b1)));

			




	
	
	
		
 
  b2_edit->setText( QString("%1").arg(sbool(par.b2)));

			




	
	
	
		
 
  b3_edit->setText( QString("%1").arg(sbool(par.b3)));

			




	
	
	
		
 
  b4_edit->setText( QString("%1").arg(sbool(par.b4)));

			




	
	
	
		
 
  dir1_edit->setText( QString("%1").arg(par.dir1) );

			




	
	
	
		
 
  dir2_edit->setText( QString("%1").arg(par.dir2) );

			




	
	
	
		
 
  export_interval_edit->setText( QString("%1").arg(par.export_interval) );

			




	
	
	
		
 
  export_fn_prefix_edit->setText( QString("%1").arg(par.export_fn_prefix) );

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
/* finis */

			




        

    


    
    

    

        

                

                    src/pardialog.h
                

                

                  
                      
                        

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/*

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  $Id$

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  This file is part of the Virtual Leaf.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  VirtualLeaf 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.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  You should have received a copy of the GNU General Public License

			




	
	
	
		
 
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 *  Copyright 2010 Roeland Merks.

			




	
	
	
		
 
 *

			




	
	
	
		
 
 */

			




	
	
	
		
 

			




	
	
	
		
 
// WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.

			




	
	
	
		
 
// All edits will be discarded.

			




	
	
	
		
 
// Do not edit. All edits will be discarded.

			




	
	
	
		
 

			




	
	
	
		
 
#ifndef PARAMETER_DIALOG_H

			




	
	
	
		
 
#define PARAMETER_DIALOG_H

			




	
	
	
		
 
#include <qdialog.h>

			




	
	
	
		
 
#include <qspinbox.h>

			




	
	
	
		
 
#include <qlineedit.h>

			




	
	
	
		
 
#include <qlayout.h>

			




	
	
	
		
 
#include <qpushbutton.h>

			




	
	
	
		
 
#include <iostream>

			




	
	
	
		
 

			




	
	
	
		
 
class ParameterDialog : public QDialog {

			




	
	
	
		
 
    Q_OBJECT

			




	
	
	
		
 
	

			




	
	
	
		
 
      public:

			




	
	
	
		
 
	ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0);

			




	
	
	
		
 
    virtual ~ParameterDialog(void);

			




	
	
	
		
 
    public slots:

			




	
	
	
		
 
    void Reset(void);

			




	
	
	
		
 

			




	
	
	
		
 
    private slots:

			




	
	
	
		
 
    void write(void);

			




	
	
	
		
 

			




	
	
	
		
 
  private:

			




	
	
	
		
 
  QLineEdit *arrowcolor_edit;

			




	
	
	
		
 
  QLineEdit *arrowsize_edit;

			




	
	
	
		
 
  QLineEdit *textcolor_edit;

			




	
	
	
		
 
  QLineEdit *cellnumsize_edit;

			




	
	
	
		
 
  QLineEdit *nodenumsize_edit;

			




	
	
	
		
 
  QLineEdit *node_mag_edit;

			




	
	
	
		
 
  QLineEdit *outlinewidth_edit;

			




	
	
	
		
 
  QLineEdit *cell_outline_color_edit;

			




	
	
	
		
 
  QLineEdit *resize_stride_edit;

			




	
	
	
		
 
  QLineEdit *T_edit;

			




	
	
	
		
 
  QLineEdit *lambda_length_edit;

			




	
	
	
		
 
  QLineEdit *lambda_celllength_edit;

			




	
	
	
		
 
  QLineEdit *target_length_edit;

			




	
	
	
		
 
  QLineEdit *cell_expansion_rate_edit;

			




	
	
	
		
 
  QLineEdit *cell_div_expansion_rate_edit;

			




	
	
	
		
 
  QLineEdit *auxin_dependent_growth_edit;

			




	
	
	
		
 
  QLineEdit *ode_accuracy_edit;

			




	
	
	
		
 
  QLineEdit *mc_stepsize_edit;

			




	
	
	
		
 
  QLineEdit *mc_cell_stepsize_edit;

			




	
	
	
		
 
  QLineEdit *energy_threshold_edit;

			




	
	
	
		
 
  QLineEdit *bend_lambda_edit;

			




	
	
	
		
 
  QLineEdit *alignment_lambda_edit;

			




	
	
	
		
 
  QLineEdit *rel_cell_div_threshold_edit;

			




	
	
	
		
 
  QLineEdit *rel_perimeter_stiffness_edit;

			




	
	
	
		
 
  QLineEdit *collapse_node_threshold_edit;

			




	
	
	
		
 
  QLineEdit *morphogen_div_threshold_edit;

			




	
	
	
		
 
  QLineEdit *morphogen_expansion_threshold_edit;

			




	
	
	
		
 
  QLineEdit *copy_wall_edit;

			




	
	
	
		
 
  QLineEdit *source_edit;

			




	
	
	
		
 
  QLineEdit *D_edit;

			




	
	
	
		
 
  QLineEdit *initval_edit;

			




	
	
	
		
 
  QLineEdit *k1_edit;

			




	
	
	
		
 
  QLineEdit *k2_edit;

			




	
	
	
		
 
  QLineEdit *r_edit;

			




	
	
	
		
 
  QLineEdit *kr_edit;

			




	
	
	
		
 
  QLineEdit *km_edit;

			




	
	
	
		
 
  QLineEdit *Pi_tot_edit;

			




	
	
	
		
 
  QLineEdit *transport_edit;

			




	
	
	
		
 
  QLineEdit *ka_edit;

			




	
	
	
		
 
  QLineEdit *pin_prod_edit;

			




	
	
	
		
 
  QLineEdit *pin_prod_in_epidermis_edit;

			




	
	
	
		
 
  QLineEdit *pin_breakdown_edit;

			




	
	
	
		
 
  QLineEdit *pin_breakdown_internal_edit;

			




	
	
	
		
 
  QLineEdit *aux1prod_edit;

			




	
	
	
		
 
  QLineEdit *aux1prodmeso_edit;

			




	
	
	
		
 
  QLineEdit *aux1decay_edit;

			




	
	
	
		
 
  QLineEdit *aux1decaymeso_edit;

			




	
	
	
		
 
  QLineEdit *aux1transport_edit;

			




	
	
	
		
 
  QLineEdit *aux_cons_edit;

			




	
	
	
		
 
  QLineEdit *aux_breakdown_edit;

			




	
	
	
		
 
  QLineEdit *kaux1_edit;

			




	
	
	
		
 
  QLineEdit *kap_edit;

			




	
	
	
		
 
  QLineEdit *leaf_tip_source_edit;

			




	
	
	
		
 
  QLineEdit *sam_efflux_edit;

			




	
	
	
		
 
  QLineEdit *sam_auxin_edit;

			




	
	
	
		
 
  QLineEdit *sam_auxin_breakdown_edit;

			




	
	
	
		
 
  QLineEdit *van3prod_edit;

			




	
	
	
		
 
  QLineEdit *van3autokat_edit;

			




	
	
	
		
 
  QLineEdit *van3sat_edit;

			




	
	
	
		
 
  QLineEdit *k2van3_edit;

			




	
	
	
		
 
  QLineEdit *dt_edit;

			




	
	
	
		
 
  QLineEdit *rd_dt_edit;

			




	
	
	
		
 
  QLineEdit *datadir_edit;

			




	
	
	
		
 
  QLineEdit *movie_edit;

			




	
	
	
		
 
  QLineEdit *nit_edit;

			




	
	
	
		
 
  QLineEdit *maxt_edit;

			




	
	
	
		
 
  QLineEdit *storage_stride_edit;

			




	
	
	
		
 
  QLineEdit *xml_storage_stride_edit;

			




	
	
	
		
 
  QLineEdit *rseed_edit;

			




	
	
	
		
 
  QLineEdit *constituous_expansion_limit_edit;

			




	
	
	
		
 
  QLineEdit *vessel_inh_level_edit;

			




	
	
	
		
 
  QLineEdit *vessel_expansion_rate_edit;

			




	
	
	
		
 
  QLineEdit *d_edit;

			




	
	
	
		
 
  QLineEdit *e_edit;

			




	
	
	
		
 
  QLineEdit *f_edit;

			




	
	
	
		
 
  QLineEdit *c_edit;

			




	
	
	
		
 
  QLineEdit *mu_edit;

			




	
	
	
		
 
  QLineEdit *nu_edit;

			




	
	
	
		
 
  QLineEdit *rho0_edit;

			




	
	
	
		
 
  QLineEdit *rho1_edit;

			




	
	
	
		
 
  QLineEdit *c0_edit;

			




	
	
	
		
 
  QLineEdit *gamma_edit;

			




	
	
	
		
 
  QLineEdit *eps_edit;

			




	
	
	
		
 
  QLineEdit *k_edit;

			




	
	
	
		
 
  QLineEdit *i1_edit;

			




	
	
	
		
 
  QLineEdit *i2_edit;

			




	
	
	
		
 
  QLineEdit *i3_edit;

			




	
	
	
		
 
  QLineEdit *i4_edit;

			




	
	
	
		
 
  QLineEdit *i5_edit;

			




	
	
	
		
 
  QLineEdit *s1_edit;

			




	
	
	
		
 
  QLineEdit *s2_edit;

			




	
	
	
		
 
  QLineEdit *s3_edit;

			




	
	
	
		
 
  QLineEdit *b1_edit;

			




	
	
	
		
 
  QLineEdit *b2_edit;

			




	
	
	
		
 
  QLineEdit *b3_edit;

			




	
	
	
		
 
  QLineEdit *b4_edit;

			




	
	
	
		
 
  QLineEdit *dir1_edit;

			




	
	
	
		
 
  QLineEdit *dir2_edit;

			




	
	
	
		
 
  QLineEdit *export_interval_edit;

			




	
	
	
		
 
  QLineEdit *export_fn_prefix_edit;

			




	
	
	
		
 
};

			




	
	
	
		
 
#endif

			




	
	
	
		
 

			




        

    



    


    



    



      

      





    
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