EI/VirtualLeaf Changeset - caa535c40937 · Centrum Wiskunde & Informatica (CWI)

Changeset - caa535c40937

Parent rev.

Child rev.

[Not reviewed]

default

1 34 4

Michael Guravage - 15 years ago 2010-06-25 16:50:35
michael.guravage@cwi.nl

Made changes to conform to the version submitted with the Plant Physiology paper. See the individual ChangeLogs for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added lib/libiconv/bin/iconv.exe
added lib/libiconv/bin/libcharset-1.dll
added lib/libiconv/bin/libiconv-2.dll
added src/gpl3.txt
changed INSTALL
changed src/ChangeLog
changed src/TutorialCode/Tutorial0/ChangeLog
changed src/TutorialCode/Tutorial0/tutorial0.pro
changed src/TutorialCode/Tutorial1A/ChangeLog
changed src/TutorialCode/Tutorial1A/tutorial1A.pro
changed src/TutorialCode/Tutorial1B/ChangeLog
changed src/TutorialCode/Tutorial1B/tutorial1B.pro
changed src/TutorialCode/Tutorial1C/ChangeLog
changed src/TutorialCode/Tutorial1C/tutorial1C.pro
changed src/TutorialCode/Tutorial1D/ChangeLog
changed src/TutorialCode/Tutorial1D/tutorial1D.pro
changed src/TutorialCode/Tutorial2/ChangeLog
changed src/TutorialCode/Tutorial2/tutorial2.pro
changed src/TutorialCode/Tutorial3/ChangeLog
changed src/TutorialCode/Tutorial3/tutorial3.pro
changed src/TutorialCode/Tutorial4/ChangeLog
changed src/TutorialCode/Tutorial4/tutorial4.pro
changed src/TutorialCode/Tutorial5/ChangeLog
changed src/TutorialCode/Tutorial5/tutorial5.pro
changed src/VirtualLeaf-install.nsi
changed src/VirtualLeaf.pro
changed src/build_models/ChangeLog
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/canvas.cpp
changed src/libplugin.pro
changed src/output.cpp
changed src/output.h
changed src/parameter.cpp
changed src/parameter.h
changed src/perl/ChangeLog
changed src/perl/make_parameter_source.pl
removed doc/gpl3.txt

38 files changed with 181 insertions and 92 deletions:

INSTALL

lib/libiconv/bin/iconv.exe

bin+new file

lib/libiconv/bin/libcharset-1.dll

bin+new file

lib/libiconv/bin/libiconv-2.dll

bin+new file

src/ChangeLog

src/TutorialCode/Tutorial0/ChangeLog

src/TutorialCode/Tutorial0/tutorial0.pro

src/TutorialCode/Tutorial1A/ChangeLog

src/TutorialCode/Tutorial1A/tutorial1A.pro

src/TutorialCode/Tutorial1B/ChangeLog

src/TutorialCode/Tutorial1B/tutorial1B.pro

src/TutorialCode/Tutorial1C/ChangeLog

src/TutorialCode/Tutorial1C/tutorial1C.pro

src/TutorialCode/Tutorial1D/ChangeLog

src/TutorialCode/Tutorial1D/tutorial1D.pro

src/TutorialCode/Tutorial2/ChangeLog

src/TutorialCode/Tutorial2/tutorial2.pro

src/TutorialCode/Tutorial3/ChangeLog

src/TutorialCode/Tutorial3/tutorial3.pro

src/TutorialCode/Tutorial4/ChangeLog

src/TutorialCode/Tutorial4/tutorial4.pro

src/TutorialCode/Tutorial5/ChangeLog

src/TutorialCode/Tutorial5/tutorial5.pro

src/VirtualLeaf-install.nsi

src/VirtualLeaf.pro

src/build_models/ChangeLog

src/build_models/plugin_auxingrowth.pro

src/build_models/plugin_meinhardt.pro

src/build_models/plugin_test.pro

src/canvas.cpp

src/gpl3.txt

rename

src/libplugin.pro

src/output.cpp

src/output.h

src/parameter.cpp

src/parameter.h

src/perl/ChangeLog

src/perl/make_parameter_source.pl

0 comments (0 inline, 0 general)

INSTALL

➞

Show inline comments

 Basic Installation
 ==================
 Linux::
  qmake -makefile libplugin.pro
  rm -f make.out
  make clean all 2>&1 | tee make.out
  cd build_models
  rm -f make.out
  for i in *.pro; do echo $i; qmake -makefile $i; make clean all 2>&1 | tee -a make.out; done
  cd -
  qmake -makefile VirtualLeaf.pro
  make clean all 2>&1 | tee -a make.out
 MacOSX::
  tbw
 Windows::
  tbw
 You will find platform specific instructions how to compile and
 install the VirtualLeaf in installation.pdf in the doc directory.

lib/libiconv/bin/iconv.exe

➞

Show inline comments

		new file 100755
		binary diff not shown

lib/libiconv/bin/libcharset-1.dll

➞

Show inline comments

		new file 100755
		binary diff not shown

lib/libiconv/bin/libiconv-2.dll

➞

Show inline comments

		new file 100755
		binary diff not shown

src/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* gpl3.txt: Moved gpl3.txt from doc to src directory.
 	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 	* libplugin.pro: Ditto.
 	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.
 	* parameter.h: Ditto.
 	* output.h: Declared new function (AppendHomeDirIfPathRelative).
 	* output.cpp (AppendHomeDirIfPathRelative): Added new function.
 	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").
 	* VirtualLeaf-install.nsi: Add missing libiconv/bin directory.
 	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.
 	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.
 -06-24    <guravage@caterpie.sen.cwi.nl>
 	* libplugin.pro: Use correct library path.
 	* VirtualLeaf.pro: Ditto.
 	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* simitembase.cpp: Removed NULL assignments to unused variables.
 	* VirtualLeaf.cpp: Ditto.
 	* apoplastitem.cpp: Ditto.
 	* canvas.cpp: Ditto.
 	* cell.cpp: Ditto.
 	* cellbase.h: Ditto.
 	* forwardeuler.cpp: Ditto.
 	* mainbase.h: Ditto.
 	* nodeitem.cpp: Ditto.
 	* qcanvasarrow.h: Ditto.
 	* simitembase.cpp: Ditto.
 	* Makefile (clean): Add -f Makefile argument to each make invocation.
 	* VirtualLeaf-install.nsi: New gpl license text.
 	* VirtualLeaf.pro: Disabled console mode.
 	* mesh.cpp (Clear): Added parentheses to qDebug statments.
 	(TestIllegalWalls): Replaced qDebug().
 	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.
 	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.
 -06-22    <guravage@caterpie.sen.cwi.nl>
 	* Makefile (tutorials): Add tutorials target.
 -06-21    <guravage@caterpie.sen.cwi.nl>
 	* parameter.cpp: Added particular reassignment of datadir.
 	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.
 -06-18    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (gpl): Added gpl slot to display GPL license.
 	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.
 	* libplugin.pro: Ditto.
 	* Makefile (clean): add if stmt not to `touch` on windows.
 -06-17    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed perl references.
 	* libplugin.pro: Ditto.
 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.
 	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.
 	* xmlwrite.h (XMLIO): Ditto!
 	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;
 	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur
 	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.
 	(XMLReadCells): Removed unused count variable.
 	(XMLReadSimtime): Removed unused cur variable.
 	(XMLRead): Removed unused v_str variable.
 	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.
 	(SimItemBase) Ditto.
 	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.
 	* output.cpp (OpenWriteFile): Removed unused par variable.
 	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.
 	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.
 	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.
 	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.
 	(mousePressEvent): Removed unused item variable.
 	* apoplastitem.cpp
 	(ApoplastItem): Removed unused par variable.
 	(OnClick): Use NULL assignment merely to obviate compilation warning.
 	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.
 	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.
 	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.
 	* VirtualLeaf.cpp ditto.
 	* canvas.cpp ditto.
 	* cell.cpp ditto.
 	* data_plot.cpp ditto.
 	* forwardeuler.cpp ditto.
 	* mesh.cpp ditto.
 	* mesh.h
 	* random.cpp ditto.
 	* wall.cpp ditto.
 	* wallbase.cpp ditto.
 	* wallitem.cpp ditto.
 -06-07    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.
 	* libplugin.pro: ditto.
 -06-03    <guravage@caterpie.sen.cwi.nl>
 	* pardialog.h: Added default versions of this automatically generated file.
 	* pardialog.cpp: ditto.
 	* parameter.h: ditto.
 	* parameter.cpp: ditto.
 	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.
  	* libplugin.pro: dito.
 	* Makefile: Added top-level Makefile
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

src/TutorialCode/Tutorial0/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial0.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial0.pro: Corrected windows library paths.

src/TutorialCode/Tutorial0/tutorial0.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial0
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1A/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1A.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1A.pro: corrected windows library path.

src/TutorialCode/Tutorial1A/tutorial1A.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial1A
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1B/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1B.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1B.pro: Corrected windows library path.

src/TutorialCode/Tutorial1B/tutorial1B.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial1B
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1C/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1C.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1C.pro: Corrected windows library path.

src/TutorialCode/Tutorial1C/tutorial1C.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial1C
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1D/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1D.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial1D.pro: Corrected windows library path.

src/TutorialCode/Tutorial1D/tutorial1D.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial1D
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial2/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial2.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial2.pro: Corrected windows library path.

src/TutorialCode/Tutorial2/tutorial2.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial2
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial3/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial3.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial3.pro: Corrected windows library path.

src/TutorialCode/Tutorial3/tutorial3.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial3
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial4/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial4.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial4.pro: Corrected windows library path.

src/TutorialCode/Tutorial4/tutorial4.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial4
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial5/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial5.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial5.pro: Corrected windows library path.

src/TutorialCode/Tutorial5/tutorial5.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 TARGET = tutorial5
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/VirtualLeaf-install.nsi

➞

Show inline comments

 # $Id$
 # appends \ to the path if missing
 # example: !insertmacro GetCleanDir "c:\blabla"
 # Pop $0 => "c:\blabla\"
 !macro GetCleanDir INPUTDIR
   ; ATTENTION: USE ON YOUR OWN RISK!
   ; Please report bugs here: http://stefan.bertels.org/
   !define Index_GetCleanDir 'GetCleanDir_Line${__LINE__}'
   Push $R0
   Push $R1
   StrCpy $R0 "${INPUTDIR}"
   StrCmp $R0 "" ${Index_GetCleanDir}-finish
   StrCpy $R1 "$R0" "" -1
   StrCmp "$R1" "\" ${Index_GetCleanDir}-finish
   StrCpy $R0 "$R0\"
 ${Index_GetCleanDir}-finish:
   Pop $R1
   Exch $R0
   !undef Index_GetCleanDir
 !macroend
 # similar to "RMDIR /r DIRECTORY", but does not remove DIRECTORY itself
 # example: !insertmacro RemoveFilesAndSubDirs "$INSTDIR"
 !macro RemoveFilesAndSubDirs DIRECTORY
   # ATTENTION: USE ON YOUR OWN RISK!
   # Please report bugs here: http://stefan.bertels.org/
   !define Index_RemoveFilesAndSubDirs 'RemoveFilesAndSubDirs_${__LINE__}'
   Push $R0
   Push $R1
   Push $R2
   !insertmacro GetCleanDir "${DIRECTORY}"
   Pop $R2
   FindFirst $R0 $R1 "$R2*.*"
 ${Index_RemoveFilesAndSubDirs}-loop:
   StrCmp $R1 "" ${Index_RemoveFilesAndSubDirs}-done
   StrCmp $R1 "." ${Index_RemoveFilesAndSubDirs}-next
   StrCmp $R1 ".." ${Index_RemoveFilesAndSubDirs}-next
   IfFileExists "$R2$R1\*.*" ${Index_RemoveFilesAndSubDirs}-directory
   ; file
   Delete "$R2$R1"
   goto ${Index_RemoveFilesAndSubDirs}-next
 ${Index_RemoveFilesAndSubDirs}-directory:
   ; directory
   RMDir /r "$R2$R1"
 ${Index_RemoveFilesAndSubDirs}-next:
   FindNext $R0 $R1
   Goto ${Index_RemoveFilesAndSubDirs}-loop
 ${Index_RemoveFilesAndSubDirs}-done:
   FindClose $R0
   Pop $R2
   Pop $R1
   Pop $R0
   !undef Index_RemoveFilesAndSubDirs
 !macroend
 !define PRODUCT_NAME "The Virtual Leaf"
 !define PRODUCT_VERSION "1.0"
 !define PRODUCT_PUBLISHER "Center for Mathematics and Computer Science (CWI)"
 !define PRODUCT_WEB_SITE "www.cwi.nl"
 !define EXECUTABLE "VirtualLeaf.exe"
 !define PROGICON "leaficon.ico"
 !define SETUP_BITMAP "leaficon.ico"
 # MUI 1.67 compatible ------
 !include "MUI.nsh"
 !include "EnvVarUpdate.nsh"
 # MUI Settings
 !define MUI_ABORTWARNING
 !define MUI_ICON "leaficon.ico"
 !define MUI_UNICON "leaficon.ico"
 # Welcome page
 !insertmacro MUI_PAGE_WELCOME
 # License page
 !insertmacro MUI_PAGE_LICENSE "..\doc\gpl3.txt"
 # Components page
 !insertmacro MUI_PAGE_COMPONENTS
 # Directory page
 !insertmacro MUI_PAGE_DIRECTORY
 # Instfiles page
 !insertmacro MUI_PAGE_INSTFILES
 # Finish page
 !insertmacro MUI_PAGE_FINISH
 # Uninstaller pages
 !insertmacro MUI_UNPAGE_CONFIRM
 !insertmacro MUI_UNPAGE_INSTFILES
 !insertmacro MUI_UNPAGE_FINISH
 # Language files
 !insertmacro MUI_LANGUAGE "English"
 # MUI end ------
 # set the name of the installer
 outfile "VirtualLeaf-install.exe"
 Name "${PRODUCT_NAME} ${PRODUCT_VERSION}"
 ShowInstDetails show
 ShowUnInstDetails show
 # define the directory to install to
 installDir C:\VirtualLeaf
 # Request application privileges
 RequestExecutionLevel user
 section "Virtual Leaf executable"
   #sectionIn RO
   # define the output path for the Virtual Leaf executable
   setOutPath $INSTDIR
   writeUninstaller $INSTDIR\uninstaller.exe
   file ..\bin\VirtualLeaf.exe
   # Required DLLs
   setOutPath $INSTDIR\bin
   file C:\libiconv\bin\libiconv-2.dll
   file C:\libxml2\lib\libxml2.dll
   file C:\libz\bin\zlib1.dll
   file ..\lib\libiconv\bin\libiconv-2.dll
   file ..\lib\libxml2\lib\libxml2.dll
   file ..\lib\libz\bin\zlib1.dll
   # Is the pegging of these DLLs to a specific QT version a problem?
   file C:\Qt\2010.02.1\mingw\bin\mingwm10.dll
   file C:\Qt\2010.02.1\mingw\bin\libgcc_s_dw2-1.dll
   file C:\Qt\2010.02.1\qt\bin\Qt3Support4.dll
   file C:\Qt\2010.02.1\qt\bin\QtCore4.dll
   file C:\Qt\2010.02.1\qt\bin\QtGui4.dll
   file C:\Qt\2010.02.1\qt\bin\QtNetwork4.dll
   file C:\Qt\2010.02.1\qt\bin\QtSql4.dll
   file C:\Qt\2010.02.1\qt\bin\QtXml4.dll
   # Prepend the Virtual Leaf bin directory to the installers PATH
   ${EnvVarUpdate} $0 "PATH" "P" "HKCU" "$INSTDIR\bin"
 sectionEnd
 section "Virtual Leaf plugins"
   # define the output path for the Virtual Leaf models
   setOutPath $INSTDIR\models
   file ..\bin\models\*
 sectionEnd
 section "Virtual Leaf data"
   # define the output path for the Virtual Leaf models
   setOutPath $INSTDIR\leaves
   file ..\data\leaves\*
 sectionEnd
 # create a section to define what the uninstaller does.
 # the section will always be named "Uninstall"
 section "Uninstall"
   # Always delete uninstaller first
   delete $INSTDIR\uninstaller.exe
   # Now delete installed file
   !insertmacro RemoveFilesAndSubDirs "$INSTDIR"
   # Last but not least - delete the path
   ${un.EnvVarUpdate} $0 "PATH" "R" "HKCU" "$INSTDIR\bin"
 sectionEnd
 # finis

src/VirtualLeaf.pro

➞

Show inline comments

+#
 #  $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += qt
 QMAKE_CXXFLAGS += -fexceptions
 QMAKE_CXXFLAGS += -Wall
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 #REACTIONS = reactions_auxin_growth.h
 #REACTIONS = reactions_meinhardt.h
 #REACTIONS = reactions_pce_growth.h
 DEFINES += QTGRAPHICS
 DEFINES += REACTIONS_HEADER=$${REACTIONS}
 DEFINES += REACTIONS_HEADER_STRING=\"$${REACTIONS}\"
 DEFINES += FLEMING
 BINDIR = ../bin
 LIBDIR = ../lib
 DESTDIR = $$BINDIR
 TARGET = VirtualLeaf
 TEMPLATE = app
 PARTMPL = $${TARGET}par.tmpl
 MAINSRC = $${TARGET}.cpp
 QT -= network sql xml
 QT += qt3support
 !win32 {
  GRAPHICS = qt #qwt
+}
 win32 {
  CONFIG -= console
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  GRAPHICS = qt
  RC_FILE = VirtualLeaf.rc
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
  LIBS += -L$${LIBXML2DIR}\lib -lxml2 -L$${LIBICONVDIR}\lib -L$${LIBZDIR}\lib  -lz -lm -lwsock32 -liconv
+}
 macx:release {
  LIBS+= -dead_strip
+}
 unix {
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 # Input
 HEADERS += \
 # apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.h \
  infobar.h \
  mainbase.h \
  mainbase.h \
  matrix.h \
  mesh.h \
  miscq.h \
  modelcatalogue.h \
  Neighbor.h \
  node.h \
  nodeitem.h \
  nodeset.h \
  OptionFileDialog.h \
  output.h \
  parameter.h \
  pardialog.h \
  parse.h \
  pi.h \
  qcanvasarrow.h \
  random.h \
  rungekutta.h \
  simitembase.h \
  simplugin.h \
  sqr.h \
  tiny.h \
  transporterdialog.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  wall.h \
  wallitem.h \
  warning.h \
  xmlwrite.h \
  $${PARTMPL}
 SOURCES += \
 # apoplastitem.cpp \
  canvas.cpp \
  cellbase.cpp \
  cell.cpp \
  cellitem.cpp \
  forwardeuler.cpp \
  mainbase.cpp \
  matrix.cpp \
  mesh.cpp \
  miscq.cpp \
  modelcatalogue.cpp \
  Neighbor.cpp \
  node.cpp \
  nodeitem.cpp \
  nodeset.cpp \
  OptionFileDialog.cpp \
  output.cpp \
  parameter.cpp \
  pardialog.cpp \
  parse.cpp \
  random.cpp \
  rungekutta.cpp \
  simitembase.cpp \
  transporterdialog.cpp \
  UniqueMessage.cpp \
  vector.cpp \
  wallbase.cpp \
  wall.cpp \
  wallitem.cpp \
  warning.cpp \
  xmlwrite.cpp \
  $$MAINSRC
 contains( TARGET, leaf_fleming ) {
  DEFINES += FLEMING
+}
 contains(GRAPHICS, qwt) {
  #macx:LIBS += -L$$QWTDIR/lib -lqwt
  #win32:LIBS += -L$$QWTDIR/lib -lqwt5
  #LIBS += -L$$QWTDIR/lib -lqwt
  INCLUDEPATH += $$QWTDIR/include
  DEFINES += HAVE_QWT
  HEADERS += data_plot.h
  SOURCES += data_plot.cpp
+}
 contains( GRAPHICS, qt ) {
  message( "Building Qt executable" )
  QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive
+}
 contains( GRAPHICS, xfig ) {
  message("Building Xfig executable (background runnable).")
  QMAKE_CXXFLAGS += -DXFIGGRAPHICS
+}
 contains( GRAPHICS, x11 ) {
  !unix {
   error("X11 graphics only available on Unix systems.")
+ }
  message("Building X11 executable")
  SOURCES += x11graph.cpp
  HEADERS += x11graph.h
  QMAKE_CXXFLAGS += -DX11GRAPHICS
  CONFIG -= qt
  CONFIG += x11
  unix:LIBS += -lpng
+}
 #contains( GRAPHICS, qwt ) {
 # 	QMAKE_POST_LINK = "install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \
 #}
 # MACOSX packaging
 macx {
 ICON = leaficon.icns
 QMAKE_POST_LINK = "\
 	#install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	cp leaficon.icns $${DESTDIR}/$${TARGET}.app; \
 	cp gpl3.txt $${DESTDIR}/$${TARGET}.app/Contents/MacOS/.                                    ; \
 	mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	cp -R /Library/Frameworks/QtCore.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	cp -R /Library/Frameworks/QtGui.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	cp -R /Library/Frameworks/Qt3Support.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	#cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	#install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \
 	install_name_tool -change /usr/local/qwt/lib/libqwt.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\
 	install_name_tool -id @executable_path/../Frameworks/QtCore.framework/Versions/Current/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtCore.framework/Versions/4.0/QtCore; \
 	install_name_tool -id @executable_path/../Frameworks/QtGui.framework/Versions/Current/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtGui.framework/Versions/4.0/QtGui; \
 	install_name_tool -id @executable_path/../Frameworks/Qt3Support.framework/Versions/Current/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
 	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	install_name_tool -change Frameworks/Qt3Support.framework/Versions/Current/Qt3Support @executable_path/../Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
 	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
 	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; "
+}
 # finis

src/build_models/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* plugin_auxingrowth.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 	* plugin_test.pro: Ditto.
 	* plugin_meinhardt.pro: Ditto.
 -06-24    <guravage@caterpie.sen.cwi.nl>
 	* plugin_auxingrowth.pro: Use correct library path.
 	* plugin_meinhardt.pro: Ditto.
 	* plugin_test.pro: Ditto.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* auxingrowthplugin.cpp: Removed NULL assignments to unused variables.
 	* meinhardtplugin.cpp: Ditto.
 	* testplugin.cpp: Ditto.
 -06-22    <guravage@caterpie.sen.cwi.nl>
 	* Makefile (clean): Add windows equivalent of UNIX touch.
 -06-18    <guravage@caterpie.sen.cwi.nl>
 	* plugin_auxingrowth.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.
 	* plugin_meinhardt.pro: Ditto.
 	* plugin_test.pro: Ditto.
 	* Makefile (clean): add if stmt not to `touch` on windows.
 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* testplugin.cpp (CelltoCellTransport) Use NULL assignment merely to obviate compilation warnings.
 	(WallDynamics): Ditto.
 	(CellDynamics): Ditto.
 	(OnDivide): Ditto.
 	* meinhardtplugin.cpp (OnDivide): Use NULL assignment merely to obviate compilation warnings.
 	* (WallDynamics): Ditto.
 	* auxingrowthplugin.cpp (OnDivide): Use NULL assignment merely to obviate compilation warnings.
 -06-03    <guravage@caterpie.sen.cwi.nl>
 	* Makefile: Added top-level Makefile.
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* plugin_test.pro: Added -fPIC option to QMAKE_CXXFLAGS.
 	* plugin_meinhardt.pro: ditto
 	* plugin_auxingrowth.pro: ditto

src/build_models/plugin_auxingrowth.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = auxingrowth
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/plugin_meinhardt.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = meinhardt
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/plugin_test.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = test
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/canvas.cpp

➞

Show inline comments

@@ @@ -573,769 +573,768 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   connect( timer, SIGNAL(timeout()), SLOT(TimeStepWrap()) );
   stopSimulation();
   statusBar()->addWidget(new QLabel("Ready."));
   setCaption(caption);
   gifanim = 0;
   infobar = new InfoBar();
   addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void)
+{
   infobar->SetText(mesh.ModelID());
+}
 void Main::UserMessage(QString message, int timeout)
+{
   statusBar()->showMessage(message, timeout);
+}
 void Main::init()
+{
   clear();
   static int r=24;
   srand(++r);
   mainCount++;
+}
 Main::~Main()
+{
   delete printer;
   if ( !--mainCount ) {
+  }
   //EndGifAnim();
+}
 void Main::newView()
+{
   // Open a new view... have it delete when closed.
   Main *m = new Main(canvas, mesh, 0, 0, Qt::WDestructiveClose);
   qApp->setMainWidget(m);
   m->show();
   qApp->setMainWidget(0);
+}
 void Main::EditParameters()
+{
   ParameterDialog *pardial = new ParameterDialog(this, "stridediag");
   // Make sure the values in the parameter dialog are updated after a file is read
   // each method changing the parameters (reading XML or PAR files) should
   // emit this signal
   QObject::connect(   this, SIGNAL( ParsChanged() ), pardial, SLOT( Reset() ) );
+}
 void Main::savePars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "Parameter files (*.par)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     ofstream parfile((const char *)fileName);
     par.Write(parfile);
+  }
   startSimulation();
+}
 void Main::readPars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::ExistingFile );
   fd->setFilter( "Parameter files (*.par)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     par.Read((const char *)fileName);
+  }
   emit ParsChanged();
+}
 void Main::saveStateXML()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "XML (*.xml)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
 			       tr("A file called %1 already exists."
 				  "Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       return saveStateXML();
     } else {
       mesh.XMLSave((const char *)fileName, XMLSettingsTree());
+    }
+  }
+}
 void Main::snapshot()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
 			       tr("A file called %1 already exists."
 				  "Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       return snapshot();
     } else {
       // extract extension from filename
       QString extension = getExtension(fileName);
       // Save bitmaps at 1024x768
       Save((const char *)fileName, extension, 1024, 768);
+    }
+  }
+}
 void Main::readPrevStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     if (f==xml_files.begin()) {
       QMessageBox mb( "Read previous leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *(--f);
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char *)next_file);
+  }
+}
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime)
+{
   try {
     xmlNode *settings;
     mesh.XMLRead((const char *)filename, &settings, geometry, pars, simtime);
 #ifdef QDEBUG
     qDebug() << "Reading done."<< endl;
 #endif
     XMLReadSettings(settings);
     xmlFree(settings);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     FitLeafToCanvas();
     currentFile =  QString(filename);
     Plot();
     QString status_message = QString("Successfully read leaf from file %1. Time is %2 h.").arg(currentFile).arg(mesh.getTimeHours().c_str());
     cerr << status_message.toStdString() << endl;
     setCaption(caption_with_file.arg(filename));
     statusBar()->message(status_message);
     emit ParsChanged();
 #ifdef QDEBUG
     qDebug() << "Done. Returning 0." << endl;
 #endif
     return 0;
   } catch (const char *error_message) {
     QMessageBox mb( "Read leaf from XML file",
 		    QString(error_message),
 		    QMessageBox::Critical,
 		    QMessageBox::Ok | QMessageBox::Default,
 		    Qt::NoButton,
 		    Qt::NoButton);
     mb.exec();
     return 1;
+  }
+}
 void Main::readNextStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     ++f;
     if (f==xml_files.end()) {
       QMessageBox mb( "Read next leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *f;
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readLastStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     next_file = xml_files.back();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readFirstStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     next_file = xml_files.front();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readStateXML()
+{
   //  extern Mesh mesh;
   stopSimulation();
 #ifdef QDEBUG
   qDebug() << "Trying to open an OptionFileDialog" << endl;
 #endif
   OptionFileDialog *fd = new OptionFileDialog( this, "read dialog", TRUE );
   fd->setMode( OptionFileDialog::ExistingFile );
   fd->setFilter( "XML files (*.xml)");
   if (working_dir) {
     fd->setDir(*working_dir);
+  }
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if (working_dir) {
       delete working_dir;
+    }
     working_dir = fd->dir();
     if (readStateXML((const char *)fileName,fd->readGeometryP(), fd->readParametersP()) )
       return readStateXML(); // user can try again
+  }
+}
 void Main::clear()
+{
   editor->clear();
+}
 void Main::about()
+{
   static QMessageBox* about = new QMessageBox
     ( "VirtualLeaf V1.0",
       "<h3>VirtualLeaf V1.0</h3>"
       "<p>"
       "An Open Source framework for cell-based modeling of plant tissue growth and development <br>"
       "(c) 2005-2008, Roeland Merks <i>et al.</i><br>"
       "    <a href=\"http://www.psb.vib-ugent.be\">VIB Department Plant Systems Biology</a>, "
       "Ghent, Belgium <br>"
       "(c) 2008-2010, <a href=\"http://www.cwi.nl/~merks\">Roeland Merks <i>et al.</i></a> <br>"
       "    <a href=\"http://www.cwi.nl\">Centrum Wiskunde & Informatica</a> and <a href=\"http://www.ncsb.nl\">Netherlands Consortium for Systems Biology</a>, Amsterdam, Netherlands <br>"
 "<br>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.<br>"
       "<br>If you use this code for your projects, please cite our paper:"
 "<br>Merks, Guravage, Inze, and Beemster. An Open Source framework for cell-based modeling of plant tissue growth and development. <i>Plant Physiology,</i> submitted.<br> . <br>"
       "<br>Please share your model plugins and extensions at <a href=\"http://virtualleaf.googlecode.com\">http://virtualleaf.googlecode.com</a>.",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   about->setButtonText( 1, "Dismiss" );
   about->show();
+}
 void Main::gpl()
+{
   static QMessageBox* gpl = new QMessageBox ( "GPL License", "",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   QDir docDir(QApplication::applicationDirPath());
   docDir.cd("../doc");
   QString path = docDir.filePath("gpl3.txt");
   std::ifstream file(path.toStdString().c_str());
   std::string str;
   if (file) {
     file.seekg(0, std::ios::end);
     str.reserve(file.tellg());
     file.seekg(0, std::ios::beg);
     str.assign((std::istreambuf_iterator<char>(file)),
 	       std::istreambuf_iterator<char>());
     gpl->setDetailedText(QString(str.c_str()));
+  }
   gpl->setText(QString( "<h3>GNU GENERAL PUBLIC LICENSE</h3>"
 			"<p>Version 3, 29 June 2007</p>"
 			"<p>Copyright &copy; 2007 Free Software Foundation, Inc. "
 			"&lt;<a href=\"http://fsf.org/\">http://fsf.org/</a>&gt;</p><p>"
 			"Everyone is permitted to copy and distribute verbatim copies "
 			"of this license document, but changing it is not allowed.</p>"
 			"<h2>GNU GENERAL PUBLIC LICENSE</h2>"));
   gpl->setButtonText( 1, "Dismiss" );
   gpl->show();
+}
 void Main::aboutQt(){
   QMessageBox::aboutQt( this, "Virtual Leaf" );
+}
 void Main::toggleShowCellCenters()
+{
   Plot();
+}
 void Main::toggleShowWalls()
+{
   Plot();
+}
 void Main::toggleShowApoplasts()
+{
   Plot();
+}
 void Main::toggleShowNodes()
+{
   Plot();
+}
 void Main::toggleNodeNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellAxes(void)
+{
   Plot();
+}
 void Main::toggleCellStrain(void)
+{
   Plot();
+}
 void Main::toggleShowFluxes(void)
+{
   Plot();
+}
 void Main::toggleShowBorderCells()
+{
   Plot();
+}
 void Main::toggleHideCells(void)
+{
   Plot();
   editor->FullRedraw();
+}
 void Main::toggleMovieFrames(){}
 void Main::toggleLeafBoundary(){}
 void Main::toggleDynCells() {}
 void Main::startSimulation(void)
+{
   timer->start( 0 );
   statusBar()->message("Simulation started");
   running = true;
+}
 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;
   TimeStep();
   t++;
   // check number of timesteps
   if (t==par.nit) {
     emit SimulationDone();
+  }
+}
 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();
+}
 void Main::CleanMeshChemicals(void)
+{
   vector<double> clean_chem(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_chem[i]=par.initval[i];
+  }
   mesh.CleanChemicals(clean_chem);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::CleanMeshTransporters(void)
+{
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_transporters[i]=0.;
+  }
   mesh.CleanTransporters(clean_transporters);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::RandomizeMesh(void)
+{
   vector<double> max_chem(Cell::NChem());
   vector<double> max_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     max_transporters[i]=0.;
     max_chem[i]=par.initval[i];
+  }
   // Amount of PIN1 at walls
   max_transporters[1] = 0.01;
   mesh.RandomizeChemicals(max_chem, max_transporters);
   Plot();
+}
 void Main::XMLReadSettings(xmlNode *settings)
+{
   MainBase::XMLReadSettings(settings);
   view->setItemChecked(com_id, showcentersp);
   view->setItemChecked(mesh_id, showmeshp);
   view->setItemChecked(border_id, showbordercellp);
   view->setItemChecked(node_number_id, shownodenumbersp);
   view->setItemChecked(cell_number_id, showcellnumbersp);
   view->setItemChecked(cell_axes_id, showcellsaxesp);
   view->setItemChecked(cell_strain_id, showcellstrainp);
   view->setItemChecked(movie_frames_id, movieframesp);
   view->setItemChecked(only_boundary_id, showboundaryonlyp);
   view->setItemChecked(fluxes_id, showfluxesp);
   view->setItemChecked(hide_cells_id, hidecellsp);
   options->setItemChecked(dyn_cells_id, dynamicscellsp);
   view->setItemChecked( cell_walls_id, showwallsp);
  // view->setItemChecked( apoplasts_id, showapoplastsp);
   editor->setTransform(viewport);
+}
 xmlNode *Main::XMLSettingsTree(void)
+{
   showcentersp = view->isItemChecked(com_id);
   showmeshp = view->isItemChecked(mesh_id);
   showbordercellp =  view->isItemChecked(border_id);
   shownodenumbersp =  view->isItemChecked(node_number_id);
   showcellnumbersp =  view->isItemChecked(cell_number_id);
   showcellsaxesp = view->isItemChecked( cell_axes_id );

src/gpl3.txt

➞

Show inline comments

file renamed from doc/gpl3.txt to src/gpl3.txt

src/libplugin.pro

➞

Show inline comments

+#
 #  $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += staticlib
 QMAKE_CXXFLAGS += -fexceptions
 QMAKE_CXXFLAGS += -Wall
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 win32:QMAKE_CXXFLAGS -= O2
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QMAKE_CXXFLAGS_DEBUG -= -finstrument-functions
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = ../lib
 LIBDIR = ../lib
 PARTMPL = VirtualLeafpar.tmpl
 QT += qt3support
 TARGET = vleaf
 TEMPLATE = lib
 HEADERS = \
  cellbase.h \
  matrix.h \
  output.h \
  parameter.h \
  parse.h \
  random.h \
  simplugin.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  warning.h
 SOURCES = \
  cellbase.cpp \
  matrix.cpp \
  output.cpp \
  parameter.cpp \
  parse.cpp \
  random.cpp \
  simplugin.cpp \
  UniqueMessage.cpp \
  vector.cpp \
  wallbase.cpp \
  warning.cpp
 unix {
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
+#

src/output.cpp

➞

Show inline comments

 /*
+ *
  *  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 <string>
 #include <stdio.h>
 #include <string.h>
 #include <stdlib.h>
 #include <errno.h>
 #include <sys/types.h>
 #include <sys/stat.h>
 #include "warning.h"
 #include "parameter.h"
 #include "output.h"
 #include <QDir>
 #include <QFileInfo>
 static const std::string _module_id("$Id$");
 using namespace MyWarning;
 #define FNAMESIZE 100
 int OpenFileAndCheckExistance(FILE **fp,const char *fname,char *ftype) {
   *fp=fopen(fname,ftype);
   if (*fp==NULL)
     return FALSE;
   if (!strncmp(ftype,"a",1)) {
     if (ftell(*fp)>0L) return TRUE;
     else return FALSE;
   } else return TRUE;
+}
 int FileExistsP(const char *fname) {
   FILE *fp;
   fp=fopen(fname,"r");
   if (fp==NULL)
     return FALSE;
   fclose(fp);
   return TRUE;
+}
 int YesNoP(const char *message) {
   char answer[100];
   fprintf(stderr,"%s (y/n) ",message);
   fflush(stderr);
   scanf("%s",answer);
   while (strcmp(answer,"y") && strcmp(answer,"n")) {
     fprintf(stderr,"\n\bPlease answer 'y' or 'n'. ");
     fflush(stderr);
     scanf("%s",answer);
+  }
   if (!strcmp(answer,"y")) return TRUE;
   return FALSE;
+}
 FILE *OpenWriteFile(const char *filename)
+{
   char fname[FNAMESIZE];
   FILE *fp;
   fprintf(stderr,"Opening %s for writing\n",filename);
   if(FileExistsP(filename)==TRUE) {
     if (false/*par.interactive*/) {
       char *message=(char *)malloc(2000*sizeof(char));
       if (!YesNoP("File exists, overwrite?")) {
 	sprintf(message," Could not open file %s for writing, exiting... \n"
 		,filename);
 	//exit(0);
 	throw(message);
+      }
     } else {
       /* Rename old file */
       sprintf(fname, "%s~",filename);
       rename(filename, fname);
+    }
+  }
   strncpy(fname, filename, FNAMESIZE-1);
   if ((fp=fopen(fname,"w"))==NULL) {
     char *message=(char *)malloc(2000*sizeof(char));
     sprintf(message," Could not open file %s for writing: "
 	    ,fname);
     perror("");
     throw(message);
+  }
   return fp;
+}
 FILE *OpenReadFile(const char *filename)
+{
   FILE *fp;
   fprintf(stderr,"Opening %s for reading\n",filename);
   if((OpenFileAndCheckExistance(&fp,filename,"r"))==FALSE) {
     char *message=(char *)malloc(2000*sizeof(char));
     sprintf(message," File %s not found or empty, exiting... \n" ,filename);
     throw(message);
+  }
   return fp;
+}
 char *ReadLine(FILE *fp)
+{
   /* does almost the same as fgetln(), but DEC Unix doesn't understand
      fgetln(). Also I want my function to return a real C string,
      terminated by a \0. */
   /* The function reads a line from file *fp, and returns a pointer to the
      line read, which can be freed with a normal free(). The length of the
      string is written in *len */
 #define INITIAL_BUFSIZE 100
   char *tmpstring;
   int character;
   long bufsize;
   char *line;
   int pos;
   CheckFile(fp);
   /* first allocate a string with a standard length */
   bufsize=INITIAL_BUFSIZE;
   MEMORYCHECK(tmpstring=(char *)malloc(bufsize*sizeof(char)));
   pos=0;
   while ((character=getc(fp))!=EOF && /* read a character and check */
 	 character!='\n') {
     tmpstring[pos]=(char)character;
     (pos)++;
     if (pos >= bufsize) {
       /* line is longer than initial_bufsize, reallocate space */
       bufsize+=INITIAL_BUFSIZE;
       MEMORYCHECK(tmpstring=(char *)realloc(tmpstring,bufsize*sizeof(char)));
+    }
+  }
   if (character==EOF) {
     if (pos==0) {
       /* EOF was reached, while no characters were read */
       free(tmpstring);
       return NULL;
+    }
     if (ferror(fp)) {
       error("I/O error in ReadLine(%ld): %s\n",fp, strerror(errno));
+    }
+  }
   /* Allocate enough memory for the line */
   MEMORYCHECK(line=(char *)malloc((++(pos))*sizeof(char)));
   strncpy(line,tmpstring,(pos)-1);
   free(tmpstring);
   line[pos-1]='\0';
   return line;
+}
 void CheckFile(FILE *fp)
+{
   if (ftell(fp)<0) {
     /* file is probably not open, or another error occured */
     error("File error (fp=%ld): %d %s\n",fp,errno,strerror(errno));
+  }
   /* File pointer is ok */
+}
 char *Chext(char *filename) {
   /* Chop the extension from a filename */
   /* Search backwards until a dot */
   /* Remember to free the memory allocated by this function */
   /* ( free(result) ) */
   /* not yet tested */
   int i;
   char *result;
   for (i=strlen(filename)-1;i>=0;i--) {
     if (filename[i]=='.')
       break;
+  }
   /* No . found */
   if (i==0) {
     result=strdup(filename);
   } else {
     /* . found */
     result=(char *)malloc((i+1)*sizeof(char));
     strncpy(result, filename, i);
+  }
   return result;
+}
 void MakeDir(const char *dirname) {
 #ifdef QTGRAPHICS
   QFileInfo file_info(dirname);
   //check for existance
   if (file_info.exists()) {
     if (file_info.isDir()) {
       // OK
       cerr << "Using existing directory " << dirname << " for data storage." << endl;
       return;
     } else {
       char *message = new char[MESS_BUF_SIZE+1];
       snprintf(message, MESS_BUF_SIZE, "%s is not a directory", dirname);
       cerr << message << endl;
       throw(message);
+    }
+  }
   // make directory
   QDir dir;
   if (!dir.mkdir(QString(dirname))) {
     char *message = new char[MESS_BUF_SIZE+1];
     snprintf(message,MESS_BUF_SIZE,"%s: Error in making directory %s",strerror(errno),dirname);
     warning(message);
     //strerror(message);
     //exit(1);
     return;
+  }
   // check
 #else
   int status;
   char message[MESS_BUF_SIZE];
   status=mkdir(dirname, S_IRWXU); // S_IRWXU: Read, Write, Execute by Owner
   if (status<0) { // error occurred
     //check for existance
     if (errno==EEXIST) {
       // Check whether it is a directory
       struct stat buf;
       stat(dirname, &buf);
       if (S_ISDIR(buf.st_mode)) {
 	// OK
 	extern  Parameter par;
 	if (false /* && par.interactive*/) {
 	  fprintf(stderr,"Using existing directory %s for data storage.\n",dirname);
 	  if (!YesNoP("OK?")) {
 	    // User doesn't agree. Exit
 	    exit(1);
+	  }
 	} else {
 	  fprintf(stderr,"Using existing directory %s for data storage.\n",dirname);
+	}
       } else {
 	snprintf(message, MESS_BUF_SIZE, "%s is not a directory", dirname);
 	perror(message);
 	exit(1);
+      }
     } else {
       // a different error occurred. Print error and quit
       snprintf(message,MESS_BUF_SIZE,"Error in making directory %s",dirname);
       perror(message);
       exit(1);
+    }
+  }
 #endif
+}
 char* AppendHomeDirIfPathRelative(char *datadir) {
   QDir dataDir(datadir);
   if (dataDir.isRelative()){
     if (datadir) {
       free(datadir);
+    }
     QStringList path;
     path << QDir::homePath() << dataDir.dirName();
     return strdup((char *) path.join("/").toStdString().c_str());
   } else return datadir;
+}
 /* finis */

src/output.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 #ifndef _OUTPUT_H_
 #define _OUTPUT_H_
 #ifdef __cplusplus
 extern "C" {
 #endif
   int OpenFileAndCheckExistance(FILE **fp,const char *fname,char *ftype);
   int YesNoP(const char *message);
   FILE *OpenWriteFile(const char *filename);
   FILE *OpenGZippedWriteFile(const char *filename);
   FILE *OpenReadFile(const char *filename);
   char *ReadLine(FILE *fp);
   void CheckFile(FILE *fp);
   int FileExistsP(const char *fname);
   char *Chext(char *filename);
   void MakeDir(const char *dirname);
   char *AppendHomeDirIfPathRelative(char *datadir);
   bool CanWeWriteP(char *filename);
 #ifdef __cplusplus
+}
 #endif
 #define MESS_BUF_SIZE 160
 #ifndef FALSE
 #define FALSE 0
 #define TRUE 1
 #endif
 #endif
 /* finis */

src/parameter.cpp

➞

Show inline comments

 /*
+ *
  *  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 "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(".");
   // reassign datadir outside the loop
   QDir dataDir(datadir);
   if (dataDir.isRelative()){
     QStringList path;
     path << QDir::homePath() << dataDir.dirName();
     datadir = strdup((char *) path.join("/").toStdString().c_str());
+  }
+}
 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);
+}
 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);
+}
 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)
     os << " datadir = " << datadir << 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;
   os << " vessel_inh_level = " << vessel_inh_level << endl;
   os << " vessel_expansion_rate = " << vessel_expansion_rate << endl;
   os << " d = " << d << endl;
   os << " e = " << e << endl;
   os << " f = " << f << endl;
   os << " c = " << c << endl;
   os << " mu = " << mu << endl;
   os << " nu = " << nu << endl;
   os << " rho0 = " << rho0 << endl;
   os << " rho1 = " << rho1 << endl;
   os << " c0 = " << c0 << endl;
   os << " gamma = " << gamma << endl;
   os << " eps = " << eps << endl;
   os << " k = "<< k[0] << ", " << k[1] << ", " << k[2] << ", " << k[3] << ", " << k[4] << ", " << k[5] << ", " << k[6] << ", " << k[7] << ", " << k[8] << ", " << k[9] << ", " << k[10] << ", " << k[11] << ", " << k[12] << ", " << k[13] << ", " << k[14] << endl;
   os << " i1 = " << i1 << endl;
   os << " i2 = " << i2 << endl;
   os << " i3 = " << i3 << endl;
   os << " i4 = " << i4 << endl;
   os << " i5 = " << i5 << endl;
   if (s1)
     os << " s1 = " << s1 << endl;
   if (s2)
     os << " s2 = " << s2 << endl;
   if (s3)
     os << " s3 = " << s3 << endl;
   os << " b1 = " << sbool(b1) << endl;
   os << " b2 = " << sbool(b2) << endl;
   os << " b3 = " << sbool(b3) << endl;
   os << " b4 = " << sbool(b4) << endl;
   if (dir1)
     os << " dir1 = " << dir1 << endl;
   if (dir2)
     os << " dir2 = " << dir2 << endl;
+}
 void Parameter::XMLAdd(xmlNode *root) const {
   xmlNode *xmlparameter = xmlNewChild(root, NULL, BAD_CAST "parameter", NULL);
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "arrowcolor" );
     ostringstream text;
     if (arrowcolor)
       text << arrowcolor;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "arrowsize" );
     ostringstream text;
     text << arrowsize;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "textcolor" );
     ostringstream text;
     if (textcolor)
       text << textcolor;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cellnumsize" );
     ostringstream text;
     text << cellnumsize;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "nodenumsize" );
     ostringstream text;
     text << nodenumsize;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "node_mag" );
     ostringstream text;
     text << node_mag;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "outlinewidth" );
     ostringstream text;
     text << outlinewidth;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_outline_color" );
     ostringstream text;
     if (cell_outline_color)
       text << cell_outline_color;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "resize_stride" );
     ostringstream text;
     text << resize_stride;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "T" );
     ostringstream text;
     text << T;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_length" );
     ostringstream text;
     text << lambda_length;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_celllength" );
     ostringstream text;
     text << lambda_celllength;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "target_length" );
     ostringstream text;
     text << target_length;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_expansion_rate" );
     ostringstream text;
     text << cell_expansion_rate;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_div_expansion_rate" );
     ostringstream text;
     text << cell_div_expansion_rate;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "auxin_dependent_growth" );
     ostringstream text;
     text << sbool(auxin_dependent_growth);
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "ode_accuracy" );
     ostringstream text;
     text << ode_accuracy;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "mc_stepsize" );
     ostringstream text;
     text << mc_stepsize;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "mc_cell_stepsize" );
     ostringstream text;
     text << mc_cell_stepsize;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "energy_threshold" );
     ostringstream text;
     text << energy_threshold;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "bend_lambda" );
     ostringstream text;
     text << bend_lambda;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "alignment_lambda" );
     ostringstream text;
     text << alignment_lambda;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rel_cell_div_threshold" );
     ostringstream text;
     text << rel_cell_div_threshold;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rel_perimeter_stiffness" );
     ostringstream text;
     text << rel_perimeter_stiffness;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "collapse_node_threshold" );
     ostringstream text;
     text << collapse_node_threshold;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "morphogen_div_threshold" );
     ostringstream text;
     text << morphogen_div_threshold;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "morphogen_expansion_threshold" );
     ostringstream text;
     text << morphogen_expansion_threshold;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "copy_wall" );
     ostringstream text;
     text << sbool(copy_wall);
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "source" );
     ostringstream text;
     text << source;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "D" );
     xmlNode *xmlvalarray = xmlNewChild(xmlpar, NULL, BAD_CAST "valarray", NULL);
+    {
       ostringstream text;
       text << D[0];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[1];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[2];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[3];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[4];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[5];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[6];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[7];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[8];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[9];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[10];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[11];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[12];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[13];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << D[14];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "initval" );
     xmlNode *xmlvalarray = xmlNewChild(xmlpar, NULL, BAD_CAST "valarray", NULL);
+    {
       ostringstream text;
       text << initval[0];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[1];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[2];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[3];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[4];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[5];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[6];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[7];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[8];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[9];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[10];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[11];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[12];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[13];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << initval[14];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k1" );
     ostringstream text;
     text << k1;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k2" );
     ostringstream text;
     text << k2;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "r" );
     ostringstream text;
     text << r;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "kr" );
     ostringstream text;
     text << kr;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "km" );
     ostringstream text;
     text << km;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "Pi_tot" );
     ostringstream text;
     text << Pi_tot;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "transport" );
     ostringstream text;
     text << transport;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "ka" );
     ostringstream text;
     text << ka;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_prod" );
     ostringstream text;
     text << pin_prod;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_prod_in_epidermis" );
     ostringstream text;
     text << pin_prod_in_epidermis;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_breakdown" );
     ostringstream text;
     text << pin_breakdown;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_breakdown_internal" );
     ostringstream text;
     text << pin_breakdown_internal;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1prod" );
     ostringstream text;
     text << aux1prod;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1prodmeso" );
     ostringstream text;
     text << aux1prodmeso;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1decay" );
     ostringstream text;
     text << aux1decay;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1decaymeso" );
     ostringstream text;
     text << aux1decaymeso;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1transport" );
     ostringstream text;
     text << aux1transport;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux_cons" );
     ostringstream text;
     text << aux_cons;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux_breakdown" );
     ostringstream text;
     text << aux_breakdown;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "kaux1" );
     ostringstream text;
     text << kaux1;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "kap" );
     ostringstream text;
     text << kap;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "leaf_tip_source" );
     ostringstream text;
     text << leaf_tip_source;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "sam_efflux" );
     ostringstream text;
     text << sam_efflux;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "sam_auxin" );
     ostringstream text;
     text << sam_auxin;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "sam_auxin_breakdown" );
     ostringstream text;
     text << sam_auxin_breakdown;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "van3prod" );
     ostringstream text;
     text << van3prod;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "van3autokat" );
     ostringstream text;
     text << van3autokat;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "van3sat" );
     ostringstream text;
     text << van3sat;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k2van3" );
     ostringstream text;
     text << k2van3;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dt" );
     ostringstream text;
     text << dt;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rd_dt" );
     ostringstream text;
     text << rd_dt;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "datadir" );
     ostringstream text;
     if (datadir)
       text << datadir;
     if (datadir) {
       QDir dataDir = QDir::home().relativeFilePath(datadir);
       text << dataDir.dirName().toStdString();
+    }
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "movie" );
     ostringstream text;
     text << sbool(movie);
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "nit" );
     ostringstream text;
     text << nit;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "maxt" );
     ostringstream text;
     text << maxt;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "storage_stride" );
     ostringstream text;
     text << storage_stride;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "xml_storage_stride" );
     ostringstream text;
     text << xml_storage_stride;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rseed" );
     ostringstream text;
     text << rseed;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "constituous_expansion_limit" );
     ostringstream text;
     text << constituous_expansion_limit;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "vessel_inh_level" );
     ostringstream text;
     text << vessel_inh_level;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "vessel_expansion_rate" );
     ostringstream text;
     text << vessel_expansion_rate;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "d" );
     ostringstream text;
     text << d;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "e" );
     ostringstream text;
     text << e;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "f" );
     ostringstream text;
     text << f;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "c" );
     ostringstream text;
     text << c;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "mu" );
     ostringstream text;
     text << mu;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "nu" );
     ostringstream text;
     text << nu;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rho0" );
     ostringstream text;
     text << rho0;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rho1" );
     ostringstream text;
     text << rho1;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "c0" );
     ostringstream text;
     text << c0;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "gamma" );
     ostringstream text;
     text << gamma;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "eps" );
     ostringstream text;
     text << eps;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k" );
     xmlNode *xmlvalarray = xmlNewChild(xmlpar, NULL, BAD_CAST "valarray", NULL);
+    {
       ostringstream text;
       text << k[0];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[1];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[2];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[3];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[4];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[5];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[6];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[7];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[8];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[9];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[10];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[11];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[12];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[13];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+    {
       ostringstream text;
       text << k[14];
       xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
       xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i1" );
     ostringstream text;
     text << i1;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i2" );
     ostringstream text;
     text << i2;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i3" );
     ostringstream text;
     text << i3;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i4" );
     ostringstream text;
     text << i4;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i5" );
     ostringstream text;
     text << i5;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "s1" );
     ostringstream text;
     if (s1)
       text << s1;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "s2" );
     ostringstream text;
     if (s2)
       text << s2;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "s3" );
     ostringstream text;
     if (s3)
       text << s3;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b1" );
     ostringstream text;
     text << sbool(b1);
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b2" );
     ostringstream text;
     text << sbool(b2);
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b3" );
     ostringstream text;
     text << sbool(b3);
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b4" );
     ostringstream text;
     text << sbool(b4);
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dir1" );
     ostringstream text;
     if (dir1)
       text << dir1;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dir2" );
     ostringstream text;
     if (dir2)
       text << dir2;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+}
 void Parameter::AssignValToPar(const char *namec, const char *valc) {
   QLocale standardlocale(QLocale::C);
   bool ok;
   if (!strcmp(namec, "arrowcolor")) {
     if (arrowcolor) { free(arrowcolor); }
     arrowcolor=strdup(valc);
+  }
   if (!strcmp(namec, "arrowsize")) {
     arrowsize = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'arrowsize' from XML file.",valc); }
+  }
   if (!strcmp(namec, "textcolor")) {
     if (textcolor) { free(textcolor); }
     textcolor=strdup(valc);
+  }
   if (!strcmp(namec, "cellnumsize")) {
     cellnumsize = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'cellnumsize' from XML file.",valc); }
+  }
   if (!strcmp(namec, "nodenumsize")) {
     nodenumsize = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'nodenumsize' from XML file.",valc); }
+  }
   if (!strcmp(namec, "node_mag")) {
     node_mag = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'node_mag' from XML file.",valc); }
+  }
   if (!strcmp(namec, "outlinewidth")) {
     outlinewidth = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'outlinewidth' from XML file.",valc); }
+  }
   if (!strcmp(namec, "cell_outline_color")) {
     if (cell_outline_color) { free(cell_outline_color); }
     cell_outline_color=strdup(valc);
+  }
   if (!strcmp(namec, "resize_stride")) {
     resize_stride = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'resize_stride' from XML file.",valc); }
+  }
   if (!strcmp(namec, "T")) {
     T = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'T' from XML file.",valc); }
+  }
   if (!strcmp(namec, "lambda_length")) {
     lambda_length = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'lambda_length' from XML file.",valc); }
+  }
   if (!strcmp(namec, "lambda_celllength")) {
     lambda_celllength = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'lambda_celllength' from XML file.",valc); }
+  }
   if (!strcmp(namec, "target_length")) {
     target_length = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'target_length' from XML file.",valc); }
+  }
   if (!strcmp(namec, "cell_expansion_rate")) {
     cell_expansion_rate = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'cell_expansion_rate' from XML file.",valc); }
+  }
   if (!strcmp(namec, "cell_div_expansion_rate")) {
     cell_div_expansion_rate = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'cell_div_expansion_rate' from XML file.",valc); }
+  }
   if (!strcmp(namec, "auxin_dependent_growth")) {
     auxin_dependent_growth = strtobool(valc);
+  }
   if (!strcmp(namec, "ode_accuracy")) {
     ode_accuracy = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'ode_accuracy' from XML file.",valc); }
+  }
   if (!strcmp(namec, "mc_stepsize")) {
     mc_stepsize = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'mc_stepsize' from XML file.",valc); }
+  }
   if (!strcmp(namec, "mc_cell_stepsize")) {
     mc_cell_stepsize = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'mc_cell_stepsize' from XML file.",valc); }
+  }
   if (!strcmp(namec, "energy_threshold")) {
     energy_threshold = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'energy_threshold' from XML file.",valc); }
+  }
   if (!strcmp(namec, "bend_lambda")) {
     bend_lambda = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'bend_lambda' from XML file.",valc); }
+  }
   if (!strcmp(namec, "alignment_lambda")) {
     alignment_lambda = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'alignment_lambda' from XML file.",valc); }
+  }
   if (!strcmp(namec, "rel_cell_div_threshold")) {
     rel_cell_div_threshold = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rel_cell_div_threshold' from XML file.",valc); }
+  }
   if (!strcmp(namec, "rel_perimeter_stiffness")) {
     rel_perimeter_stiffness = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rel_perimeter_stiffness' from XML file.",valc); }
+  }
   if (!strcmp(namec, "collapse_node_threshold")) {
     collapse_node_threshold = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'collapse_node_threshold' from XML file.",valc); }
+  }
   if (!strcmp(namec, "morphogen_div_threshold")) {
     morphogen_div_threshold = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'morphogen_div_threshold' from XML file.",valc); }
+  }
   if (!strcmp(namec, "morphogen_expansion_threshold")) {
     morphogen_expansion_threshold = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'morphogen_expansion_threshold' from XML file.",valc); }
+  }
   if (!strcmp(namec, "copy_wall")) {
     copy_wall = strtobool(valc);
+  }
   if (!strcmp(namec, "source")) {
     source = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'source' from XML file.",valc); }
+  }
   if (!strcmp(namec, "k1")) {
     k1 = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'k1' from XML file.",valc); }
+  }
   if (!strcmp(namec, "k2")) {
     k2 = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'k2' from XML file.",valc); }
+  }
   if (!strcmp(namec, "r")) {
     r = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'r' from XML file.",valc); }
+  }
   if (!strcmp(namec, "kr")) {
     kr = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'kr' from XML file.",valc); }
+  }
   if (!strcmp(namec, "km")) {
     km = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'km' from XML file.",valc); }
+  }
   if (!strcmp(namec, "Pi_tot")) {
     Pi_tot = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'Pi_tot' from XML file.",valc); }
+  }
   if (!strcmp(namec, "transport")) {
     transport = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'transport' from XML file.",valc); }
+  }
   if (!strcmp(namec, "ka")) {
     ka = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'ka' from XML file.",valc); }
+  }
   if (!strcmp(namec, "pin_prod")) {
     pin_prod = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_prod' from XML file.",valc); }
+  }
   if (!strcmp(namec, "pin_prod_in_epidermis")) {
     pin_prod_in_epidermis = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_prod_in_epidermis' from XML file.",valc); }
+  }
   if (!strcmp(namec, "pin_breakdown")) {
     pin_breakdown = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_breakdown' from XML file.",valc); }
+  }
   if (!strcmp(namec, "pin_breakdown_internal")) {
     pin_breakdown_internal = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_breakdown_internal' from XML file.",valc); }
+  }
   if (!strcmp(namec, "aux1prod")) {
     aux1prod = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1prod' from XML file.",valc); }
+  }
   if (!strcmp(namec, "aux1prodmeso")) {
     aux1prodmeso = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1prodmeso' from XML file.",valc); }
+  }
   if (!strcmp(namec, "aux1decay")) {
     aux1decay = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1decay' from XML file.",valc); }
+  }
   if (!strcmp(namec, "aux1decaymeso")) {
     aux1decaymeso = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1decaymeso' from XML file.",valc); }
+  }
   if (!strcmp(namec, "aux1transport")) {
     aux1transport = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1transport' from XML file.",valc); }
+  }
   if (!strcmp(namec, "aux_cons")) {
     aux_cons = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux_cons' from XML file.",valc); }
+  }
   if (!strcmp(namec, "aux_breakdown")) {
     aux_breakdown = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux_breakdown' from XML file.",valc); }
+  }
   if (!strcmp(namec, "kaux1")) {
     kaux1 = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'kaux1' from XML file.",valc); }
+  }
   if (!strcmp(namec, "kap")) {
     kap = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'kap' from XML file.",valc); }
+  }
   if (!strcmp(namec, "leaf_tip_source")) {
     leaf_tip_source = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'leaf_tip_source' from XML file.",valc); }
+  }
   if (!strcmp(namec, "sam_efflux")) {
     sam_efflux = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'sam_efflux' from XML file.",valc); }
+  }
   if (!strcmp(namec, "sam_auxin")) {
     sam_auxin = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'sam_auxin' from XML file.",valc); }
+  }
   if (!strcmp(namec, "sam_auxin_breakdown")) {
     sam_auxin_breakdown = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'sam_auxin_breakdown' from XML file.",valc); }
+  }
   if (!strcmp(namec, "van3prod")) {
     van3prod = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3prod' from XML file.",valc); }
+  }
   if (!strcmp(namec, "van3autokat")) {
     van3autokat = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3autokat' from XML file.",valc); }
+  }
   if (!strcmp(namec, "van3sat")) {
     van3sat = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3sat' from XML file.",valc); }
+  }
   if (!strcmp(namec, "k2van3")) {
     k2van3 = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'k2van3' from XML file.",valc); }
+  }
   if (!strcmp(namec, "dt")) {
     dt = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'dt' from XML file.",valc); }
+  }
   if (!strcmp(namec, "rd_dt")) {
     rd_dt = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rd_dt' from XML file.",valc); }
+  }
   if (!strcmp(namec, "datadir")) {
     if (datadir) { free(datadir); }
     datadir=strdup(valc);
     datadir = AppendHomeDirIfPathRelative(datadir);
+  }
   if (!strcmp(namec, "movie")) {
     movie = strtobool(valc);
+  }
   if (!strcmp(namec, "nit")) {
     nit = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'nit' from XML file.",valc); }
+  }
   if (!strcmp(namec, "maxt")) {
     maxt = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'maxt' from XML file.",valc); }
+  }
   if (!strcmp(namec, "storage_stride")) {
     storage_stride = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'storage_stride' from XML file.",valc); }
+  }
   if (!strcmp(namec, "xml_storage_stride")) {
     xml_storage_stride = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'xml_storage_stride' from XML file.",valc); }
+  }
   if (!strcmp(namec, "rseed")) {
     rseed = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'rseed' from XML file.",valc); }
+  }
   if (!strcmp(namec, "constituous_expansion_limit")) {
     constituous_expansion_limit = standardlocale.toInt(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'constituous_expansion_limit' from XML file.",valc); }
+  }
   if (!strcmp(namec, "vessel_inh_level")) {
     vessel_inh_level = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'vessel_inh_level' from XML file.",valc); }
+  }
   if (!strcmp(namec, "vessel_expansion_rate")) {
     vessel_expansion_rate = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'vessel_expansion_rate' from XML file.",valc); }
+  }
   if (!strcmp(namec, "d")) {
     d = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'd' from XML file.",valc); }
+  }
   if (!strcmp(namec, "e")) {
     e = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'e' from XML file.",valc); }
+  }
   if (!strcmp(namec, "f")) {
     f = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'f' from XML file.",valc); }
+  }
   if (!strcmp(namec, "c")) {
     c = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'c' from XML file.",valc); }
+  }
   if (!strcmp(namec, "mu")) {
     mu = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'mu' from XML file.",valc); }
+  }
   if (!strcmp(namec, "nu")) {
     nu = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'nu' from XML file.",valc); }
+  }
   if (!strcmp(namec, "rho0")) {
     rho0 = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rho0' from XML file.",valc); }
+  }
   if (!strcmp(namec, "rho1")) {
     rho1 = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rho1' from XML file.",valc); }
+  }
   if (!strcmp(namec, "c0")) {
     c0 = standardlocale.toDouble(valc, &ok);
     if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'c0' from XML file.",valc); }
+  }
   if (!strcmp(namec, "gamma")) {
     gamma = standardlocale.toDouble(valc, &ok);
     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);
+  }
+}
 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++);
+    }
+  }
   // reassign datadir outside the loop
   if (!strcmp(namec, "datadir")) {
     if (datadir) { free(datadir); }
     QDir dataDir(datadir);
     if (dataDir.isRelative()){
       QStringList path;
       path << QDir::homePath() << dataDir.dirName();
       datadir = strdup((char *) path.join("/").toStdString().c_str());
+    }
+  }
+}
 ostream &operator<<(ostream &os, Parameter &p) {
   p.Write(os);
   return os;
+}
 /* finis */

src/parameter.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 #ifndef _PARAMETER_H_
 #define _PARAMETER_H_
 #include "vector.h"
 #include <vector>
 #include <libxml/parser.h>
 #include <libxml/tree.h>
 class Parameter {
+ 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);
    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;
   double c;
   double mu;
   double nu;
   double rho0;
   double rho1;
   double c0;
   double gamma;
   double eps;
   double * k;
   int i1;
   int i2;
   int i3;
   int i4;
   int i5;
   char * s1;
   char * s2;
   char * s3;
   bool b1;
   bool b2;
   bool b3;
   bool b4;
   char * dir1;
   char * dir2;
  private:
 };
+ };
 ostream &operator<<(ostream &os, Parameter &p);
 const char *sbool(const bool &p);
  ostream &operator<<(ostream &os, Parameter &p);
  const char *sbool(const bool &p);
 #endif
 /* finis */

src/perl/ChangeLog

➞

Show inline comments

 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* make_parameter_source.pl: Added datadir changes.
 -06-21    <guravage@caterpie.sen.cwi.nl>
 	* make_pardialog_source.pl: Reformatted. If datadir is relative append it to the user's home directory.
 	* make_parameter_source.pl: Ditto.
 	* make_xmlwritecode.pl: Ditto.

src/perl/make_parameter_source.pl

➞

Show inline comments

 #!/usr/bin/perl
+#
 # $Id$
+#
 #  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.
+#
 # input: parameter file + types
 # format: par_name = default_value/type
 # output: C++ source code of class Parameter
 # and sample parameter file
 %funname = (
     "double" => fgetpar,
     "float" => fgetpar,
     "int" => igetpar,
     "bool" => bgetpar,
     "char *" => sgetpar,
     "string" => sgetpar,
     "double *" => dgetparlist,
     );
 %typetrans = (
     "double" => "double",
     "float" => "double",
     "int" => "int",
     "bool" => "bool",
     "char *" => "char *",
     "string" => "char *",
     "directory" => "char *",
     "doublelist" => "double *",
     "label" => "label",
     "title" => "title",
     );
 open parfile,"<$ARGV[0]";
 open cppfile,">parameter.cpp";
 $i=0;
 while (<parfile>) {
 #ignore comments
     if (/^#/) {
 	next;
+	}
     @line=split(/=/);
 #ignore empty lines
     if ($#line<1) {
 	next;
+    }
     $param[$i]=$line[0];
     $value_type=$line[1];
     @typel=split(/ \/ /,$value_type);
     $value[$i] = $typel[0];
     $type[$i] = $typel[1];
 #get rid of spaces
     $param[$i] =~ s/ //g;
     $value[$i] =~ s/ //g;
     $type[$i] =~ s/ //g;
     $type[$i] =~s/\n//g;
     $convtype[$i]=$typetrans{$type[$i]};
     if ($convtype[$i] eq "char *") {
 	$value[$i] = "\"$value[$i]\"";
+    }
     #print cppfile "param = $param, value = $value, type = $type\n";
     $i++;
+}
 $lines=$i;
 print cppfile <<END_HEADER;
 // WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.
     // All edits will be discarded.
 // 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;
 Parameter::Parameter() {
 END_HEADER
 for ($i=0;$i<$lines;$i++) {
     if ($convtype[$i] ne "label" && $convtype[$i] ne "title") {
 	if ($convtype[$i] eq "char *") {
 	    print cppfile "  $param[$i] = strdup($value[$i]);\n";
 	    if ($param[$i] eq "datadir") {
 		print cppfile "  datadir = AppendHomeDirIfPathRelative(datadir);\n";
+	    }
 	} else {
 	    if ($convtype[$i] eq "double *") {
                 #comma separated list expected
 		@paramlist = split(/,/, $value[$i]);
 		$length = $#paramlist+1;
 		print cppfile "  $param[$i] = new double\[$length\];\n";
 		for ($j=0;$j<=$#paramlist;$j++) {
 		    print cppfile "  $param[$i]\[$j\] = $paramlist[$j];\n";
+		}
 	    } else {
 		print cppfile "  $param[$i] = $value[$i];\n";
+	    }
+	}
+    }
+}
 print cppfile <<END_HEADER3;
   // reassign datadir outside the loop
   QDir dataDir(datadir);
   if (dataDir.isRelative()){
     QStringList path;
     path << QDir::homePath() << dataDir.dirName();
     datadir = strdup((char *) path.join("/").toStdString().c_str());
+  }
+}
 Parameter::~Parameter() {
 // destruct parameter object
 // free string parameter
 CleanUp();
+}
 void Parameter::CleanUp(void) {
 END_HEADER3
 for ($i=0;$i<$lines;$i++) {
     if ($convtype[$i] eq "char *" || $convtype[$i] eq "double *") {
 	print cppfile "  if ($param[$i]) \n";
 	print cppfile "     free($param[$i]);\n";
+    }
+}
 print cppfile <<END_HEADER4;
+}
 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);
 END_HEADER4
 for ($i=0;$i<$lines;$i++) {
     if ($convtype[$i] eq "label" || $convtype[$i] eq "title") {
 	next;
+    }
     if ($convtype[$i] eq "double *") {
 	@paramlist = split(/,/,$value[$i]);
 	$length = $#paramlist+1;
 	print cppfile "  $param[$i] = $funname{$convtype[$i]}(fp, \"$param[$i]\", $length, true);\n";
     } else {
 	print cppfile "  $param[$i] = $funname{$convtype[$i]}(fp, \"$param[$i]\", $value[$i], true);\n";
 	if ($param[$i] eq "datadir") {
 	    print cppfile "  datadir = AppendHomeDirIfPathRelative(datadir);\n";
+	}
+    }
     if ($type[$i] eq "directory") {
 	print cppfile "  if (strcmp($param[$i], \".\"))\n";
 	print cppfile "    MakeDir($param[$i]);\n";
+    }
+}
   print cppfile <<END_MIDPART;
+}
 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 {
 END_MIDPART
 for ($i=0;$i<$lines;$i++) {
     if ($convtype[$i] eq "label"  || $convtype[$i] eq "title") {
 	next;
+    }
     if ($convtype[$i] eq "double *") {
 	print cppfile "  os << \" $param[$i] = \"";
 	@paramlist = split(/,/,$value[$i]);
 	for ($j=0;$j<$#paramlist;$j++) {
 	    print cppfile "<< $param[$i]\[$j\] << \", \" ";
+	}
 	print cppfile "<< $param[$i]\[$#paramlist\] << endl;\n";
     } else {
 	if ($convtype[$i] eq "bool") {
 	    print cppfile "  os << \" $param[$i] = \" << sbool($param[$i]) << endl;\n";
 	} else {
 	    if ($convtype[$i] eq "char *") {
 		print cppfile "\n  if ($param[$i]) \n";
 		print cppfile "  ";
 	    if (($convtype[$i] eq "char *") and ($param[$i] eq "datadir")) {
                 print cppfile "  if (datadir) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      os << \" datadir = \" << dataDir.dirName().toStdString() << endl;
+                                 }
                                  else {
                                      os << \"datadir = .\" << endl;
                                  }\n";
 	    } else {
 		if ($convtype[$i] eq "char *") {
 		    print cppfile "\n  if ($param[$i]) \n";
+		}
 		print cppfile "  os << \" $param[$i] = \" << $param[$i] << endl;\n";
+	    }
 	    print cppfile "  os << \" $param[$i] = \" << $param[$i] << endl;\n";
+	}
+    }
+}
 print cppfile "}\n";
 print cppfile <<END_TRAIL2;
 void Parameter::XMLAdd(xmlNode *root) const {
     xmlNode *xmlparameter = xmlNewChild(root, NULL, BAD_CAST "parameter", NULL);
 END_TRAIL2
 for ($i=0;$i<$lines;$i++) {
     if ($convtype[$i] eq "label" || $convtype[$i] eq "title") {
 	next;
+    }
     print cppfile "{\n";
     print cppfile "  xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST \"par\", NULL);\n";
     print cppfile "  xmlNewProp(xmlpar, BAD_CAST \"name\", BAD_CAST \"$param[$i]\" );\n";
     if ($convtype[$i] eq "double *") {
 	@paramlist = split(/,/,$value[$i]);
 	print cppfile "  xmlNode *xmlvalarray = xmlNewChild(xmlpar, NULL, BAD_CAST \"valarray\", NULL);\n";
 	for ($j=0;$j<=$#paramlist;$j++) {
 	    print cppfile "  {\n";
 	    print cppfile "    ostringstream text;\n";
 	    print cppfile "    text << $param[$i]\[$j\];\n";
 	    print cppfile "    xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST \"val\", NULL);\n";
 	    print cppfile "    xmlNewProp(xmlval, BAD_CAST \"v\", BAD_CAST text.str().c_str());\n";
 	    print cppfile "  }\n";
+	}
 	print cppfile "}\n";
 	next;
     } else {
 	print cppfile "  ostringstream text;\n";
 	if ($convtype[$i] eq "bool") {
 	    print cppfile "text << sbool($param[$i]);\n";
 	} else {
 	    if ($convtype[$i] eq "char *") {
 		print cppfile "\n  if ($param[$i]) \n";
 		print cppfile "  ";
 	    if (($convtype[$i] eq "char *") and ($param[$i] eq "datadir")) {
                 print cppfile "\n  if ($param[$i]) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      text << dataDir.dirName().toStdString();
                                    }\n";
 	    } else {
 		if ($convtype[$i] eq "char *") {
 		    print cppfile "\n  if ($param[$i]) \n";
+		}
 		print cppfile "    text << $param[$i];\n";
+	    }
 	    print cppfile "  text << $param[$i];\n";
+	}
+    }
     print cppfile "xmlNewProp(xmlpar, BAD_CAST \"val\", BAD_CAST text.str().c_str());\n";
     print cppfile "}\n";
+}
 print cppfile "}\n";
 print cppfile "void Parameter::AssignValToPar(const char *namec, const char *valc) {\n";
 print cppfile;
 print cppfile "  QLocale standardlocale(QLocale::C);\n";
 print cppfile "  bool ok;\n";
 for ($i=0;$i<$lines;$i++) {
     if ($convtype[$i] eq "label" || $convtype[$i] eq "title") {
 	next;
+    }
     if ($convtype[$i] eq "double *") {
 	next;
     } else {
 	print cppfile "if (!strcmp(namec, \"$param[$i]\")) {\n";
 	if ($convtype[$i] eq "bool") {
 	    print cppfile "$param[$i] = strtobool(valc);\n";
 	} else {
 	    if ($convtype[$i] eq "char *") {
 		print cppfile "  if ($param[$i]) { free($param[$i]); }\n";
 		print cppfile "  $param[$i]=strdup(valc);\n";
 		if ($param[$i] eq "datadir") {
 		    print cppfile "  datadir = AppendHomeDirIfPathRelative(datadir);\n";
+		}
 	    } else {
 		if ($convtype[$i] eq "int") {
 		    print cppfile "  $param[$i] = standardlocale.toInt(valc, &ok);\n";
 		    print cppfile "  if (!ok) { MyWarning::error(\"Read error: cannot convert string \\\"%s\\\" to integer while reading parameter '$param[$i]' from XML file.\",valc); }\n";
 		    # print cppfile "  $param[$i] = (int)strtol(valc, 0, 10);\n";
 		} else {
 		    # print cppfile "  $param[$i] = strtod(valc, 0);\n";
 		    print cppfile "  $param[$i] = standardlocale.toDouble(valc, &ok);\n";
 		    print cppfile "  if (!ok) { MyWarning::error(\"Read error: cannot convert string \\\"%s\\\" to double while reading parameter '$param[$i]' from XML file.\",valc); }\n";
+		}
+	    }
+	}
+    }
     print cppfile "}\n";
+}
 print cppfile "}\n";
 print cppfile "void Parameter::AssignValArrayToPar(const char *namec, vector<double> valarray) {\n";
 print cppfile;
 for ($i=0;$i<$lines;$i++) {
     if ($convtype[$i] eq "double *") {
 	@paramlist = split(/,/,$value[$i]);
 	print cppfile "if (!strcmp(namec, \"$param[$i]\")) {\n";
 	print cppfile "  int i=0;\n";
 	print cppfile "  vector<double>::const_iterator v=valarray.begin();\n";
 	print cppfile "  while (v!=valarray.end() && i <= $#paramlist ) {\n";
 	print cppfile "     $param[$i]\[i++\]=*(v++);\n";
 	print cppfile "  }\n";
 	print cppfile "}\n";
+    }
+}
 print cppfile <<END_DATADIR;
 // reassign datadir outside the loop
 if (!strcmp(namec, "datadir")) {
   if (datadir) { free(datadir); }
   QDir dataDir(datadir);
   if (dataDir.isRelative()){
     QStringList path;
     path << QDir::homePath() << dataDir.dirName();
     datadir = strdup((char *) path.join("/").toStdString().c_str());
+  }
+ }
 END_DATADIR
 print cppfile "}\n";
 print cppfile <<END_TRAILER;
 ostream &operator<<(ostream &os, Parameter &p) {
     p.Write(os);
     return os;
+}
 END_TRAILER
 # parameter.h
 open hfile, ">parameter.h";
 print hfile <<END_HEADER2;
 // WARNING: This file is automatically generated by make_parameter_source.pl. 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);
 END_HEADER2
    for ($i=0;$i<$lines;$i++) {
      if ($convtype[$i] ne "label" && $convtype[$i] ne "title") {
        print hfile "  $convtype[$i] $param[$i];\n";
+     }
+   }
    print hfile <<END_TRAILER2;
  private:
  };
  ostream &operator<<(ostream &os, Parameter &p);
  const char *sbool(const bool &p);
 #endif
 END_TRAILER2
 # finally, a parameter file with the default values, based on the template
 open parfile,">default.par";
 for ($i=0;$i<$lines;$i++) {
   if ($type[$i] ne "title" && $type[$i] ne "label") {
     $value[$i] =~ s/\"//g;
       print parfile "  $param[$i] = $value[$i]\n";
+  }
+}
 # finis

0 comments (0 inline, 0 general)