# HG changeset patch # User Michael Guravage # Date 2010-06-22 16:52:13 # Node ID 21afbd2a2c01011eb34723aa180c9020d4dd5e44 # Parent 4f82fc35a2b3b9d8cea10defea1c81c2f098c11d Renamed tutorial examples and added makefile, etc. -- user: Michael Guravage branch 'default' added doc/gpl3.txt added doc/installation.pdf added doc/installation.rst added src/TutorialCode/Makefile added src/TutorialCode/Tutorial0/Makefile added src/TutorialCode/Tutorial0/tutorial0.cpp added src/TutorialCode/Tutorial0/tutorial0.h added src/TutorialCode/Tutorial0/tutorial0.pro added src/TutorialCode/Tutorial1A/Makefile added src/TutorialCode/Tutorial1A/tutorial1A.cpp added src/TutorialCode/Tutorial1A/tutorial1A.h added src/TutorialCode/Tutorial1A/tutorial1A.pro added src/TutorialCode/Tutorial1B/Makefile added src/TutorialCode/Tutorial1B/tutorial1B.cpp added src/TutorialCode/Tutorial1B/tutorial1B.h added src/TutorialCode/Tutorial1B/tutorial1B.pro added src/TutorialCode/Tutorial1C/Makefile added src/TutorialCode/Tutorial1C/tutorial1C.cpp added src/TutorialCode/Tutorial1C/tutorial1C.h added src/TutorialCode/Tutorial1C/tutorial1C.pro added src/TutorialCode/Tutorial1D/Makefile added src/TutorialCode/Tutorial1D/tutorial1D.cpp added src/TutorialCode/Tutorial1D/tutorial1D.h added src/TutorialCode/Tutorial1D/tutorial1D.pro added src/TutorialCode/Tutorial2/Makefile added src/TutorialCode/Tutorial2/tutorial2.cpp added src/TutorialCode/Tutorial2/tutorial2.h added src/TutorialCode/Tutorial2/tutorial2.pro added src/TutorialCode/Tutorial3/Makefile added src/TutorialCode/Tutorial3/tutorial3.cpp added src/TutorialCode/Tutorial3/tutorial3.h added src/TutorialCode/Tutorial3/tutorial3.pro added src/TutorialCode/Tutorial4/Makefile added src/TutorialCode/Tutorial4/tutorial4.cpp added src/TutorialCode/Tutorial4/tutorial4.h added src/TutorialCode/Tutorial4/tutorial4.pro added src/TutorialCode/Tutorial5/Makefile added src/TutorialCode/Tutorial5/tutorial5.cpp added src/TutorialCode/Tutorial5/tutorial5.h added src/TutorialCode/Tutorial5/tutorial5.pro added src/perl/ChangeLog changed src/ChangeLog changed src/Makefile changed src/build_models/ChangeLog changed src/build_models/Makefile changed src/canvas.cpp changed src/parameter.cpp changed src/parameter.h changed src/pardialog.cpp changed src/pardialog.h changed src/perl/make_parameter_source.pl changed src/perl/make_pardialog_source.pl changed src/perl/make_xmlwritecode.pl changed src/vleafmodel.h removed doc/GPL removed src/TutorialCode/Tutorial0/mymodel.cpp removed src/TutorialCode/Tutorial0/mymodel.h removed src/TutorialCode/Tutorial0/mymodel.pro removed src/TutorialCode/Tutorial1/mymodel.cpp removed src/TutorialCode/Tutorial1/mymodel.h removed src/TutorialCode/Tutorial1/mymodel.pro removed src/TutorialCode/Tutorial1A/mymodel.cpp removed src/TutorialCode/Tutorial1A/mymodel.h removed src/TutorialCode/Tutorial1A/mymodel.pro removed src/TutorialCode/Tutorial1B/mymodel.cpp removed src/TutorialCode/Tutorial1B/mymodel.h removed src/TutorialCode/Tutorial1B/mymodel.pro removed src/TutorialCode/Tutorial1C/mymodel.cpp removed src/TutorialCode/Tutorial1C/mymodel.h removed src/TutorialCode/Tutorial1C/mymodel.pro removed src/TutorialCode/Tutorial1D/mymodel.cpp removed src/TutorialCode/Tutorial1D/mymodel.h removed src/TutorialCode/Tutorial1D/mymodel.pro removed src/TutorialCode/Tutorial2/mymodel.cpp removed src/TutorialCode/Tutorial2/mymodel.h removed src/TutorialCode/Tutorial2/mymodel.pro removed src/TutorialCode/Tutorial3/mymodel.cpp removed src/TutorialCode/Tutorial3/mymodel.h removed src/TutorialCode/Tutorial3/mymodel.pro removed src/TutorialCode/Tutorial4/mymodel removed src/TutorialCode/Tutorial4/mymodel.cpp removed src/TutorialCode/Tutorial4/mymodel.h removed src/TutorialCode/Tutorial4/mymodel.pro removed src/TutorialCode/Tutorial5/mymodel removed src/TutorialCode/Tutorial5/mymodel.cpp removed src/TutorialCode/Tutorial5/mymodel.h removed src/TutorialCode/Tutorial5/mymodel.pro diff --git a/doc/GPL b/doc/GPL deleted file mode 100644 --- a/doc/GPL +++ /dev/null @@ -1,75 +0,0 @@ -GNU GENERAL PUBLIC LICENSE Version 2, June 1991 - -Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. - -Preamble The licenses for most software are designed to take away your freedom to share and change it. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. + + Copyright (C) + + This program 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. + + This program 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 this program. If not, see . Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: + + Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . + + The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . diff --git a/doc/installation.pdf b/doc/installation.pdf new file mode 100644 --- /dev/null +++ b/doc/installation.pdf @@ -0,0 +1,436 @@ +%PDF-1.3 +%“Œ‹ž ReportLab Generated PDF document http://www.reportlab.com +% 'BasicFonts': class PDFDictionary +1 0 obj +% The standard fonts dictionary +<< /F1 2 0 R + /F2 3 0 R + /F3 5 0 R >> +endobj +% 'F1': class PDFType1Font +2 0 obj +% Font Helvetica +<< /BaseFont /Helvetica + /Encoding /WinAnsiEncoding + /Name /F1 + /Subtype /Type1 + /Type /Font >> +endobj +% 'F2': class PDFType1Font +3 0 obj +% Font Helvetica-Bold +<< /BaseFont /Helvetica-Bold + /Encoding /WinAnsiEncoding + /Name /F2 + /Subtype /Type1 + /Type /Font >> +endobj +% 'Annot.NUMBER1': class PDFDictionary +4 0 obj +<< /A << /S /URI + /Type /Action + /URI (http://qt.nokia.com/downloads/downloads#lgpl/) >> + /Border [ 0 + 0 + 0 ] + /Rect [ 332.4149 + 657.5936 + 411.372 + 669.5936 ] + /Subtype /Link + /Type /Annot >> +endobj +% 'F3': class PDFType1Font +5 0 obj +% Font Courier +<< /BaseFont /Courier + /Encoding /WinAnsiEncoding + /Name /F3 + /Subtype /Type1 + /Type /Font >> +endobj +% 'Page1': class PDFPage +6 0 obj +% Page dictionary +<< /Annots [ 4 0 R ] + /Contents 17 0 R + /MediaBox [ 0 + 0 + 595.2756 + 841.8898 ] + /Parent 16 0 R + /Resources << /Font 1 0 R + /ProcSet [ /PDF + /Text + /ImageB + /ImageC + /ImageI ] >> + /Rotate 0 + /Trans << >> + /Type /Page >> +endobj +% 'Page2': class PDFPage +7 0 obj +% Page dictionary +<< /Contents 18 0 R + /MediaBox [ 0 + 0 + 595.2756 + 841.8898 ] + /Parent 16 0 R + /Resources << /Font 1 0 R + /ProcSet [ /PDF + /Text + /ImageB + /ImageC + /ImageI ] >> + /Rotate 0 + /Trans << >> + /Type /Page >> +endobj +% 'R8': class PDFCatalog +8 0 obj +% Document Root +<< /Outlines 10 0 R + /PageLabels 19 0 R + /PageMode /UseNone + /Pages 16 0 R + /Type /Catalog >> +endobj +% 'R9': class PDFInfo +9 0 obj +<< /Author () + /CreationDate (D:20100622164642-01'00') + /Keywords () + /Producer (ReportLab http://www.reportlab.com) + /Subject (\(unspecified\)) + /Title (Installation Instructions) >> +endobj +% 'R10': class PDFOutlines +10 0 obj +<< /Count 5 + /First 11 0 R + /Last 15 0 R + /Type /Outlines >> +endobj +% 'Outline.0': class OutlineEntryObject +11 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 717.0236 + 0 ] + /Next 12 0 R + /Parent 10 0 R + /Title (Requirements) >> +endobj +% 'Outline.1': class OutlineEntryObject +12 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 618.0236 + 0 ] + /Next 13 0 R + /Parent 10 0 R + /Prev 11 0 R + /Title (All Platforms) >> +endobj +% 'Outline.2': class OutlineEntryObject +13 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 507.0236 + 0 ] + /Next 14 0 R + /Parent 10 0 R + /Prev 12 0 R + /Title (Linux) >> +endobj +% 'Outline.3': class OutlineEntryObject +14 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 260.4236 + 0 ] + /Next 15 0 R + /Parent 10 0 R + /Prev 13 0 R + /Title (Windows) >> +endobj +% 'Outline.4': class OutlineEntryObject +15 0 obj +<< /Dest [ 7 0 R + /XYZ + 62.69291 + 753.0236 + 0 ] + /Parent 10 0 R + /Prev 14 0 R + /Title (MacOS) >> +endobj +% 'R16': class PDFPages +16 0 obj +% page tree +<< /Count 2 + /Kids [ 6 0 R + 7 0 R ] + /Type /Pages >> +endobj +% 'R17': class PDFStream +17 0 obj +% page stream +<< /Length 5681 >> +stream +1 0 0 1 0 0 cm BT /F1 12 Tf 14.4 TL ET +q +1 0 0 1 62.69291 729.0236 cm +q +0 0 0 rg +BT 1 0 0 1 0 9.64 Tm /F2 20 Tf 24 TL 122.1449 0 Td (Installation Instructions) Tj T* -122.1449 0 Td ET +Q +Q +q +1 0 0 1 62.69291 696.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (Requirements) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 630.0236 cm +q +BT 1 0 0 1 0 52.82 Tm .076098 Tw 12 TL /F1 10 Tf 0 0 0 rg (The Virtual Leaf is written with the QT Cross platform application and UI framework, and can run on Linux,) Tj T* 0 Tw 1.85686 Tw (Apple Macintosh and Windows machines. 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To compile the Virtual Leaf you will need to install the QT +software development kit which you can download from the `QT download +site `_. Whether +installed globally by a system administrator our locally in your own +user space, make sure the QT bin directory containing qmake is in your +execution path. + + +All Platforms +------------- + +Compilation is effected with make, either the native ``make`` on UNIX +and MAC systems or the ``mingw32-make`` distributed with the windows +version of QT. In the Virtual Leaf ``src`` directory you will find a +``Makefile``, the root of a hierarchy of makefiles, that will guide +the compilation and installation of the VirtualLeaf executable, its +default plugins and the tutorial examples. To facilitate cross +platform compatibility, the makefiles expect an environment variable +named ``MAKE`` to name the make utility to use. The fallback default +is 'make.' Platform specific instructions follow. + + +Linux +----- + +Prepend the QT bin directory to your path, for example:: + + > PATH=/opt/QT/qt/bin:$PATH + +If you wish to use some other make utility than make, instantiate an +environment variable named ``MAKE``, for example:: + + > export MAKE=gmake. + +Go to the ``src`` directory and invoke make, for example:: + + > cd /home/michael/VirtualLeaf/v1.0/src + > make + +When complete, you will find the ``VirtualLeaf`` binary in +``v1.0/bin`` and the plugins in ``v1.0/bin/models``. + + +Windows +------- + +For convenience sake the libiconv, libxml2 and libz header files and +libraries are distributed with the Virtual Leaf code, and Virtual Leaf +will compile correctly with them. If, however, you wish to compile +with other versions of these libraries, you will need to reassign the +``LIBZML2DIR``, ``LIBICONVDIR`` and ``LIBZDIR`` variables in all the +project files. + +After installing QT you should be able to invoke a QT command window +from the start menu. This shell automatically includes the necessary +QT folder in your execution PATH. Within this command window, go to the +Virtual Leaf's src directory, + +In the start menu, right click on My Computer and choose properties +from the drop down list. In the advanced tab click on environment +variables. Append the QT + + +MacOS +----- + + + diff --git a/src/ChangeLog b/src/ChangeLog --- a/src/ChangeLog +++ b/src/ChangeLog @@ -1,3 +1,13 @@ +2010-06-22 + + * Makefile (tutorials): Add tutorials target. + +2010-06-21 + + * parameter.cpp: Added particular reassignment of datadir. + + * canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists. + 2010-06-18 * canvas.cpp (gpl): Added gpl slot to display GPL license. diff --git a/src/Makefile b/src/Makefile --- a/src/Makefile +++ b/src/Makefile @@ -2,10 +2,15 @@ QMAKE = $(HOME)/Trolltech/Qt-4.4.1/bin/qmake -# Set $(MAKE) to the name of the make command on your machine, e.g. 'make' on Linux and 'mingw32-make' on windows. -MAKE = make # mingw32-make +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. -all: VirtualLeaf libplugin plugins +ifeq ($(MAKE),) + MAKE=make +endif + +all: VirtualLeaf libplugin plugins tutorials VirtualLeaf: Makefile.VirtualLeaf $(MAKE) -f Makefile.VirtualLeaf @@ -22,13 +27,21 @@ Makefile.libplugin: libplugin.pro plugins: $(MAKE) -C build_models +tutorials: + $(MAKE) -C build_models + $(MAKE) -C TutorialCode + clean: $(MAKE) -f Makefile.libplugin clean $(MAKE) -f Makefile.VirtualLeaf clean $(MAKE) -C build_models clean + $(MAKE) -C TutorialCode clean ifeq ($(MAKE),make) touch VirtualLeaf.pro touch libplugin.pro +else + copy /b VirtualLeaf.pro +,, + copy /b libplugin.pro +,, endif #finis diff --git a/src/TutorialCode/Makefile b/src/TutorialCode/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Makefile @@ -0,0 +1,51 @@ +# $Id$ + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial_0 tutorial_1A tutorial_1B tutorial_1C tutorial_1D tutorial_2 tutorial_3 tutorial_4 tutorial_5 + +tutorial_0: + $(MAKE) -C Tutorial0 + +tutorial_1A: + $(MAKE) -C Tutorial1A + +tutorial_1B: + $(MAKE) -C Tutorial1B + +tutorial_1C: + $(MAKE) -C Tutorial1C + +tutorial_1D: + $(MAKE) -C Tutorial1D + +tutorial_2: + $(MAKE) -C Tutorial2 + +tutorial_3: + $(MAKE) -C Tutorial3 + +tutorial_4: + $(MAKE) -C Tutorial4 + +tutorial_5: + $(MAKE) -C Tutorial5 + +clean: + $(MAKE) -C Tutorial0 clean + $(MAKE) -C Tutorial1A clean + $(MAKE) -C Tutorial1B clean + $(MAKE) -C Tutorial1C clean + $(MAKE) -C Tutorial1D clean + $(MAKE) -C Tutorial2 clean + $(MAKE) -C Tutorial3 clean + $(MAKE) -C Tutorial4 clean + $(MAKE) -C Tutorial5 clean + +# finis diff --git a/src/TutorialCode/Tutorial0/Makefile b/src/TutorialCode/Tutorial0/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial0/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial0 + +tutorial0: Makefile.tutorial0 + $(MAKE) -f Makefile.tutorial0 + +Makefile.tutorial0: tutorial0.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial0 clean +ifeq ($(MAKE),make) + touch tutorial0.pro +else + copy /b tutorial0.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial0/mymodel.cpp b/src/TutorialCode/Tutorial0/tutorial0.cpp rename from src/TutorialCode/Tutorial0/mymodel.cpp rename to src/TutorialCode/Tutorial0/tutorial0.cpp --- a/src/TutorialCode/Tutorial0/mymodel.cpp +++ b/src/TutorialCode/Tutorial0/tutorial0.cpp @@ -28,42 +28,42 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial0.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial0::ModelID(void) { // specify the name of your model here return QString( "My first model in VirtualLeaf" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial0::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial0::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial0::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial0::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial0::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial0::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial0::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial0, Tutorial0) diff --git a/src/TutorialCode/Tutorial0/mymodel.h b/src/TutorialCode/Tutorial0/tutorial0.h rename from src/TutorialCode/Tutorial0/mymodel.h rename to src/TutorialCode/Tutorial0/tutorial0.h --- a/src/TutorialCode/Tutorial0/mymodel.h +++ b/src/TutorialCode/Tutorial0/tutorial0.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial0 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial0/mymodel.pro b/src/TutorialCode/Tutorial0/tutorial0.pro rename from src/TutorialCode/Tutorial0/mymodel.pro rename to src/TutorialCode/Tutorial0/tutorial0.pro --- a/src/TutorialCode/Tutorial0/mymodel.pro +++ b/src/TutorialCode/Tutorial0/tutorial0.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial0 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1/mymodel.cpp b/src/TutorialCode/Tutorial1/mymodel.cpp deleted file mode 100644 --- a/src/TutorialCode/Tutorial1/mymodel.cpp +++ /dev/null @@ -1,70 +0,0 @@ -/* - * - * 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 . - * - * Copyright 2010 Roeland Merks. - * - */ - -#include -#include - -#include "simplugin.h" - -#include "parameter.h" - -#include "wallbase.h" -#include "cellbase.h" -#include "mymodel.h" - -static const std::string _module_id("$Id$"); - -QString MyModel::ModelID(void) { - // specify the name of your model here - return QString( "Cell growth" ); -} - -// return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } - -// To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { - // rules to be executed after cell division go here - // (e.g., cell differentiation rules) -} - -void MyModel::SetCellColor(CellBase *c, QColor *color) { - // add cell coloring rules here - -} - -void MyModel::CellHouseKeeping(CellBase *c) { - // add cell behavioral rules here - c->EnlargeTargetArea(par->cell_expansion_rate); -} - -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { - // add biochemical transport rules here -} -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { - // add biochemical networks for reactions occuring at walls here -} -void MyModel::CellDynamics(CellBase *c, double *dchem) { - // add biochemical networks for intracellular reactions here -} - - -Q_EXPORT_PLUGIN2(mymodel, MyModel) diff --git a/src/TutorialCode/Tutorial1/mymodel.h b/src/TutorialCode/Tutorial1/mymodel.h deleted file mode 100644 --- a/src/TutorialCode/Tutorial1/mymodel.h +++ /dev/null @@ -1,60 +0,0 @@ -/* - * $Id$ - * - * 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 . - * - * Copyright 2010 Roeland Merks. - * - */ - - -#include -#include -#include -#include "simplugin.h" - - -class MyModel : public QObject, SimPluginInterface { - Q_OBJECT - Q_INTERFACES(SimPluginInterface); - -public: - virtual QString ModelID(void); - - // Executed after the cellular mechanics steps have equillibrized - virtual void CellHouseKeeping (CellBase *c); - // Differential equations describing transport of chemicals from cell to cell - virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2); - - // Differential equations describing chemical reactions taking place at or near the cell walls - // (e.g. PIN accumulation) - virtual void WallDynamics(Wall *w, double *dw1, double *dw2); - - // Differential equations describing chemical reactions inside the cells - virtual void CellDynamics(CellBase *c, double *dchem); - - // to be executed after a cell division - virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2); - - // to be executed for coloring a cell - virtual void SetCellColor(CellBase *c, QColor *color); - // return number of chemicals - virtual int NChem(void); -}; - - - - diff --git a/src/TutorialCode/Tutorial1/mymodel.pro b/src/TutorialCode/Tutorial1/mymodel.pro deleted file mode 100644 --- a/src/TutorialCode/Tutorial1/mymodel.pro +++ /dev/null @@ -1,61 +0,0 @@ -# -# $Id$ -# -# 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 . -# -# Copyright 2010 Roeland Merks. -# - - -TARGET = mymodel -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$${INCDIR} -QMAKE_CXXFLAGS_DEBUG += -g3 -QMAKE_CXXFLAGS_DEBUG += -DQDEBUG -QT += qt3support -SOURCES = $${TARGET}.cpp -TEMPLATE = lib - -unix { - LIBS += -L$${LIBDIR} -lvleaf - QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2 - QMAKE_LFLAGS += -fPIC -} - -win32 { - LIBXML2DIR = C:\libxml2 - LIBICONVDIR = C:\libiconv - LIBZDIR = C:\libz - LIBS += -L$${LIBDIR} -lvleaf - QMAKE_CXXFLAGS += -DLIBXML_STATIC - QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include - -} - -# finish diff --git a/src/TutorialCode/Tutorial1A/Makefile b/src/TutorialCode/Tutorial1A/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1A/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1A + +tutorial1A: Makefile.tutorial1A + $(MAKE) -f Makefile.tutorial1A + +Makefile.tutorial1A: tutorial1A.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1A clean +ifeq ($(MAKE),make) + touch tutorial1A.pro +else + copy /b tutorial1A.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1A/mymodel.cpp b/src/TutorialCode/Tutorial1A/tutorial1A.cpp rename from src/TutorialCode/Tutorial1A/mymodel.cpp rename to src/TutorialCode/Tutorial1A/tutorial1A.cpp --- a/src/TutorialCode/Tutorial1A/mymodel.cpp +++ b/src/TutorialCode/Tutorial1A/tutorial1A.cpp @@ -28,43 +28,43 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1A.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1A::ModelID(void) { // specify the name of your model here - return QString( "Cell growth" ); + return QString( "1A: Cell growth" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1A::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1A::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1A::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1A::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1A::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1A::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1A::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1A, Tutorial1A) diff --git a/src/TutorialCode/Tutorial1A/mymodel.h b/src/TutorialCode/Tutorial1A/tutorial1A.h rename from src/TutorialCode/Tutorial1A/mymodel.h rename to src/TutorialCode/Tutorial1A/tutorial1A.h --- a/src/TutorialCode/Tutorial1A/mymodel.h +++ b/src/TutorialCode/Tutorial1A/tutorial1A.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1A : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1A/mymodel.pro b/src/TutorialCode/Tutorial1A/tutorial1A.pro rename from src/TutorialCode/Tutorial1A/mymodel.pro rename to src/TutorialCode/Tutorial1A/tutorial1A.pro --- a/src/TutorialCode/Tutorial1A/mymodel.pro +++ b/src/TutorialCode/Tutorial1A/tutorial1A.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1A VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1B/Makefile b/src/TutorialCode/Tutorial1B/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1B/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1B + +tutorial1B: Makefile.tutorial1B + $(MAKE) -f Makefile.tutorial1B + +Makefile.tutorial1B: tutorial1B.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1B clean +ifeq ($(MAKE),make) + touch tutorial1B.pro +else + copy /b tutorial1B.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1B/mymodel.cpp b/src/TutorialCode/Tutorial1B/tutorial1B.cpp rename from src/TutorialCode/Tutorial1B/mymodel.cpp rename to src/TutorialCode/Tutorial1B/tutorial1B.cpp --- a/src/TutorialCode/Tutorial1B/mymodel.cpp +++ b/src/TutorialCode/Tutorial1B/tutorial1B.cpp @@ -28,30 +28,30 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1B.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1B::ModelID(void) { // specify the name of your model here - return QString( "Cell growth and cell division" ); + return QString( "1B: Cell growth and cell division" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1B::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1B::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1B::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1B::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { @@ -59,15 +59,15 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1B::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1B::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1B::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1B, Tutorial1B) diff --git a/src/TutorialCode/Tutorial1B/mymodel.h b/src/TutorialCode/Tutorial1B/tutorial1B.h rename from src/TutorialCode/Tutorial1B/mymodel.h rename to src/TutorialCode/Tutorial1B/tutorial1B.h --- a/src/TutorialCode/Tutorial1B/mymodel.h +++ b/src/TutorialCode/Tutorial1B/tutorial1B.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1B : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1B/mymodel.pro b/src/TutorialCode/Tutorial1B/tutorial1B.pro rename from src/TutorialCode/Tutorial1B/mymodel.pro rename to src/TutorialCode/Tutorial1B/tutorial1B.pro --- a/src/TutorialCode/Tutorial1B/mymodel.pro +++ b/src/TutorialCode/Tutorial1B/tutorial1B.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1B VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1C/Makefile b/src/TutorialCode/Tutorial1C/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1C/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1C + +tutorial1C: Makefile.tutorial1C + $(MAKE) -f Makefile.tutorial1C + +Makefile.tutorial1C: tutorial1C.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1C clean +ifeq ($(MAKE),make) + touch tutorial1C.pro +else + copy /b tutorial1C.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1C/mymodel.cpp b/src/TutorialCode/Tutorial1C/tutorial1C.cpp rename from src/TutorialCode/Tutorial1C/mymodel.cpp rename to src/TutorialCode/Tutorial1C/tutorial1C.cpp --- a/src/TutorialCode/Tutorial1C/mymodel.cpp +++ b/src/TutorialCode/Tutorial1C/tutorial1C.cpp @@ -28,29 +28,29 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1C.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1C::ModelID(void) { // specify the name of your model here - return QString( "Cell growth and cell division" ); + return QString( "1C: Vertical cell division" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1C::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1C::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1C::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1C::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { @@ -58,15 +58,15 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1C::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1C::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1C::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1C, Tutorial1C) diff --git a/src/TutorialCode/Tutorial1C/mymodel.h b/src/TutorialCode/Tutorial1C/tutorial1C.h rename from src/TutorialCode/Tutorial1C/mymodel.h rename to src/TutorialCode/Tutorial1C/tutorial1C.h --- a/src/TutorialCode/Tutorial1C/mymodel.h +++ b/src/TutorialCode/Tutorial1C/tutorial1C.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1C : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1C/mymodel.pro b/src/TutorialCode/Tutorial1C/tutorial1C.pro rename from src/TutorialCode/Tutorial1C/mymodel.pro rename to src/TutorialCode/Tutorial1C/tutorial1C.pro --- a/src/TutorialCode/Tutorial1C/mymodel.pro +++ b/src/TutorialCode/Tutorial1C/tutorial1C.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1C VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1D/Makefile b/src/TutorialCode/Tutorial1D/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1D/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1D + +tutorial1D: Makefile.tutorial1D + $(MAKE) -f Makefile.tutorial1D + +Makefile.tutorial1D: tutorial1D.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1D clean +ifeq ($(MAKE),make) + touch tutorial1D.pro +else + copy /b tutorial1D.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1D/mymodel.cpp b/src/TutorialCode/Tutorial1D/tutorial1D.cpp rename from src/TutorialCode/Tutorial1D/mymodel.cpp rename to src/TutorialCode/Tutorial1D/tutorial1D.cpp --- a/src/TutorialCode/Tutorial1D/mymodel.cpp +++ b/src/TutorialCode/Tutorial1D/tutorial1D.cpp @@ -28,32 +28,32 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1D.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1D::ModelID(void) { // specify the name of your model here - return QString( "Growth, division, coloring" ); + return QString( "1D: Growth, division, coloring" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1D::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1D::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1D::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here if (c->Area()/c->BaseArea()>1.8) { color->setNamedColor("blue"); } else { color->setNamedColor("green"); } } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1D::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { @@ -61,15 +61,15 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1D::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1D::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1D::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1D, Tutorial1D) diff --git a/src/TutorialCode/Tutorial1D/mymodel.h b/src/TutorialCode/Tutorial1D/tutorial1D.h rename from src/TutorialCode/Tutorial1D/mymodel.h rename to src/TutorialCode/Tutorial1D/tutorial1D.h --- a/src/TutorialCode/Tutorial1D/mymodel.h +++ b/src/TutorialCode/Tutorial1D/tutorial1D.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1D : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1D/mymodel.pro b/src/TutorialCode/Tutorial1D/tutorial1D.pro rename from src/TutorialCode/Tutorial1D/mymodel.pro rename to src/TutorialCode/Tutorial1D/tutorial1D.pro --- a/src/TutorialCode/Tutorial1D/mymodel.pro +++ b/src/TutorialCode/Tutorial1D/tutorial1D.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1D VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial2/Makefile b/src/TutorialCode/Tutorial2/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial2/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial2 + +tutorial2: Makefile.tutorial2 + $(MAKE) -f Makefile.tutorial2 + +Makefile.tutorial2: tutorial2.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial2 clean +ifeq ($(MAKE),make) + touch tutorial2.pro +else + copy /b tutorial2.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial2/mymodel.cpp b/src/TutorialCode/Tutorial2/tutorial2.cpp rename from src/TutorialCode/Tutorial2/mymodel.cpp rename to src/TutorialCode/Tutorial2/tutorial2.cpp --- a/src/TutorialCode/Tutorial2/mymodel.cpp +++ b/src/TutorialCode/Tutorial2/tutorial2.cpp @@ -28,20 +28,20 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial2.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial2::ModelID(void) { // specify the name of your model here - return QString( "Growth hormones" ); + return QString( "2: Growth hormones" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 1; } +int Tutorial2::NChem(void) { return 1; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial2::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) @@ -78,7 +78,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial2::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // white: high concentration of growth hormone, black low concentration @@ -86,7 +86,7 @@ void MyModel::SetCellColor(CellBase *c, color->setRgbF(val, val, val); } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial2::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here if (CellBase::NCells()==1) // first cell expands unconditionally @@ -99,17 +99,17 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial2::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; dchem_c2[0]-=phi; } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial2::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial2::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here if (c->CellType()==1) { dchem[0] = par->leaf_tip_source; @@ -117,4 +117,4 @@ void MyModel::CellDynamics(CellBase *c, } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial2, Tutorial2) diff --git a/src/TutorialCode/Tutorial2/mymodel.h b/src/TutorialCode/Tutorial2/tutorial2.h rename from src/TutorialCode/Tutorial2/mymodel.h rename to src/TutorialCode/Tutorial2/tutorial2.h --- a/src/TutorialCode/Tutorial2/mymodel.h +++ b/src/TutorialCode/Tutorial2/tutorial2.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial2 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial2/mymodel.pro b/src/TutorialCode/Tutorial2/tutorial2.pro rename from src/TutorialCode/Tutorial2/mymodel.pro rename to src/TutorialCode/Tutorial2/tutorial2.pro --- a/src/TutorialCode/Tutorial2/mymodel.pro +++ b/src/TutorialCode/Tutorial2/tutorial2.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial2 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial3/Makefile b/src/TutorialCode/Tutorial3/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial3/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial3 + +tutorial3: Makefile.tutorial3 + $(MAKE) -f Makefile.tutorial3 + +Makefile.tutorial3: tutorial3.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial3 clean +ifeq ($(MAKE),make) + touch tutorial3.pro +else + copy /b tutorial3.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial3/mymodel.cpp b/src/TutorialCode/Tutorial3/tutorial3.cpp rename from src/TutorialCode/Tutorial3/mymodel.cpp rename to src/TutorialCode/Tutorial3/tutorial3.cpp --- a/src/TutorialCode/Tutorial3/mymodel.cpp +++ b/src/TutorialCode/Tutorial3/tutorial3.cpp @@ -28,20 +28,20 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial3.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial3::ModelID(void) { // specify the name of your model here - return QString( "Growth hormones" ); + return QString( "3: Directed phytohormone transport" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } +int Tutorial3::NChem(void) { return 2; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial3::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) @@ -78,7 +78,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial3::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // white: high concentration of growth hormone, black low concentration @@ -86,7 +86,7 @@ void MyModel::SetCellColor(CellBase *c, color->setRgbF(val, val, val); } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial3::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here if (CellBase::NCells()==1) // first cell expands unconditionally @@ -99,7 +99,7 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial3::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; @@ -119,10 +119,10 @@ void MyModel::CelltoCellTransport(Wall * } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial3::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial3::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here if (c->CellType()==1) { dchem[0] = par->leaf_tip_source; @@ -130,4 +130,4 @@ void MyModel::CellDynamics(CellBase *c, } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial3, Tutorial3) diff --git a/src/TutorialCode/Tutorial3/mymodel.h b/src/TutorialCode/Tutorial3/tutorial3.h rename from src/TutorialCode/Tutorial3/mymodel.h rename to src/TutorialCode/Tutorial3/tutorial3.h --- a/src/TutorialCode/Tutorial3/mymodel.h +++ b/src/TutorialCode/Tutorial3/tutorial3.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial3 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial3/mymodel.pro b/src/TutorialCode/Tutorial3/tutorial3.pro rename from src/TutorialCode/Tutorial3/mymodel.pro rename to src/TutorialCode/Tutorial3/tutorial3.pro --- a/src/TutorialCode/Tutorial3/mymodel.pro +++ b/src/TutorialCode/Tutorial3/tutorial3.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial3 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial4/Makefile b/src/TutorialCode/Tutorial4/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial4/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial4 + +tutorial4: Makefile.tutorial4 + $(MAKE) -f Makefile.tutorial4 + +Makefile.tutorial4: tutorial4.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial4 clean +ifeq ($(MAKE),make) + touch tutorial4.pro +else + copy /b tutorial4.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial4/mymodel b/src/TutorialCode/Tutorial4/mymodel deleted file mode 100644 --- a/src/TutorialCode/Tutorial4/mymodel +++ /dev/null @@ -1,147 +0,0 @@ -/* - * - * 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 . - * - * Copyright 2010 Roeland Merks. - * - */ - -#include -#include -#include -#include "simplugin.h" - -#include "parameter.h" - -#include "wallbase.h" -#include "cellbase.h" -#include "mymodel.h" -#include "flux_function.h" - -static const std::string _module_id("$Id$"); - -QString MyModel::ModelID(void) { - // specify the name of your model here - return QString( "new auxin transport 2" ); -} - -// return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } - -// To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { - - // After divisions, parent and daughter cells get a standard stock of PINs. - daughter1->SetChemical(1, par->initval[1]); - daughter2->SetChemical(1, par->initval[1]); - - -} - -void MyModel::SetCellColor(CellBase *c, QColor *color) { - // add cell coloring rules here - // Red: PIN1 - // Green: Auxin - color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.), 0); - -} - -void MyModel::CellHouseKeeping(CellBase *c) { - // add cell behavioral rules here - - c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); - - if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { - c->Divide(); - } -} - -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { - // add biochemical transport rules here - double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); - dchem_c1[0]+=phi; - dchem_c2[0]-=phi; - - // Active fluxes (PIN1 mediated transport) - - // (Transporters measured in moles, here) - // efflux from cell 1 to cell 2 - double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) ); - - // efflux from cell 2 to cell 1 - double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) ); - - dchem_c1[0] += trans21 - trans12; - dchem_c2[0] += trans12 - trans21; - - // Influx at leaf "AuxinSource" (as specified in initial condition) - if (w->AuxinSource()) { - double aux_flux = par->leaf_tip_source * w->Length(); - dchem_c1[0] += aux_flux; - dchem_c2[0] += aux_flux; - } -} - -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { - // PIN1 localization at wall - // Note: chemical 0 is Auxin (intracellular storage only) - // PIN1 is Chemical 1 (both in walls and intracellular storage) - //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$ - // Note that Pij is measured in term of concentration (mol/L) - // Pi in terms of quantity (mol) - - // Equations as in Merks et al., Trends in Plant Science 2007 - - // calculate PIN translocation rate from cell to membrane - double adj_auxin = adjacent_cell->Chemical(0); - double receptor_level = adj_auxin * par->r / (par->kr + adj_auxin); - double pin_atwall; // pick the correct side of the Wall - - if (w->C1() == this_cell) pin_atwall = w->Transporters1(1); - else pin_atwall=w->Transporters2(1); - - // note: pin_flux is net flux from endosome to wall - double pin_flux = par->k1 * this_cell->Chemical(1) * receptor_level / ( par->km + this_cell->Chemical(1) ) - par->k2 * pin_atwall; - return pin_flux; - - -} - - -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { - // add biochemical networks for reactions occuring at walls here - dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls - dw1[1] = PINflux(w->C1(),w->C2(),w); - dw2[1] = PINflux(w->C2(),w->C1(),w); - //static ofstream pf("pin_flux.dat"); - //pf << dw1[1] << " " << dw2[1] << " " << w->C1()->Chemical(1) << " " << w->C2()->Chemical(1) << endl; - -} - -void MyModel::CellDynamics(CellBase *c, double *dchem) { - // add biochemical networks for intracellular reactions here - - // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); - - // auxin degradation - dchem[0] = - par->aux_breakdown * c->Chemical(0); - - -} - - -Q_EXPORT_PLUGIN2(mymodel, MyModel) diff --git a/src/TutorialCode/Tutorial4/mymodel.cpp b/src/TutorialCode/Tutorial4/tutorial4.cpp rename from src/TutorialCode/Tutorial4/mymodel.cpp rename to src/TutorialCode/Tutorial4/tutorial4.cpp --- a/src/TutorialCode/Tutorial4/mymodel.cpp +++ b/src/TutorialCode/Tutorial4/tutorial4.cpp @@ -28,21 +28,21 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial4.h" #include "flux_function.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial4::ModelID(void) { // specify the name of your model here - return QString( "new auxin transport 2" ); + return QString( "4: Dynamic PIN orientation" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } +int Tutorial4::NChem(void) { return 2; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial4::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // After divisions, parent and daughter cells get a standard stock of PINs. daughter1->SetChemical(1, par->initval[1]); @@ -51,7 +51,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial4::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // Red: PIN1 // Green: Auxin @@ -59,7 +59,7 @@ void MyModel::SetCellColor(CellBase *c, } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial4::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); @@ -69,7 +69,7 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial4::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; @@ -95,7 +95,7 @@ void MyModel::CelltoCellTransport(Wall * } } -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { +double Tutorial4::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { // PIN1 localization at wall // Note: chemical 0 is Auxin (intracellular storage only) // PIN1 is Chemical 1 (both in walls and intracellular storage) @@ -121,7 +121,7 @@ double MyModel::PINflux(CellBase *this_c } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial4::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls dw1[1] = PINflux(w->C1(),w->C2(),w); @@ -131,15 +131,15 @@ void MyModel::WallDynamics(Wall *w, doub } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial4::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); + dchem[1] = - SumFluxFromWalls( c, Tutorial4::PINflux ); } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial4, Tutorial4) diff --git a/src/TutorialCode/Tutorial4/mymodel.h b/src/TutorialCode/Tutorial4/tutorial4.h rename from src/TutorialCode/Tutorial4/mymodel.h rename to src/TutorialCode/Tutorial4/tutorial4.h --- a/src/TutorialCode/Tutorial4/mymodel.h +++ b/src/TutorialCode/Tutorial4/tutorial4.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial4 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial4/mymodel.pro b/src/TutorialCode/Tutorial4/tutorial4.pro rename from src/TutorialCode/Tutorial4/mymodel.pro rename to src/TutorialCode/Tutorial4/tutorial4.pro --- a/src/TutorialCode/Tutorial4/mymodel.pro +++ b/src/TutorialCode/Tutorial4/tutorial4.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial4 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial5/Makefile b/src/TutorialCode/Tutorial5/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial5/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial5 + +tutorial5: Makefile.tutorial5 + $(MAKE) -f Makefile.tutorial5 + +Makefile.tutorial5: tutorial5.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial5 clean +ifeq ($(MAKE), make) + touch tutorial5.pro +else + copy /b tutorial5.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial5/mymodel b/src/TutorialCode/Tutorial5/mymodel deleted file mode 100644 --- a/src/TutorialCode/Tutorial5/mymodel +++ /dev/null @@ -1,147 +0,0 @@ -/* - * - * 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 . - * - * Copyright 2010 Roeland Merks. - * - */ - -#include -#include -#include -#include "simplugin.h" - -#include "parameter.h" - -#include "wallbase.h" -#include "cellbase.h" -#include "mymodel.h" -#include "flux_function.h" - -static const std::string _module_id("$Id$"); - -QString MyModel::ModelID(void) { - // specify the name of your model here - return QString( "new auxin transport 2" ); -} - -// return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } - -// To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { - - // After divisions, parent and daughter cells get a standard stock of PINs. - daughter1->SetChemical(1, par->initval[1]); - daughter2->SetChemical(1, par->initval[1]); - - -} - -void MyModel::SetCellColor(CellBase *c, QColor *color) { - // add cell coloring rules here - // Red: PIN1 - // Green: Auxin - color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.), 0); - -} - -void MyModel::CellHouseKeeping(CellBase *c) { - // add cell behavioral rules here - - c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); - - if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { - c->Divide(); - } -} - -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { - // add biochemical transport rules here - double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); - dchem_c1[0]+=phi; - dchem_c2[0]-=phi; - - // Active fluxes (PIN1 mediated transport) - - // (Transporters measured in moles, here) - // efflux from cell 1 to cell 2 - double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) ); - - // efflux from cell 2 to cell 1 - double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) ); - - dchem_c1[0] += trans21 - trans12; - dchem_c2[0] += trans12 - trans21; - - // Influx at leaf "AuxinSource" (as specified in initial condition) - if (w->AuxinSource()) { - double aux_flux = par->leaf_tip_source * w->Length(); - dchem_c1[0] += aux_flux; - dchem_c2[0] += aux_flux; - } -} - -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { - // PIN1 localization at wall - // Note: chemical 0 is Auxin (intracellular storage only) - // PIN1 is Chemical 1 (both in walls and intracellular storage) - //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$ - // Note that Pij is measured in term of concentration (mol/L) - // Pi in terms of quantity (mol) - - // Equations as in Merks et al., Trends in Plant Science 2007 - - // calculate PIN translocation rate from cell to membrane - double adj_auxin = adjacent_cell->Chemical(0); - double receptor_level = adj_auxin * par->r / (par->kr + adj_auxin); - double pin_atwall; // pick the correct side of the Wall - - if (w->C1() == this_cell) pin_atwall = w->Transporters1(1); - else pin_atwall=w->Transporters2(1); - - // note: pin_flux is net flux from endosome to wall - double pin_flux = par->k1 * this_cell->Chemical(1) * receptor_level / ( par->km + this_cell->Chemical(1) ) - par->k2 * pin_atwall; - return pin_flux; - - -} - - -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { - // add biochemical networks for reactions occuring at walls here - dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls - dw1[1] = PINflux(w->C1(),w->C2(),w); - dw2[1] = PINflux(w->C2(),w->C1(),w); - //static ofstream pf("pin_flux.dat"); - //pf << dw1[1] << " " << dw2[1] << " " << w->C1()->Chemical(1) << " " << w->C2()->Chemical(1) << endl; - -} - -void MyModel::CellDynamics(CellBase *c, double *dchem) { - // add biochemical networks for intracellular reactions here - - // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); - - // auxin degradation - dchem[0] = - par->aux_breakdown * c->Chemical(0); - - -} - - -Q_EXPORT_PLUGIN2(mymodel, MyModel) diff --git a/src/TutorialCode/Tutorial5/mymodel.cpp b/src/TutorialCode/Tutorial5/tutorial5.cpp rename from src/TutorialCode/Tutorial5/mymodel.cpp rename to src/TutorialCode/Tutorial5/tutorial5.cpp --- a/src/TutorialCode/Tutorial5/mymodel.cpp +++ b/src/TutorialCode/Tutorial5/tutorial5.cpp @@ -20,20 +20,20 @@ */ #include "vleafmodel.h" - +#include "tutorial5.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial5::ModelID(void) { // specify the name of your model here - return QString( "auxin flux and growth" ); + return QString( "5: Auxin-driven growth" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } +int Tutorial5::NChem(void) { return 2; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial5::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // After divisions, parent and daughter cells get a standard stock of PINs. daughter1->SetChemical(1, par->initval[1]); @@ -45,7 +45,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial5::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // Red: PIN1 // Green: Auxin @@ -53,7 +53,7 @@ void MyModel::SetCellColor(CellBase *c, } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial5::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); @@ -63,7 +63,7 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial5::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; @@ -89,7 +89,7 @@ void MyModel::CelltoCellTransport(Wall * } } -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { +double Tutorial5::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { // PIN1 localization at wall // Note: chemical 0 is Auxin (intracellular storage only) // PIN1 is Chemical 1 (both in walls and intracellular storage) @@ -115,7 +115,7 @@ double MyModel::PINflux(CellBase *this_c } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial5::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls dw1[1] = PINflux(w->C1(),w->C2(),w); @@ -123,11 +123,11 @@ void MyModel::WallDynamics(Wall *w, doub } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial5::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); + dchem[1] = - SumFluxFromWalls( c, Tutorial5::PINflux ); // auxin degradation dchem[0] = - par->aux_breakdown * c->Chemical(0); @@ -136,4 +136,4 @@ void MyModel::CellDynamics(CellBase *c, } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial5, Tutorial5) diff --git a/src/TutorialCode/Tutorial5/mymodel.h b/src/TutorialCode/Tutorial5/tutorial5.h rename from src/TutorialCode/Tutorial5/mymodel.h rename to src/TutorialCode/Tutorial5/tutorial5.h --- a/src/TutorialCode/Tutorial5/mymodel.h +++ b/src/TutorialCode/Tutorial5/tutorial5.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial5 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial5/mymodel.pro b/src/TutorialCode/Tutorial5/tutorial5.pro rename from src/TutorialCode/Tutorial5/mymodel.pro rename to src/TutorialCode/Tutorial5/tutorial5.pro --- a/src/TutorialCode/Tutorial5/mymodel.pro +++ b/src/TutorialCode/Tutorial5/tutorial5.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial5 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/build_models/ChangeLog b/src/build_models/ChangeLog --- a/src/build_models/ChangeLog +++ b/src/build_models/ChangeLog @@ -1,3 +1,8 @@ +2010-06-22 + + * Makefile (clean): Add windows equivalent of UNIX touch. + + 2010-06-18 * plugin_auxingrowth.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories. diff --git a/src/build_models/Makefile b/src/build_models/Makefile --- a/src/build_models/Makefile +++ b/src/build_models/Makefile @@ -2,8 +2,13 @@ QMAKE = $(HOME)/Trolltech/Qt-4.4.1/bin/qmake -# Set $(MAKE) to the name of the make command on your machine, e.g. 'make' on Linux and 'mingw32-make' on windows. -MAKE = make # mingw32-make +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif all: plugin_auxingrowth plugin_meinhardt plugin_test @@ -33,6 +38,11 @@ ifeq ($(MAKE),make) touch plugin_auxingrowth.pro touch plugin_meinhardt.pro touch plugin_test.pro +else + copy /b plugin_auxingrowth.pro +,, + copy /b plugin_meinhardt.pro +,, + copy /b plugin_test.pro +,, + endif #finis diff --git a/src/canvas.cpp b/src/canvas.cpp --- a/src/canvas.cpp +++ b/src/canvas.cpp @@ -20,6 +20,8 @@ */ #include +#include +#include #include #include #include @@ -41,6 +43,8 @@ #include #include #include +#include + #include #include @@ -558,7 +562,7 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q helpmenu->insertSeparator(); helpmenu->insertItem("&About", this, SLOT(about()) ); //, Key_F1); helpmenu->insertSeparator(); - helpmenu->insertItem("&GPL", this, SLOT(gpl()) ); + helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) ); menu->insertItem("&Help",helpmenu); statusBar(); setCentralWidget(editor); @@ -665,8 +669,6 @@ void Main::readPars() } emit ParsChanged(); - /* if (timer_active) - timer->start( 0 );*/ } @@ -948,30 +950,37 @@ void Main::about() } -#include -#include -#include void Main::gpl() { - static QMessageBox* gpl = new QMessageBox ( "License", "", + static QMessageBox* gpl = new QMessageBox ( "GPL License", "", QMessageBox::Information, 1, 0, 0, this, 0, FALSE ); - std::ifstream t("../doc/GPL"); + QDir docDir(QApplication::applicationDirPath()); + docDir.cd("../doc"); + QString path = docDir.filePath("gpl3.txt"); + + std::ifstream file(path.toStdString().c_str()); std::string str; - t.seekg(0, std::ios::end); - str.reserve(t.tellg()); - t.seekg(0, std::ios::beg); + if (file) { + file.seekg(0, std::ios::end); + str.reserve(file.tellg()); + file.seekg(0, std::ios::beg); + + str.assign((std::istreambuf_iterator(file)), + std::istreambuf_iterator()); - str.assign((std::istreambuf_iterator(t)), - std::istreambuf_iterator()); - gpl->setText(QString("

GNU GENERAL PUBLIC LICENSE

" - "

Version 2, June 1991

" - "

Copyright (C) 1989, 1991 Free Software Foundation, Inc. " - "59 Temple Place, Suite 330, Boston, MA 02111-1307 USA: " - "Everyone is permitted to copy and distribute verbatim copies " - "of this license document, but changing it is not allowed.

")); - gpl->setDetailedText(QString(str.c_str())); + gpl->setDetailedText(QString(str.c_str())); + } + + gpl->setText(QString( "

GNU GENERAL PUBLIC LICENSE

" + "

Version 3, 29 June 2007

" + "

Copyright © 2007 Free Software Foundation, Inc. " + "<http://fsf.org/>

" + "Everyone is permitted to copy and distribute verbatim copies " + "of this license document, but changing it is not allowed.

" + "

GNU GENERAL PUBLIC LICENSE

")); + gpl->setButtonText( 1, "Dismiss" ); gpl->show(); } diff --git a/src/parameter.cpp b/src/parameter.cpp --- a/src/parameter.cpp +++ b/src/parameter.cpp @@ -31,6 +31,8 @@ #include "xmlwrite.h" #include "warning.h" #include +#include +#include using namespace std; @@ -45,7 +47,7 @@ Parameter::Parameter() { node_mag = 1.0; outlinewidth = 1.0; cell_outline_color = strdup("forestgreen"); - resize_stride = 10; + resize_stride = 0; T = 1.0; lambda_length = 100.; lambda_celllength = 0.; @@ -180,14 +182,19 @@ Parameter::Parameter() { 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(); } @@ -216,17 +223,18 @@ void Parameter::CleanUp(void) { 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; @@ -241,7 +249,7 @@ void Parameter::Read(const char *filenam 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", 10, 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); @@ -468,6 +476,7 @@ void Parameter::Write(ostream &os) const if (dir2) os << " dir2 = " << dir2 << endl; } + void Parameter::XMLAdd(xmlNode *root) const { xmlNode *xmlparameter = xmlNewChild(root, NULL, BAD_CAST "parameter", NULL); { @@ -1838,43 +1847,18 @@ void Parameter::AssignValArrayToPar(cons 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()); + } + } } -/* void Parameter::XMLRead(xmlNode *root) { - - xmlNode *cur = root->xmlChildrenNode; - while (cur!=NULL) { - if ((!xmlStrcmp(cur->name, (const xmlChar *)"parameter"))){ - xmlNode *par_node = cur->xmlChildrenNode; - while (par_node!=NULL) { - { - if (!xmlStrcmp(par_node->name, (const xmlChar *)"par")) { - xmlChar *namec = xmlGetProp(par_node, BAD_CAST "name"); - xmlChar *valc = xmlGetProp(par_node, BAD_CAST "val"); - if (valc) { - AssignValToPar((const char*)namec,(const char*)valc); - } else { - // Probably a valarray - xmlNode *sub_par_node = par_node->xmlChildrenNode; - vector valarray; - while (sub_par_node != NULL) { - if (!xmlStrcmp(sub_par_node->name, (const xmlChar *)"valarray")) { - valarray = XMLIO::XMLReadValArray(sub_par_node); - } - sub_par_node = sub_par_node->next; - } - AssignValArrayToPar((const char*)namec, valarray); - } - } - } - par_node = par_node->next; - } - - } - cur=cur->next; - } - }*/ - ostream &operator<<(ostream &os, Parameter &p) { p.Write(os); return os; diff --git a/src/parameter.h b/src/parameter.h --- a/src/parameter.h +++ b/src/parameter.h @@ -30,7 +30,7 @@ #include class Parameter { - + public: Parameter(); ~Parameter(); diff --git a/src/pardialog.cpp b/src/pardialog.cpp --- a/src/pardialog.cpp +++ b/src/pardialog.cpp @@ -137,7 +137,7 @@ ParameterDialog::ParameterDialog(QWidget dir2_edit = new QLineEdit( QString("%1").arg(par.dir2), this, "dir2_edit" ); // make a 1x1 grid; it will auto-expand QGridLayout *grid = new QGridLayout( this, 1, 1 ); - + // add the first four widgets with (row, column) addressing setWindowTitle( QString( " Parameter values for The Virtual Leaf") ); grid->addWidget( new QLabel( "

Parameter values for The Virtual Leaf

",this), 0, 0, 1, -1, Qt::AlignCenter); @@ -463,7 +463,7 @@ ParameterDialog::~ParameterDialog(void) } void ParameterDialog::write(void) { - + extern Parameter par; QString tmpval; par.arrowcolor = strdup((const char *)arrowcolor_edit->text()); @@ -694,6 +694,7 @@ void ParameterDialog::write(void) { par.dir1 = strdup((const char *)dir1_edit->text()); par.dir2 = strdup((const char *)dir2_edit->text()); Reset(); + } void ParameterDialog::Reset(void) { extern Parameter par; @@ -803,5 +804,4 @@ void ParameterDialog::Reset(void) { dir2_edit->setText( QString("%1").arg(par.dir2) ); } - /* finis */ diff --git a/src/pardialog.h b/src/pardialog.h --- a/src/pardialog.h +++ b/src/pardialog.h @@ -1,26 +1,3 @@ -/* - * - * $Id$ - * - * 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 . - * - * Copyright 2010 Roeland Merks. - * - */ - #ifndef PARAMETER_DIALOG_H #define PARAMETER_DIALOG_H #include @@ -31,18 +8,18 @@ #include class ParameterDialog : public QDialog { - Q_OBJECT + Q_OBJECT + + public: + ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0); + virtual ~ParameterDialog(void); + public slots: + void Reset(void); - public: - ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0); - virtual ~ParameterDialog(void); - public slots: - void Reset(void); + private slots: + void write(void); - private slots: - void write(void); - - private: + private: QLineEdit *arrowcolor_edit; QLineEdit *arrowsize_edit; QLineEdit *textcolor_edit; @@ -142,7 +119,4 @@ class ParameterDialog : public QDialog { QLineEdit *dir1_edit; QLineEdit *dir2_edit; }; - #endif - -/* finis */ diff --git a/src/perl/ChangeLog b/src/perl/ChangeLog new file mode 100644 --- /dev/null +++ b/src/perl/ChangeLog @@ -0,0 +1,6 @@ +2010-06-21 + + * 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. + diff --git a/src/perl/make_parameter_source.pl b/src/perl/make_parameter_source.pl --- a/src/perl/make_parameter_source.pl +++ b/src/perl/make_parameter_source.pl @@ -103,293 +103,273 @@ print cppfile < +#include +#include - using namespace std; - +using namespace std; Parameter::Parameter() { - END_HEADER +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"; - } 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"; - } +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"; + } 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 < valarray) {\n"; - print cppfile; +print cppfile "void Parameter::AssignValArrayToPar(const char *namec, vector valarray) {\n"; +print cppfile; - for ($i=0;$i<$lines;$i++) { +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::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"; - } - } + 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::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 <xmlChildrenNode; - while (cur!=NULL) { - if ((!xmlStrcmp(cur->name, (const xmlChar *)"parameter"))){ - xmlNode *par_node = cur->xmlChildrenNode; - while (par_node!=NULL) { - { - if (!xmlStrcmp(par_node->name, (const xmlChar *)"par")) { - xmlChar *namec = xmlGetProp(par_node, BAD_CAST "name"); - xmlChar *valc = xmlGetProp(par_node, BAD_CAST "val"); - if (valc) { - AssignValToPar((const char*)namec,(const char*)valc); - } else { - // Probably a valarray - xmlNode *sub_par_node = par_node->xmlChildrenNode; - vector valarray; - while (sub_par_node != NULL) { - if (!xmlStrcmp(sub_par_node->name, (const xmlChar *)"valarray")) { - valarray = XMLIO::XMLReadValArray(sub_par_node); - } - sub_par_node = sub_par_node->next; - } - AssignValArrayToPar((const char*)namec, valarray); - } - } - } - par_node = par_node->next; - } +print cppfile <next; - } - - }*/ +print cppfile "}\n"; + +print cppfile <parameter.h"; - print hfile <parameter.h"; +print hfile < #include - 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 valarray); - END_HEADER2 + 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 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"; - } - } + for ($i=0;$i<$lines;$i++) { + if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { + print hfile " $convtype[$i] $param[$i];\n"; + } + } - print hfile <default.par"; +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"; - } - } +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 diff --git a/src/perl/make_pardialog_source.pl b/src/perl/make_pardialog_source.pl --- a/src/perl/make_pardialog_source.pl +++ b/src/perl/make_pardialog_source.pl @@ -98,140 +98,139 @@ print cppfile <addWidget( new QLabel( \"$value[$i]\", this), $row, $col, 1, 2 );\n"; +$numrows = 30; +$c = 0; +for ($i=0;$i<$lines;$i++) { + $col = 2*int($c/($numrows-3)); + $row = $c % ($numrows-3) + $ntitles * 3; + if ($convtype[$i] eq "label") { + print cppfile " grid->addWidget( new QLabel( \"$value[$i]\", this), $row, $col, 1, 2 );\n"; + $c++; + } else { + if ($convtype[$i] eq "title") { + if ($ntitles) { + print stderr "Sorry, only one title allowed. Aborting source construction...\n"; + exit(1); + } + print cppfile " setWindowTitle( QString( \"$value[$i]\") );\n"; + print cppfile " grid->addWidget( new QLabel( \"

$value[$i]

\",this), $row, $col, 1, -1, Qt::AlignCenter);\n"; + print cppfile " grid->addWidget( new QLabel( \"\", this), $row+1, $col, 1, -1);\n"; + $ntitles++; + } else { + print cppfile " grid->addWidget( new QLabel( \"$param[$i]\", this ),$row, $col );\n"; + print cppfile " grid->addWidget( $param[$i]_edit, $row, $col+1 );\n"; $c++; - } else { - if ($convtype[$i] eq "title") { - if ($ntitles) { - print stderr "Sorry, only one title allowed. Aborting source construction...\n"; - exit(1); - } - print cppfile " setWindowTitle( QString( \"$value[$i]\") );\n"; - print cppfile " grid->addWidget( new QLabel( \"

$value[$i]

\",this), $row, $col, 1, -1, Qt::AlignCenter);\n"; - print cppfile " grid->addWidget( new QLabel( \"\", this), $row+1, $col, 1, -1);\n"; - $ntitles++; - } else { - print cppfile " grid->addWidget( new QLabel( \"$param[$i]\", this ),$row, $col );\n"; - print cppfile " grid->addWidget( $param[$i]_edit, $row, $col+1 );\n"; - $c++; - } } } +} - $row = $numrows+1; - $col = 2*int($i/$numrows); +$row = $numrows+1; +$col = 2*int($i/$numrows); - print cppfile <addWidget(pb, $row, $col ); - connect( pb, SIGNAL( clicked() ), this, SLOT( write() ) ); - QPushButton *pb2 = new QPushButton( \"&Close\", this ); - grid->addWidget(pb2,$row, $col+1 ); - connect( pb2, SIGNAL( clicked() ), this, SLOT( close() ) ); - QPushButton *pb3 = new QPushButton( \"&Reset\", this ); - grid->addWidget(pb3, $row, $col+2 ); - connect( pb3, SIGNAL( clicked() ), this, SLOT( Reset() ) ); - show(); +print cppfile <addWidget(pb, $row, $col ); +connect( pb, SIGNAL( clicked() ), this, SLOT( write() ) ); +QPushButton *pb2 = new QPushButton( \"&Close\", this ); +grid->addWidget(pb2,$row, $col+1 ); +connect( pb2, SIGNAL( clicked() ), this, SLOT( close() ) ); +QPushButton *pb3 = new QPushButton( \"&Reset\", this ); +grid->addWidget(pb3, $row, $col+2 ); +connect( pb3, SIGNAL( clicked() ), this, SLOT( Reset() ) ); +show(); }; ParameterDialog::~ParameterDialog(void) { - ANOTHER_LABEL +ANOTHER_LABEL - for ($i=0;$i<$lines;$i++) { - if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { - print cppfile "delete $param[$i]_edit;\n"; - } +for ($i=0;$i<$lines;$i++) { + if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { + print cppfile "delete $param[$i]_edit;\n"; } - - print cppfile <text().section(',', $j, $j);\n"; + print cppfile " par.$param[$i]\[$j\] = tmpval.toDouble();\n"; } - if ($convtype[$i] eq "double *") { - @paramlist = split(/,/,$value[$i]); - for ($j=0;$j<=$#paramlist;$j++) { - print cppfile " tmpval = $param[$i]_edit->text().section(',', $j, $j);\n"; - print cppfile " par.$param[$i]\[$j\] = tmpval.toDouble();\n"; - } + } else { + if ($convtype[$i] eq "bool") { + print cppfile " tmpval = $param[$i]_edit->text().stripWhiteSpace();\n"; + print cppfile " if (tmpval == \"true\" || tmpval == \"yes\" ) par.$param[$i] = true;\n"; + print cppfile " else if (tmpval == \"false\" || tmpval == \"no\") par.$param[$i] = false;\n"; + print cppfile " else {\n"; + print cppfile " if (QMessageBox::question(this, \"Syntax error\", tr(\"Value %1 of parameter %2 is not recognized as Boolean.\\nDo you mean TRUE or FALSE?\").arg(tmpval).arg(\"$param[$i]\"),\"True\",\"False\", QString::null, 0, 1)==0) par.$param[$i]=true;\n"; + print cppfile " else par.$param[$i]=false;\n"; + print cppfile " }\n"; } else { - if ($convtype[$i] eq "bool") { - print cppfile " tmpval = $param[$i]_edit->text().stripWhiteSpace();\n"; - print cppfile " if (tmpval == \"true\" || tmpval == \"yes\" ) par.$param[$i] = true;\n"; - print cppfile " else if (tmpval == \"false\" || tmpval == \"no\") par.$param[$i] = false;\n"; - print cppfile " else {\n"; - print cppfile " if (QMessageBox::question(this, \"Syntax error\", tr(\"Value %1 of parameter %2 is not recognized as Boolean.\\nDo you mean TRUE or FALSE?\").arg(tmpval).arg(\"$param[$i]\"),\"True\",\"False\", QString::null, 0, 1)==0) par.$param[$i]=true;\n"; - print cppfile " else par.$param[$i]=false;\n"; - print cppfile " }\n"; + if ($convtype[$i] eq "char *") { + print cppfile " par.$param[$i] = strdup((const char *)$param[$i]_edit->text());\n"; } else { - if ($convtype[$i] eq "char *") { - print cppfile " par.$param[$i] = strdup((const char *)$param[$i]_edit->text());\n"; - } else { - print cppfile " par.$param[$i] = $param[$i]_edit->text().$funname{$convtype[$i]}();\n"; - } + print cppfile " par.$param[$i] = $param[$i]_edit->text().$funname{$convtype[$i]}();\n"; } } - } + } +} - print cppfile <) { - chomp; - s/\\/\\\\/g; - s/\"/\\\"/g; - s/\&/\&/g; - $str.=$_."\\n"; - } - $str .= "\";\n"; - return $str; - } + open srcfile, "<$fname"; + while () { + chomp; + s/\\/\\\\/g; + s/\"/\\\"/g; + s/\&/\&/g; + $str.=$_."\\n"; + } + $str .= "\";\n"; + return $str; +} - print xmlsrc "xmlChar *sourcecode = (xmlChar *)\"".construct_string_constant_from_file( "$mainsource" ); - print xmlsrc <