EI/VirtualLeaf Changeset - 096de6bb6fab · Centrum Wiskunde & Informatica (CWI)

Changeset - 096de6bb6fab

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Michael Guravage - 15 years ago 2010-04-29 19:03:53
michael.guravage@cwi.nl

Restructured project files for windows build. Compiling with libxml2 yields multiple definition errors.

9 files changed with 89 insertions and 61 deletions:

.hgignore

src/VirtualLeaf.pro

src/VirtualLeaf_d.pro

src/build_models/plugin_auxingrowth.pro

src/build_models/plugin_leaf.pro

src/build_models/plugin_meinhardt.pro

src/build_models/plugin_test.pro

src/cellbase.h

src/libplugin.pro

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.hgignore

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 # use glob syntax.
 syntax: glob
 *~
 *.a
 *.cache
 *.Debug
 *.o
 *.orig
 *.out
 *.Release
 *.so
 *.vars
 *Makefile
 *make.out
 *moc_*.cpp
 *make.out
 *Makefile
 src/parameter.h
 src/parameter.cpp
 src/default.par
 src/pardialog.h
 src/pardialog.cpp
 bin*
 # switch to regexp syntax.
 syntax: regexp
 # finis

src/VirtualLeaf.pro

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+#
 #  $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 #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
 CONFIG += qt release
 PERLDIR = ./perl
 BINDIR = ../bin
 DESTDIR = $$BINDIR
 TARGET = VirtualLeaf
 PARTMPL = $${TARGET}par.tmpl
 MAINSRC = $${TARGET}.cpp
 QT -= network sql xml
 QT += qt3support
 QWTDIR = /usr/local/qwt
 QMAKE_LIBDIR += $$QWTDIR/lib
 win32:QWTDIR = "C:\Qwt-5.0.2"
 unix:LIBS +=  -lxml2 -lz -lm
 win32:LIBS += -L\"c:\Lib\" -L\"c:\Bin\" -lxml2 -lz -lm -lwsock32
 LIBXML2DIR = C:\libxml2
 !win32 {
  GRAPHICS = qt #qwt
+}
 win32 {
  CONFIG += console
  system(DEL parameter.cpp parameter.h)
  GRAPHICS = qt
  RC_FILE = VirtualLeaf.rc
  QMAKE_CXXFLAGS_RELEASE += -fexceptions -IC:\Include
  QMAKE_CXXFLAGS_DEBUG += -fexceptions -IC:\Include
  QMAKE_CXXFLAGS += -fexceptions -I$${LIBXML2DIR}\include
  QMAKE_CXXFLAGS_DEBUG += -DQDEBUG -ggdb3 -O0
  QMAKE_POST_LINK = "\
   C:\Bin\cp release\VirtualLeaf.exe \
   C:\Qt\4.5.3\bin\Qt3Support4.dll \
   C:\Qt\4.5.3\bin\QtGui4.dll \
   C:\Qt\4.5.3\bin\QtSql4.dll \
   C:\Qt\4.5.3\bin\QtXml4.dll \
   C:\Qt\4.5.3\bin\QtCore4.dll \
   C:\Qt\4.5.3\bin\QtNetwork4.dll \
   C:\Qt\4.5.3\bin\QtSvg4.dll \
   C:\bin\iconv.dll \
   C:\bin\libxml2.dll \
   C:\bin\zlib1.dll \
   C:\MinGW\bin\mingwm10.dll \
   $${DESTDIR}"
  LIBS += -lz -lm -lwsock32 -L$${LIBXML2DIR}\lib -lxml2
+}
 # Application icons
 macx {
  ICON = leaficon.icns
  # make sure that the executable can find the libqwt share library
  QMAKE_POST_LINK = "mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
   cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/.; \
   #install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
   install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \
   install_name_tool -change libqwt.5.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\
   cp leaficon.icns $${DESTDIR}/$${TARGET}.app; "
+}
 macx:release {
  LIBS+= -dead_strip
+}
 unix {
  system(rm -f parameter.cpp parameter.h)
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
  QMAKE_CXXFLAGS += -fexceptions -I/usr/include/libxml2
  QMAKE_CXXFLAGS_DEBUG += -DQDEBUG -ggdb3 -O0
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
  system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
  system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
  #system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)
  CC = /usr/bin/gcc
  QMAKE_CXXFLAGS_RELEASE += -fexceptions -I/usr/include/libxml2
  QMAKE_CXXFLAGS_DEBUG += -fexceptions -I/usr/include/libxml2 -DQDEBUG -ggdb3 -O0
  QMAKE_LFLAGS += -fPIC
+}
 # Input
 HEADERS += \
  apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.h \
  infobar.h \
  mainbase.h \
  mainbase.h \
  matrix.h \
  mesh.h \
  miscq.h \
  modelcatalogue.h \
  Neighbor.h \
  node.h \
  nodeitem.h \
  nodeset.h \
  OptionFileDialog.h \
  output.h \
  parameter.h \
  pardialog.h \
  parse.h \
  pi.h \
  qcanvasarrow.h \
  random.h \
  rungekutta.h \
  simitembase.h \
  simplugin.h \
  sqr.h \
  tiny.h \
  transporterdialog.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  wall.h \
  wallitem.h \
  warning.h \
  xmlwrite.h \
  $${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 \
  xmlwritecode.cpp \
  xmlwrite.cpp \
  $$MAINSRC
 contains( TARGET, leaf_fleming ) {
  DEFINES += FLEMING
+}
 contains(GRAPHICS, qwt) {
  macx:LIBS += -L$$QWTDIR/lib -lqwt
  win32:LIBS += -L$$QWTDIR/lib -lqwt5
  #macx:LIBS += -L$$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_RELEASE += -DQTGRAPHICS # -fpermissive
  QMAKE_CXXFLAGS_DEBUG += -DQTGRAPHICS
  QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive
+}
 contains( GRAPHICS, xfig ) {
  message("Building Xfig executable (background runnable).")
  QMAKE_CXXFLAGS_RELEASE += -DXFIGGRAPHICS
  QMAKE_CXXFLAGS_DEBUG += -DXFIGGRAPHICS
  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_RELEASE += -DX11GRAPHICS
  QMAKE_CXXFLAGS_DEBUG += -DX11GRAPHICS
  QMAKE_CXXFLAGS += -DX11GRAPHICS
  CONFIG -= qt
  CONFIG += x11
  unix:LIBS += -lpng
+}
 # finis

src/VirtualLeaf_d.pro

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+#
 #  $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 #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
 CONFIG += qt debug
 PERLDIR = ./perl
 BINDIR = ../bin
 DESTDIR = $$BINDIR
 TARGET = VirtualLeaf
 PARTMPL = $${TARGET}par.tmpl
 MAINSRC = $${TARGET}.cpp
 QT -= network sql xml
 QT += qt3support
 QWTDIR = /usr/local/qwt
 QMAKE_LIBDIR += $$QWTDIR/lib
 win32:QWTDIR = "C:\Qwt-5.0.2"
 unix:LIBS +=  -lxml2 -lz -lm
 win32:LIBS += -L\"c:\Lib\" -L\"c:\Bin\" -lxml2 -lz -lm -lwsock32
 LIBXML2DIR = C:\libxml2
 !win32 {
  GRAPHICS = qt #qwt
+}
 win32 {
  CONFIG += console
  system(DEL parameter.cpp parameter.h)
  GRAPHICS = qt
  RC_FILE = VirtualLeaf.rc
  QMAKE_CXXFLAGS_RELEASE += -fexceptions -IC:\Include
  QMAKE_CXXFLAGS_DEBUG += -fexceptions -IC:\Include
  QMAKE_CXXFLAGS += -fexceptions -I$${LIBXML2DIR}\include
  QMAKE_CXXFLAGS_DEBUG += -DQDEBUG -ggdb3 -O0
  QMAKE_POST_LINK = "\
   C:\Bin\cp release\VirtualLeaf.exe \
   C:\Qt\4.5.3\bin\Qt3Support4.dll \
   C:\Qt\4.5.3\bin\QtGui4.dll \
   C:\Qt\4.5.3\bin\QtSql4.dll \
   C:\Qt\4.5.3\bin\QtXml4.dll \
   C:\Qt\4.5.3\bin\QtCore4.dll \
   C:\Qt\4.5.3\bin\QtNetwork4.dll \
   C:\Qt\4.5.3\bin\QtSvg4.dll \
   C:\bin\iconv.dll \
   C:\bin\libxml2.dll \
   C:\bin\zlib1.dll \
   C:\MinGW\bin\mingwm10.dll \
   $${DESTDIR}"
  LIBS += -lz -lm -lwsock32 -L$${LIBXML2DIR}\lib -lxml2
+}
 # Application icons
 macx {
  ICON = leaficon.icns
  # make sure that the executable can find the libqwt share library
  QMAKE_POST_LINK = "mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
   cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/.; \
   #install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
   install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \
   install_name_tool -change libqwt.5.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\
   cp leaficon.icns $${DESTDIR}/$${TARGET}.app; "
+}
 macx:release {
  LIBS+= -dead_strip
+}
 unix {
  system(rm -f parameter.cpp parameter.h)
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
  QMAKE_CXXFLAGS += -fexceptions -I/usr/include/libxml2
  QMAKE_CXXFLAGS_DEBUG += -DQDEBUG -ggdb3 -O0
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
  system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
  system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
  #system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)
  CC = /usr/bin/gcc
  QMAKE_CXXFLAGS_RELEASE += -fexceptions -I/usr/include/libxml2
  QMAKE_CXXFLAGS_DEBUG += -fexceptions -I/usr/include/libxml2 -DQDEBUG -ggdb3 -O0
  QMAKE_LFLAGS += -fPIC
+}
 # Input
 HEADERS += \
  apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.h \
  infobar.h \
  mainbase.h \
  mainbase.h \
  matrix.h \
  mesh.h \
  miscq.h \
  modelcatalogue.h \
  Neighbor.h \
  node.h \
  nodeitem.h \
  nodeset.h \
  OptionFileDialog.h \
  output.h \
  parameter.h \
  pardialog.h \
  parse.h \
  pi.h \
  qcanvasarrow.h \
  random.h \
  rungekutta.h \
  simitembase.h \
  simplugin.h \
  sqr.h \
  tiny.h \
  transporterdialog.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  wall.h \
  wallitem.h \
  warning.h \
  xmlwrite.h \
  $${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 \
  xmlwritecode.cpp \
  xmlwrite.cpp \
  $$MAINSRC
 contains( TARGET, leaf_fleming ) {
  DEFINES += FLEMING
+}
 contains(GRAPHICS, qwt) {
  macx:LIBS += -L$$QWTDIR/lib -lqwt
  win32:LIBS += -L$$QWTDIR/lib -lqwt5
  #macx:LIBS += -L$$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_RELEASE += -DQTGRAPHICS # -fpermissive
  QMAKE_CXXFLAGS_DEBUG += -DQTGRAPHICS
  QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive
+}
 contains( GRAPHICS, xfig ) {
  message("Building Xfig executable (background runnable).")
  QMAKE_CXXFLAGS_RELEASE += -DXFIGGRAPHICS
  QMAKE_CXXFLAGS_DEBUG += -DXFIGGRAPHICS
  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_RELEASE += -DX11GRAPHICS
  QMAKE_CXXFLAGS_DEBUG += -DX11GRAPHICS
  QMAKE_CXXFLAGS += -DX11GRAPHICS
  CONFIG -= qt
  CONFIG += x11
  unix:LIBS += -lpng
+}
 # finis

src/build_models/plugin_auxingrowth.pro

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+#
 # $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 BINDIR = ../../bin
 CONFIG += plugin release
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = auxingrowth
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -I..
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix:LIBS += -L"lib" -lvleaf
 win32:LIBS += -L"lib" -lvleaf
 LIBXML2DIR = C:\libxml2
 unix {
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  QMAKE_CXXFLAGS += -fexceptions -IC:\Include
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -IC:\strawberry\c\include -I$${LIBXML2DIR}\include
+}
 # finis

src/build_models/plugin_leaf.pro

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+#
 # $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 BINDIR = ../../bin
 CONFIG += plugin release
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = leaf
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -I..
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix:LIBS += -L"lib" -lvleaf
 win32:LIBS += -L"lib" -lvleaf
 LIBXML2DIR = C:\libxml2
 unix {
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  QMAKE_CXXFLAGS += -fexceptions -IC:\Include
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -IC:\strawberry\c\include -I$${LIBXML2DIR}\include
+}
 # finis

src/build_models/plugin_meinhardt.pro

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+#
 # $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 BINDIR = ../../bin
 CONFIG += plugin release
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = meinhardt
 HEADERS = simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -I..
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix:LIBS += -L"lib" -lvleaf
 win32:LIBS += -L"lib" -lvleaf
 LIBXML2DIR = C:\libxml2
 unix {
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  QMAKE_CXXFLAGS += -fexceptions -IC:\Include
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -IC:\strawberry\c\include -I$${LIBXML2DIR}\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.
+#
 BINDIR = ../../bin
 CONFIG += plugin release
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = test
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -I..
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix:LIBS += -L"lib" -lvleaf
 win32:LIBS += -L"lib" -lvleaf
 LIBXML2DIR = C:\libxml2
 unix {
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  QMAKE_CXXFLAGS += -fexceptions -I/usr/include/libxml2
+}
 win32 {
  QMAKE_CXXFLAGS += -fexceptions -IC:\Include
  LIBS += -Llib -lvleaf
  QMAKE_CXXFLAGS += -fexceptions -I$${LIBXML2DIR}\include
+}
 # finis

src/cellbase.h

➞

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.
+ *
  */
 // CellBase derives from Vector, where Vector is simply used as a Vertex
 #ifndef _CELLBASE_H_
 #define _CELLBASE_H_
 #include <list>
 #include <vector>
 #include <iostream>
 #include <QString>
 #include <QDebug>
 #include "vector.h"
 #include "parameter.h"
 #include "wall.h"
 #include "warning.h"
 #include "assert.h"
 extern Parameter par;
 using namespace std;
 class Mesh;
 class Node;
 class CellBase;
 class NodeSet;
 struct ParentInfo {
 	Vector polarization;
 	double PINmembrane;
 	double PINendosome;
 };
 // We need a little trick here, to make sure the plugin and the main application will see the same static datamembers
 // otherwise each have their own instantation.
 // My solution is as follow. I collect all original statics in a class. The main application instantiates it and
 // has a static pointer to it. After loading the plugin I set a static pointer to the same class
 class CellsStaticDatamembers {
 public:
 	CellsStaticDatamembers(void) {
 		ncells = 0;
 		nchem = 0;
 		base_area = 0.;
 		cerr << "Constructor of CellsStaticDatamembers\n";
+	}
 	~CellsStaticDatamembers() {
 		cerr << "Oops! Desctructor of CellsStaticDatamembers called\n";
+	}
 	int ncells;
 	int nchem;
 	double base_area;
 };
 class CellBase :  public QObject, public Vector
+{
 	Q_OBJECT
 	friend class Mesh;
 	friend class CellInfo;
 	friend class Node;
 	friend class WallBase;
 	friend class SimPluginInterface;
  public:
 	CellBase(QObject *parent=0);
 	CellBase(double x,double y,double z=0); // constructor
   virtual ~CellBase() {
 	  delete[] chem;
 	  delete[] new_chem;
 	  //cerr << "CellBase " << index << " is dying. " << endl;
+  }
 	CellBase(const CellBase &src); // copy constructor
 	virtual bool BoundaryPolP(void) const { return false; }
 	//  CellBase(const Vector &src); // not allowed (we cannot know to which mesh
 	/// the CellBase will belong...)
     CellBase operator=(const CellBase &src); // assignment operator
     CellBase operator=(const Vector &src);
     void SetChemical(int chem, double conc);
     inline void SetNewChem(int chem, double conc) {
       new_chem[chem] = conc;
+    }
     void SetSource(int chem, double conc) {
       source=true;
       source_chem = chem;
       source_conc = conc;
+	}
     void UnfixNodes(void);
     void FixNodes(void);
     void UnsetSource(void) {
       source = false;
+    }
 	inline bool Source(void) { return source; }
     enum boundary_type {None, Noflux, SourceSink, SAM};
     static const char * boundary_type_names[4];
     inline const char *BoundaryStr(void) { return boundary_type_names[boundary]; }
     ostream &print(ostream &os) const;
     inline double Chemical(int c) const { // returns the value of chemical c
       return chem[c];
     #ifdef QDEBUG
       qDebug() << endl << "Entering cellbase::chemical(" << c << ")" << endl;
     #endif
       int nchem = NChem();
       #ifdef _undefined_
       if ((c<0) || (c>=nchem))
 	MyWarning::warning("CellBase::Chemical says: index c is: %d, but nchem is: %d. Merely return zero", c, nchem);
       #endif
       return ((c<0) || (c>=nchem)) ? 0 : chem[c];
+    }
     //void print_nblist(void) const;
     boundary_type SetBoundary(boundary_type bound) {
       if (bound!=None) {
 	//area=0.;
 	//length=0.;
+      }
       return boundary=bound;
+    }
     boundary_type ResetBoundary(void) {
       return boundary=None;
+    }
     boundary_type Boundary(void) const {
       return boundary;
+    }
     static int &NChem(void) {
       return static_data_members->nchem;
+    }
     double CalcArea(void) const;
     double RecalcArea(void) {
       return area = CalcArea();
+    }
     Vector Centroid(void) const;
     void SetIntegrals(void) const;
     double Length(Vector *long_axis = 0, double *width = 0) const;
     double CalcLength(Vector *long_axis = 0, double *width = 0) const;
     inline int Index(void) const {
       return index;
+    }
     void SetTargetArea(double tar_ar) {
       target_area=tar_ar;
+    }
     inline void SetTargetLength(double tar_l) {
       target_length=tar_l;
+    }
     inline void SetLambdaLength(double lambda_length) {
       lambda_celllength = lambda_length;
+    }
     inline double TargetArea(void) {
       return target_area;
+    }
     inline void SetStiffness(double stiff) {
       stiffness = stiff;
+    }
     inline double Stiffness(void) {
       return stiffness;
+    }
     inline double EnlargeTargetArea(double da) {
       return target_area+=da;
+    }
     inline double Area(void) const {
       return area;
+    }
 	inline void Divide(void) {
 		flag_for_divide = true;
+	}
     //Vector Strain(void) const;
     inline double Circumference(void) const {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum +=  (*w)->Length();
+      }
       return sum;
+    }
 	QList<WallBase *> getWalls(void) {
 		QList<WallBase *> wall_list;
 		for (list<Wall *>::iterator i=walls.begin();
 			 i!=walls.end();
 			 i++) {
 			wall_list << *i;
+		}
 		return wall_list;
+	}
   //  void XFigPrint(std::ostream &os) const;
     void Dump(ostream &os) const;
 	QString printednodelist(void);
    // void OnDivide(ParentInfo &parent_info, CellBase &daughter);
     inline bool DeadP(void) { return dead; }
     inline void MarkDead(void) { dead  = true; }
 	static double &BaseArea(void) {
 		return static_data_members->base_area;
+	}
     void CheckForDivision(void);
     // write flux from neighboring cells into "flux"
     void Flux(double *flux, double *D);
     inline bool FixedP(void) { return fixed; }
     inline bool Fix(void) {  FixNodes(); return (fixed=true); }
     inline bool Unfix(void) { UnfixNodes(); return (fixed=false);}
     inline void setCellVec(Vector cv) { cellvec = cv; }
 	bool AtBoundaryP(void) const;
     static inline int &NCells(void) {
       return static_data_members->ncells;
+    }
     inline void Mark(void) {
       marked=true;
+    }
     inline void Unmark(void) {
       marked=false;
+    }
     inline bool Marked(void) const {
       return marked;
+    }
 	//! Returns the sum of chemical "chem" of this CellBase's neighbors
     double SumChemicalsOfNeighbors(int chem) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum +=  (*w)->Length() * ( (*w)->c1!=this ? (*w)->c1->Chemical(chem) : (*w)->c2->Chemical(chem) );
+      }
       return sum;
+    }
     //! Generalization of the previous member function
     template<class P, class Op> P ReduceNeighbors(Op f) {
       P sum=0;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->c1 != this ? f( *((*w)->c1) ) : f ( *((*w)->c2) );
+      }
       return sum;
+    }
     //! The same, but now for the walls
     template<class P, class Op> P ReduceWalls(Op f, P sum) {
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += f( **w );
+      }
       return sum;
+    }
     //! The same, but now for the walls AND neighbors
     template<class P, class Op> P ReduceCellAndWalls(Op f) {
       P sum = 0;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->c1 == this ?
 	  f( *((*w)->c1), *((*w)->c2), **w ) :
 	  f( *((*w)->c2), *((*w)->c1), **w );
+      }
       return sum;
+    }
 	/* template<class Op> void LoopWalls(Op f) {
 		for (list<Wall *>::const_iterator w=walls.begin();
 			 w!=walls.end();
 			 w++) {
 			( **w)->f;
+		}
 	}*/
     //! Sum transporters at this CellBase's side of the walls
     double SumTransporters(int ch) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->getTransporter(this, ch);
+      }
       return sum;
+    }
     inline int NumberOfDivisions(void) { return div_counter; }
     //! Sum transporters at this CellBase's side of the walls
     double SumLengthTransporters(int ch) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->getTransporter(this, ch) * (*w)->Length();
+      }
       return sum;
+    }
     double SumLengthTransportersChemical(int trch, int ch) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->getTransporter(this, trch) * ( (*w)->c1!=this ? (*w)->c1->Chemical(ch) : (*w)->c2->Chemical(ch) );
+      }
       return sum;
+    }
 	inline int CellType(void) const { return cell_type; }
 	inline void SetCellType(int ct) { cell_type = ct; }
 	static void SetNChem(int new_nchem) {
 		if (NCells()) {
 			MyWarning::error("CellBase::SetNChem says: not permitted, call SetNChem after deleting all cells.");
 		} else {
 			NChem() = new_nchem;
+		}
+	}
 	inline double TargetLength() const { return target_length; }
 	static inline CellsStaticDatamembers *GetStaticDataMemberPointer(void) { return static_data_members; }
 protected:
 	// (define a list of Node* iterators)
 	typedef list < list<Node *>::iterator > ItList;
     int index;
 	inline void SetChemToNewchem(void) {
 		for (int c=0;c<CellBase::NChem();c++) {
 			chem[c]=new_chem[c];
+		}
+    }
     inline void SetNewChemToChem(void) {
 		for (int c=0;c<CellBase::NChem();c++) {
 			new_chem[c]=chem[c];
+		}
+    }
 	inline double NewChem(int c) const { return new_chem[c]; }
  protected:
     list<Node *> nodes;
     void ConstructNeighborList(void);
 	long wall_list_index (Wall *elem) const;
     // DATA MEMBERS
     // list of nodes, in clockwise order
     // a (non-ordered) list of neighboring cells (actually I think the
     // introduction of ConstructWalls() has made these
     // lists ordered (clockwise), but I am not yet 100% sure...).
     list<CellBase *> neighbors;
     list<Wall *> walls;
     double *chem;
     double *new_chem;
     boundary_type boundary;
     mutable double area;
     double target_area;
     double target_length;
     double lambda_celllength;
     double stiffness; // stiffness like in Hogeweg (2000)
     bool fixed;
     bool pin_fixed;
     bool at_boundary;
     bool dead;
 	bool flag_for_divide;
 	int cell_type;
     //double length;
     //Vector meanflux;
     //int valence;
     // for length constraint
     mutable double intgrl_xx, intgrl_xy, intgrl_yy, intgrl_x, intgrl_y;
     bool source;
     Vector cellvec;
 	// STATIC DATAMEMBERS MOVED TO CLASS
 	static CellsStaticDatamembers *static_data_members;
 	double source_conc;
     int source_chem;
     // PRIVATE MEMBER FUNCTIONS
     inline static void ClearNCells(void) {
       NCells()=0;
+    }
     bool marked;
     int div_counter;
 };
 ostream &operator<<(ostream &os, const CellBase &v);
 inline Vector PINdir(CellBase &here, CellBase &nb, Wall &w) {
 	return w.getTransporter( &here, 1)  *  w.getInfluxVector(&here);
+}
 #endif

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 += staticlib release
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = build_models/lib
 PERLDIR = ./perl
 PARTMPL = VirtualLeafpar.tmpl
 QT += qt3support
 TARGET = vleaf
 TEMPLATE = lib
 unix:LIBS +=  -lxml2 -lz -lm
 win32:LIBS += -L\"c:\Lib\" -L\"c:\Bin\" -lxml2 -lz -lm -lwsock32
 LIBXML2DIR = C:\libxml2
 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 {
  system(rm -f parameter.cpp parameter.h) # this is performed here when qmake is envoked and not in the resulting makefile.
  system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
  system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
  QMAKE_CXXFLAGS += -fexceptions -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 win32 {
   QMAKE_CXXFLAGS += -fexceptions -IC:\Include
  system(DEL parameter.cpp parameter.h)
  QMAKE_CXXFLAGS += -fexceptions -I$${LIBXML2DIR}\include
+}
 system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
 system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
 #system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)
+#

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