[med-svn] [Git][med-team/beads][upstream] New upstream version 1.1.21
Filippo Rusconi (@lopippo)
gitlab at salsa.debian.org
Wed Dec 14 16:30:26 GMT 2022
Filippo Rusconi pushed to branch upstream at Debian Med / beads
Commits:
a80ffa77 by Rusconi Filippo at 2022-12-14T16:17:05+01:00
New upstream version 1.1.21
- - - - -
17 changed files:
- CMakeLists.txt
- − debian/beads.install
- − debian/beads.links
- − debian/beads.manpages
- − debian/changelog
- − debian/compat
- − debian/control
- − debian/copyright
- − debian/rules
- − debian/source/format
- − debian/upstream/metadata
- − debian/watch
- src/CMakeLists.txt
- src/qtbeads/CMakeLists.txt
- src/qtbeads/main_window.cpp
- src/qtbeads/properties.cpp
- src/qtbeads/q_gel_image.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -5,7 +5,7 @@
# cmake .
# make
# make install
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.18.4)
# The name of our project is "beads". CMakeLists files in this project can
@@ -77,8 +77,8 @@ set(CMAKE_CXX_FLAGS_DEBUG "-g -s")
set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
-set(BEADS_VERSION "1.1.20")
-set(VERSION 1.1.20)
+set(BEADS_VERSION "1.1.21")
+set(VERSION 1.1.21)
set(CPACK_CMAKE_GENERATOR "Unix Makefiles")
set(CPACK_GENERATOR "STGZ;TGZ;TZ")
@@ -212,7 +212,7 @@ add_custom_target(targz
add_custom_target(deb
- cd beads-${BEADS_VERSION} && dpkg-buildpackage
+ cd beads-${BEADS_VERSION} && dpkg-buildpackage -b
DEPENDS targz
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Creating Debian package" VERBATIM
=====================================
debian/beads.install deleted
=====================================
@@ -1 +0,0 @@
-usr/*
=====================================
debian/beads.links deleted
=====================================
@@ -1,2 +0,0 @@
-usr/share/man/man1/beads.1 usr/share/man/man1/qtbeads.1
-
=====================================
debian/beads.manpages deleted
=====================================
@@ -1,2 +0,0 @@
-doc/man1/beads.1
-
=====================================
debian/changelog deleted
=====================================
@@ -1,339 +0,0 @@
-beads (1.1.20-1) unstable; urgency=low
-
- * New upstream version, merging upstream and Debian packaging
- development with the initial work of Andreas Tille, the ongoing
- work by Olivier Langella and Filippo Rusconi.
-
- -- Filippo Rusconi <lopippo at debian.org> Wed, 06 May 2020 11:04:30 +0200
-
-beads (1.1.19+dfsg-1) unstable; urgency=low
-
- * New version updating the CMake build system to match
- the changes operated in the libodsstream package
- (closes: #959637) and the name of the libodsstream-dev
- package name. Thanks a lot to Lucas Nussbaum
- <lucas at debian.org> and Andreas Tille
- <andreas at an3as.eu> for reporting the problem.
-
- * Standards-Version: 4.5.0 (no changes needed).
-
- * Changed the inra.fr to inrae.fr domain name of the home page.
-
- -- Filippo Rusconi <lopippo at debian.org> Tue, 05 May 2020 20:08:31 +0200
-
-beads (1.1.18-9) buster; urgency=medium
-
- * new lib PAPPSOms++
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Sat, 11 Apr 2020 11:13:23 +0200
-
-beads (1.1.18+dfsg-4) unstable; urgency=medium
-
- * Drop unneeded Build-Depends on libquazip5-headers
- Closes: #945885
- * debhelper-compat 12
- * Standards-Version: 4.4.1
- * Remove patches qt5.patch that are missing from
- debian/patches/series.
-
- -- Andreas Tille <tille at debian.org> Sun, 01 Dec 2019 07:54:06 +0100
-
-beads (1.1.18+dfsg-3) unstable; urgency=medium
-
- * Add libquazip5-headers Build-Depends explicitly which seems to have
- vanished from Depends of some build dependency
- Closes: #924472
- * Standards-Version: 4.3.0
-
- -- Andreas Tille <tille at debian.org> Wed, 13 Mar 2019 14:02:07 +0100
-
-beads (1.1.18+dfsg-2) unstable; urgency=medium
-
- * Point Vcs fields to salsa.debian.org
- * Standards-Version: 4.2.1
- * Remove trailing whitespace in debian/copyright
-
- -- Andreas Tille <tille at debian.org> Sat, 27 Oct 2018 17:41:52 +0200
-
-beads (1.1.18+dfsg-1) unstable; urgency=medium
-
- * New upstream version
- * Watch file now reports new upstream URLs (not fit for proper download
- yet since some more sophisticated name mangling is needed)
- * Standards-Version: 4.1.3
- * debhelper 11
- * Build-Depends: libodsstream-qt5-dev (>= 0.4.13-2)
- * Drop unused lintian override
-
- -- Andreas Tille <tille at debian.org> Mon, 19 Feb 2018 13:27:11 +0100
-
-beads (1.1.18-8) stretch; urgency=medium
-
- * new odsstream library
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Wed, 02 Jan 2019 22:14:14 +0100
-
-beads (1.1.18-6) stretch; urgency=medium
-
- * new pappso mspp library
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Wed, 12 Dec 2018 19:20:48 +0100
-
-beads (1.1.18-5) stretch; urgency=medium
-
- * new libodsstream library
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Thu, 16 Aug 2018 10:52:49 +0200
-
-beads (1.1.18-4) stretch; urgency=medium
-
- * new libodsstream library
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Wed, 16 May 2018 09:35:46 +0200
-
-beads (1.1.18-3) stretch; urgency=medium
-
- * new libodsstream
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Mon, 30 Apr 2018 15:43:46 +0200
-
-beads (1.1.18-2) stretch; urgency=medium
-
- * new libodsstream
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Sat, 14 Apr 2018 21:26:00 +0200
-
-beads (1.1.18-1) stretch; urgency=medium
-
- * better debian package, new libodsstream
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Tue, 13 Mar 2018 15:53:00 +0100
-
-beads (1.1.17-2) stretch; urgency=medium
-
- * better debian package
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Fri, 16 Feb 2018 06:57:23 +0100
-
-beads (1.1.17-1) stretch; urgency=medium
-
- * move to QT5
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Sun, 11 Feb 2018 18:41:58 +0100
-
-beads (1.1.16-3) stretch; urgency=medium
-
- * stretch package
-
- -- Olivier Langella <olivier.langella at u-psud.fr> Thu, 17 Aug 2017 21:41:50 +0200
-
-beads (1.1.16-2) jessie; urgency=medium
-
- * new odsstream library
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Tue, 23 May 2017 22:31:11 +0200
-
-beads (1.1.16-1) jessie; urgency=medium
-
- * updated version using libodsstream, better exports
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Mon, 24 Apr 2017 09:42:19 +0200
-
-beads (1.1.15-2) jessie; urgency=medium
-
- * package for Jessie
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 28 Aug 2015 16:02:53 +0200
-
-beads (1.1.15-1) wheezy; urgency=low
-
- * bug fixed creating new beads.conf file
-
- -- Olivier Langella <olivier.langella at moulon.inra.fr> Sat, 19 May 2012 06:18:51 +0200
-
-beads (1.1.14-2) natty; urgency=low
-
- * no more X11 dependency
- * no more pthread depency
-
- -- Olivier Langella <olivier.langella at moulon.inra.fr> Sat, 25 Jun 2011 06:18:51 +0200
-
-beads (1.1.14-1~maverick1) maverick; urgency=low
-
- * new CMakeLists.txt compilation method
- * new Cimg library 1.4.4
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 2 Nov 2010 10:18:51 +0200
-
-beads (1.1.13+dfsg-2) unstable; urgency=medium
-
- * replacing the build dependency on qttools5-dev-tools with qttools5-dev
- Closes: #880850
-
- -- Andreas Tille <tille at debian.org> Mon, 06 Nov 2017 00:31:00 +0100
-
-beads (1.1.13+dfsg-1) unstable; urgency=medium
-
- * Initial upload to Debian (Closes: #879556)
-
- -- Andreas Tille <tille at debian.org> Sun, 22 Oct 2017 22:19:26 +0200
-
-beads (1.1.13-1~maverick1) maverick; urgency=low
-
- * maverick package
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 9 Sep 2010 10:18:51 +0200
-
-beads (1.1.13-1~lucid1) lucid; urgency=low
-
- * fixed bug when trying to save results from sypro images (detected by T. Balliau)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 9 Sep 2010 10:18:51 +0200
-
-beads (1.1.12-1~lucid1) lucid; urgency=low
-
- * command line output extension detection problem fixed
- * integration of Cimg 1.3.9
- * memory leak fixed on qt properties object
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 26 Aug 2010 10:18:51 +0200
-
-beads (1.1.11-1~lucid1) lucid; urgency=low
-
- * UTF8 image file path
- * parameter "atom" renamed in "minbeads"
- * rename CONFLUENTS image to SELECT image
- * parameter "minconfl" renamed in "minpath"
- * parameter "flux" renamed in "minflux"
- * confluent_ prefix removed from minflux, minpath, winconfl, minbeads
- * prob_ prefix removed from sx, sy, sx_bottom, sy_bottom
- * rename detection_threshold to minproba
- * rename quantification_npass to npass
- * inverse image checked by default
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 18 May 2010 10:18:51 +0200
-
-beads (1.1.10-1~lucid1) lucid; urgency=low
-
- * write matchset with matched spot num
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Mon, 10 Apr 2010 10:18:51 +0200
-
-beads (1.1.9-2~lucid1) lucid; urgency=low
-
- * bug fixed writing sample name in PROTICdbML (thanks to Thierry Balliau)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 28 Apr 2010 10:18:51 +0200
-
-beads (1.1.9-1~lucid1) karmic; urgency=low
-
- * edit spot_num dialog
- * new menu item to save all beads steps in one directory (PROBABILITIES, NUMBERS, PATH...)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 28 Apr 2010 10:18:51 +0200
-
-beads (1.1.8-1~karmic1) karmic; urgency=low
-
- * poor protection of detection in BeadsResults fixed (bug found by Thierry Balliau)
- * gnumeric support
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 12 Mar 2010 10:18:51 +0200
-
-beads (1.1.7-1~karmic1) karmic; urgency=low
-
- * CMakeLists.txt changes
- * use of QXmlStreamWriter to produce well formed and well coded XML documents
- * use of QString and QDebug in the core library
- * qt about disabled
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 24 Feb 2010 10:18:51 +0200
-
-beads (1.1.6-1~karmic1) karmic; urgency=low
-
- * bug reported by Thierry Balliau fixed (depth of recursive functions)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 13 Jan 2010 02:18:51 +0200
-
-beads (1.1.5-1~karmic1) karmic; urgency=low
-
- * cimg_OS defined by cmake
- * SVG beads icon added to the main windows
- * image intensity reads correctly UTF8 file paths (uses QFileInfo)
- * action "fit to windows" is disabled
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 16 Dec 2009 02:18:51 +0200
-
-beads (1.1.4-1~karmic1) karmic; urgency=low
-
- * save picked num in PROTICdbML file
- * edit picked num on detected gel image
- * display spot number on detected gel image
- * display x,y position of the cursor on gel image
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 16 Dec 2009 02:18:51 +0200
-
-beads (1.1.3-1~karmic1) karmic; urgency=low
-
- * contour edges problem fixed
- * qt compilation with win32
- * new steps argument
- * updated man page
- * desktop menu for qtbeads
- * parameters files examples in /usr/share/beads
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Mon, 7 Dec 2009 18:18:51 +0200
-
-beads (1.1.2-1~karmic1) karmic; urgency=low
-
- * load beads parameter file
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 30 Nov 2009 10:18:51 +0200
-
-beads (1.1.1-2~karmic1) karmic; urgency=low
-
- * package dependencies fixed
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 29 Nov 2009 10:18:51 +0200
-
-beads (1.1.1-1~karmic1) karmic; urgency=low
-
- * saves results to output files (images, quantifications, svg, PROTICdbML)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 29 Nov 2009 10:18:51 +0200
-
-beads (1.1.0-1~karmic1) karmic; urgency=low
-
- * new cimg library (1.3.2)
- * first version of qtbeads, GUI for beads
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 28 Nov 2009 10:18:51 +0200
-
-beads (1.0-2~karmic1) karmic; urgency=low
-
- * repackaging for Ubuntu Karmic Koala
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Thu, 12 Nov 2009 10:18:51 +0200
-
-beads (1.0-1~hardy1) hardy; urgency=low
-
- * published in Proteomics : http://www.ncbi.nlm.nih.gov/pubmed/19003871
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 26 Nov 2008 11:18:51 +0200
-
-beads (1.0-1) intrepid; urgency=low
-
- * published in Proteomics : http://www.ncbi.nlm.nih.gov/pubmed/19003871
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 26 Nov 2008 11:18:51 +0200
-
-beads (0.1-1~hardy1) hardy; urgency=low
-
- * ppa build for Hardy and Intrepid.
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 07 Nov 2008 20:08:38 +0200
-
-beads (0.1-1) intrepid; urgency=low
-
- * Initial release.
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 25 Jun 2008 11:18:51 +0200
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-9
=====================================
debian/control deleted
=====================================
@@ -1,23 +0,0 @@
-Source: beads
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Filippo Rusconi <lopippo at debian.org>
-Homepage: http://pappso.inrae.fr/bioinfo/beads
-Build-Depends: debhelper-compat (= 12),
- cmake (>= 3.12),
- qtbase5-dev,
- cimg-dev,
- libodsstream-dev
-Standards-Version: 4.5.0
-
-Package: beads
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- imagemagick
-Description: 2-DE electrophoresis gel image spot detection
- Beads is a program for spot detection on 2-D gel images. It is based on
- an analogy with beads flowing uphill on the surface of the gel image and
- on the analysis of their paths (Langella & Zivy, 2008).
=====================================
debian/copyright deleted
=====================================
@@ -1,547 +0,0 @@
-Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: Beads
-Upstream-Contact: Olivier Langella <olivier.langella at universite-paris-saclay.fr>
-Source: http://pappso.inrae.fr/bioinfo/beads/index.php
-
-Files: *
-Copyright: 2008-2010 Michel Zivy <zivy at moulon.inra.fr>, Olivier Langella <olivier.langella at moulon.inra.fr>
-License: CeCILL
-
-Files: src/cimg/CImg.h
-Copyright: David Tschumperle (http://tschumperle.users.greyc.fr/)
-License: CeCILL
-
-Files: src/ConfigFile/*
-Copyright: 2004 Richard J. Wagner
-License: MIT
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to
- deal in the Software without restriction, including without limitation the
- rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
- sell copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
- .
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
- IN THE SOFTWARE.
-
-Files: debian/*
-Copyright: Andreas Tille <tille at debian.org>
- Olivier Langella <olivier.langella at universite-paris-saclay>
- Filippo Rusconi <lopippo at debian.org>
-License: CeCILL
-
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- .
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- Version 2.0 dated 2006-09-05.
-
=====================================
debian/rules deleted
=====================================
@@ -1,11 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-
-%:
- dh $@
-
=====================================
debian/source/format deleted
=====================================
@@ -1 +0,0 @@
-3.0 (quilt)
=====================================
debian/upstream/metadata deleted
=====================================
@@ -1,20 +0,0 @@
-Reference:
- Author: Olivier Langella and Michel Zivy
- Title: >
- A method based on bead flows for spot detection on 2-D gel images
- Journal: Proteomics
- Year: 2008
- Volume: 8
- Number: 23-24
- Pages: 4914-8
- DOI: 10.1002/pmic.200800644
- PMID: 19003871
- URL: >
- http://onlinelibrary.wiley.com/doi/10.1002/pmic.200800644/abstract
-Registry:
- - Name: OMICtools
- Entry: OMICS_25900
- - Name: SciCrunch
- Entry: NA
- - Name: bio.tools
- Entry: NA
=====================================
debian/watch deleted
=====================================
@@ -1,5 +0,0 @@
-version=4
-
-# FIXME: this needs proper URL mangling
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- https://sourcesup.renater.fr/projects/beads/ .*/.*#beads-_ at ANY_VERSION@-title-content
=====================================
src/CMakeLists.txt
=====================================
@@ -1,4 +1,5 @@
-find_package( Qt5 COMPONENTS Core Gui Xml REQUIRED )
+find_package( Qt6 COMPONENTS Core Gui Xml REQUIRED )
+find_package(QuaZip-Qt6 REQUIRED)
list( APPEND CMAKE_MODULE_PATH
${PROJECT_SOURCE_DIR}/cmake_modules
@@ -39,29 +40,29 @@ endif(MINGW32)
set( BEADS_FOR_QT_CPP
- ConfigFile/ConfigFile
- parameters
- encode/base64
+ ConfigFile/ConfigFile.cpp
+ parameters.cpp
+ encode/base64.cpp
images/imageIntensity.cpp
images/imageDirect.cpp
- images/imageCode
- images/imageCoule
- images/imagePaths
- images/imageConfluent
- images/imageProb
- images/parameterProb
- parameterDetection
- images/parameterConfluent
- detection
- images/imageDetection
- images/imageNumber
- images/parameterNumber
- images/imageContours
- spotPROTICdbDocument
- spot
- spotDocument
- spotSvgDocument
- images/imageDeNovo
+ images/imageCode.h
+ images/imageCoule.cpp
+ images/imagePaths.cpp
+ images/imageConfluent.cpp
+ images/imageProb.cpp
+ images/parameterProb.cpp
+ parameterDetection.cpp
+ images/parameterConfluent.cpp
+ detection.cpp
+ images/imageDetection.cpp
+ images/imageNumber.cpp
+ images/parameterNumber.cpp
+ images/imageContours.cpp
+ spotPROTICdbDocument.cpp
+ spot.cpp
+ spotDocument.cpp
+ spotSvgDocument.cpp
+ images/imageDeNovo.cpp
)
if(WIN32)
@@ -91,24 +92,24 @@ set_target_properties(beads
CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
)
-target_link_libraries(beads cppbeads
+target_link_libraries(beads cppbeads
${CImg_SYSTEM_LIBS}
${CImg_CFLAGS}
- Qt5::Core
- Qt5::Gui
- Qt5::Xml
+ Qt6::Core
+ Qt6::Gui
+ Qt6::Xml
OdsStream::Core
)
-add_library( cppbeads STATIC
+add_library(cppbeads STATIC
${BEADS_FOR_QT_CPP}
)
target_include_directories(cppbeads PUBLIC ${OdsStream_INCLUDE_DIRS}
${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
set_target_properties(cppbeads
- PROPERTIES OUTPUT_NAME cppbeads-qt5
+ PROPERTIES OUTPUT_NAME cppbeads-qt6
CLEAN_DIRECT_OUTPUT 1
CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
)
@@ -116,9 +117,9 @@ set_target_properties(cppbeads
target_link_libraries(cppbeads
${CImg_SYSTEM_LIBS}
${CImg_CFLAGS}
- Qt5::Core
- Qt5::Gui
- Qt5::Xml
+ Qt6::Core
+ Qt6::Gui
+ Qt6::Xml
OdsStream::Core
)
=====================================
src/qtbeads/CMakeLists.txt
=====================================
@@ -1,5 +1,5 @@
-find_package( Qt5 COMPONENTS Core Gui Xml Widgets PrintSupport REQUIRED )
+find_package( Qt6 COMPONENTS Core Gui Xml Widgets PrintSupport REQUIRED )
# add some useful macros and variables
# (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
@@ -48,13 +48,13 @@ set( QTBEADS_MOC_HDRS
# this command will generate rules that will run rcc on all files from SAMPLE_RCS
# in result SAMPLE_RC_SRCS variable will contain paths to files produced by rcc
-qt5_add_resources( QTBEADS_SRCS ${SAMPLE_RCS} )
+qt6_add_resources( QTBEADS_SRCS ${SAMPLE_RCS} )
# this will run uic on .ui files:
#QT4_WRAP_UI( SAMPLE_UI_HDRS ${SAMPLE_UIS} )
# and finally this will run moc:
-qt5_wrap_cpp( QTBEADS_MOC_SRCS ${QTBEADS_MOC_HDRS} )
+qt6_wrap_cpp( QTBEADS_MOC_SRCS ${QTBEADS_MOC_HDRS} )
# we need this to be able to include headers produced by uic in our code
# (CMAKE_BINARY_DIR holds a path to the build directory, while INCLUDE_DIRECTORIES() works just like INCLUDEPATH from qmake)
@@ -85,6 +85,6 @@ else(WIN32)
)
endif(WIN32)
-target_link_libraries(qtbeads cppbeads OdsStream::Core ${CImg_SYSTEM_LIBS} Qt5::Core Qt5::Gui Qt5::Xml Qt5::Widgets Qt5::PrintSupport)
+target_link_libraries(qtbeads cppbeads OdsStream::Core ${CImg_SYSTEM_LIBS} Qt6::Core Qt6::Gui Qt6::Xml Qt6::Widgets Qt6::PrintSupport)
=====================================
src/qtbeads/main_window.cpp
=====================================
@@ -22,10 +22,8 @@
#include "../images/imageCoule.h"
#include "../images/imageProb.h"
#include "../images/imagePaths.h"
-#include "../images/imageDetection.h"
#include "../images/imageConfluent.h"
#include "../images/imageContours.h"
-#include "../images/imageDeNovo.h"
#include "../parameters.h"
bool copy_file(QString inputfile, QString outputfile) {
@@ -149,7 +147,7 @@ void MainWindow::moveGelImage(QMouseEvent * event) {
_before_x = event->x();
_before_y = event->y();
- qDebug() << event->x() << " " << event->y() << endl;
+ qDebug() << event->x() << " " << event->y() << Qt::endl;
//scrollArea->widget()->move(event->x(), event->y());
scrollArea->horizontalScrollBar()->setSliderPosition(
scrollArea->horizontalScrollBar()->value() - dx);
@@ -245,16 +243,28 @@ void MainWindow::saveStepsDirectory() {
}
void MainWindow::print() {
- Q_ASSERT(scrollArea->getGelImage()->pixmap());
+#if QT_VERSION < 0x060000
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).isNull());
+#else
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap().isNull());
+#endif
QPrintDialog dialog(&printer, this);
if (dialog.exec()) {
QPainter painter(&printer);
QRect rect = painter.viewport();
- QSize size = scrollArea->getGelImage()->pixmap()->size();
+#if QT_VERSION < 0x060000
+ QSize size = scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).size();
size.scale(rect.size(), Qt::KeepAspectRatio);
painter.setViewport(rect.x(), rect.y(), size.width(), size.height());
- painter.setWindow(scrollArea->getGelImage()->pixmap()->rect());
- painter.drawPixmap(0, 0, *scrollArea->getGelImage()->pixmap());
+ painter.setWindow(scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).rect());
+ painter.drawPixmap(0, 0, scrollArea->getGelImage()->pixmap(Qt::ReturnByValue));
+#else
+ QSize size = scrollArea->getGelImage()->pixmap().size();
+ size.scale(rect.size(), Qt::KeepAspectRatio);
+ painter.setViewport(rect.x(), rect.y(), size.width(), size.height());
+ painter.setWindow(scrollArea->getGelImage()->pixmap().rect());
+ painter.drawPixmap(0, 0, scrollArea->getGelImage()->pixmap());
+#endif
}
}
@@ -403,7 +413,11 @@ void MainWindow::updateActions() {
}
void MainWindow::scaleImage(double factor) {
- Q_ASSERT(scrollArea->getGelImage()->pixmap());
+#if QT_VERSION < 0x060000
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).isNull());
+#else
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap().isNull());
+#endif
scrollArea->scaleImage(factor);
adjustScrollBar(scrollArea->horizontalScrollBar(), factor);
@@ -467,7 +481,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
qDebug() << "MainWindow::runDetection _properties.isInverse() "
<< _properties.isInverse();
- qDebug() << "Computing bead directions " << endl;
+ qDebug() << "Computing bead directions " << Qt::endl;
imageDirect directions;
const parameterDirect & parameter_direct =
beads_params.get_parameter_direction();
@@ -477,7 +491,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
directions.save(directory_to_save_all_steps + "/DIRECTIONS.png");
}
- qDebug() << "Beads are rolling" << endl;
+ qDebug() << "Beads are rolling" << Qt::endl;
imageCoule rolling;
rolling.compute_from_direct(directions);
if (!directory_to_save_all_steps.isEmpty()) {
@@ -485,7 +499,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
}
//using confluent method :
- qDebug() << "Computing bead paths" << endl;
+ qDebug() << "Computing bead paths" << Qt::endl;
imagePaths path;
path.compute_from_direct_and_coule(directions, rolling);
@@ -493,13 +507,13 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
path.save(directory_to_save_all_steps + "/PATHS.png");
}
- qDebug() << "Detecting merging paths and arrival positions" << endl;
+ qDebug() << "Detecting merging paths and arrival positions" << Qt::endl;
const parameterConfluent & parameter_confl =
beads_params.get_parameter_confluent();
- qDebug() << " minflux : " << parameter_confl.get_minflux() << endl;
- qDebug() << " minpath : " << parameter_confl.get_minpath() << endl;
- qDebug() << " winconfl : " << parameter_confl.get_winconfl() << endl;
- qDebug() << " minbeads : " << parameter_confl.get_minbeads() << endl;
+ qDebug() << " minflux : " << parameter_confl.get_minflux() << Qt::endl;
+ qDebug() << " minpath : " << parameter_confl.get_minpath() << Qt::endl;
+ qDebug() << " winconfl : " << parameter_confl.get_winconfl() << Qt::endl;
+ qDebug() << " minbeads : " << parameter_confl.get_minbeads() << Qt::endl;
imageConfluent confluent;
confluent.compute_from_direct_and_paths(directions, path, *p_gel_image,
@@ -508,12 +522,12 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
confluent.save(directory_to_save_all_steps + "/SELECT.png");
}
- qDebug() << "Computing probabilites of spot positions" << endl;
+ qDebug() << "Computing probabilites of spot positions" << Qt::endl;
const parameterProb & parameter_prob =
beads_params.get_parameter_prob();
- qDebug() << " threshold : " << parameter_prob.get_threshold() << endl;
- qDebug() << " sx : " << parameter_prob.get_sx() << endl;
- qDebug() << " sy : " << parameter_prob.get_sy() << endl;
+ qDebug() << " threshold : " << parameter_prob.get_threshold() << Qt::endl;
+ qDebug() << " sx : " << parameter_prob.get_sx() << Qt::endl;
+ qDebug() << " sy : " << parameter_prob.get_sy() << Qt::endl;
imageProb dest_image_prob;
@@ -523,11 +537,11 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
+ "/PROBABILITIES.png");
}
- qDebug() << "Detecting spots" << endl;
+ qDebug() << "Detecting spots" << Qt::endl;
const parameterDetection & parameter_detection =
beads_params.get_parameter_detection();
qDebug() << " minproba : " << parameter_detection.get_minproba()
- << endl;
+ << Qt::endl;
detection * p_the_detection_from_prob = new detection();
p_the_detection_from_prob->detect_from_prob(dest_image_prob,
@@ -535,7 +549,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
//imageDetection img_detect(*p_the_detection_from_prob);
- qDebug() << "Quantification" << endl;
+ qDebug() << "Quantification" << Qt::endl;
const parameterNumber & parameter_number =
beads_params.get_parameter_number();
=====================================
src/qtbeads/properties.cpp
=====================================
@@ -20,53 +20,53 @@ void create_default_parameter_file(const QFileInfo & filename) {
}
QTextStream param_stream(¶m_file);
- param_stream << "#" << filename.absoluteFilePath() << endl;
- param_stream << "# beads configuration file" << endl;
+ param_stream << "#" << filename.absoluteFilePath() << Qt::endl;
+ param_stream << "# beads configuration file" << Qt::endl;
param_stream << "# default parameters, optimized for silver staining"
- << endl;
- param_stream << endl;
- param_stream << "################################" << endl;
- param_stream << "# parameters for DIRECTIONS #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "burned_pixel_threshold = 63000" << endl;
- param_stream << endl;
- param_stream << "################################" << endl;
- param_stream << "# parameters for SELECT #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "minflux = 100" << endl;
- param_stream << "minpath = 2" << endl;
- param_stream << "winconfl = 300" << endl;
- param_stream << "minbeads = 200" << endl;
- param_stream << "confluent_intmax = 60000" << endl;
- param_stream << "confluent_minpct = 1" << endl;
- param_stream << endl;
- param_stream << "################################" << endl;
- param_stream << "# parameters for PROBABILITIES #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "prob_threshold = 10" << endl;
- param_stream << "sx = 3" << endl;
- param_stream << "sy = 3" << endl;
- param_stream << "sx_bottom = 5" << endl;
- param_stream << "sy_bottom = 5" << endl;
- param_stream << endl;
-
- param_stream << "################################" << endl;
- param_stream << "# parameters for detections #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "minproba = 400" << endl;
- param_stream << endl;
-
- param_stream << "################################" << endl;
- param_stream << "# parameters for quantification #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "quantification_enlarge_fusion = 3" << endl;
- param_stream << "npass = 10" << endl;
- param_stream << endl;
+ << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for DIRECTIONS #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "burned_pixel_threshold = 63000" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for SELECT #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "minflux = 100" << Qt::endl;
+ param_stream << "minpath = 2" << Qt::endl;
+ param_stream << "winconfl = 300" << Qt::endl;
+ param_stream << "minbeads = 200" << Qt::endl;
+ param_stream << "confluent_intmax = 60000" << Qt::endl;
+ param_stream << "confluent_minpct = 1" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for PROBABILITIES #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "prob_threshold = 10" << Qt::endl;
+ param_stream << "sx = 3" << Qt::endl;
+ param_stream << "sy = 3" << Qt::endl;
+ param_stream << "sx_bottom = 5" << Qt::endl;
+ param_stream << "sy_bottom = 5" << Qt::endl;
+ param_stream << Qt::endl;
+
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for detections #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "minproba = 400" << Qt::endl;
+ param_stream << Qt::endl;
+
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for quantification #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "quantification_enlarge_fusion = 3" << Qt::endl;
+ param_stream << "npass = 10" << Qt::endl;
+ param_stream << Qt::endl;
param_stream.flush();
param_file.close();
}
=====================================
src/qtbeads/q_gel_image.cpp
=====================================
@@ -55,7 +55,11 @@ void QGelImage::setScaleFactor(double scale_factor) {
void QGelImage::scaleImage(double factor) {
_scaleFactor *= factor;
- this->resize(_scaleFactor * this->pixmap()->size());
+#if QT_VERSION < 0x060000
+ this->resize(_scaleFactor * this->pixmap(Qt::ReturnByValue).size());
+#else
+ this->resize(_scaleFactor * this->pixmap().size());
+#endif
}
int QGelImage::getX(int real_x) const {
View it on GitLab: https://salsa.debian.org/med-team/beads/-/commit/a80ffa774f9e06bb46aafd77d595ce9d615df327
--
View it on GitLab: https://salsa.debian.org/med-team/beads/-/commit/a80ffa774f9e06bb46aafd77d595ce9d615df327
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