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sci-biology/clustalx: Switch to Qt5
Thanks to Debian. Bug: https://bugs.gentoo.org/644726 Package-Manager: Portage-2.3.24, Repoman-2.3.6
This commit is contained in:
Andreas Sturmlechner
56
sci-biology/clustalx/clustalx-2.1-r3.ebuild
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56
sci-biology/clustalx/clustalx-2.1-r3.ebuild
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@@ -0,0 +1,56 @@
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# Copyright 1999-2018 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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inherit desktop qmake-utils
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DESCRIPTION="Graphical interface for the ClustalW multiple alignment program"
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HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/"
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SRC_URI="
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http://www.clustal.org/download/current/${P}.tar.gz
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https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz"
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LICENSE="GPL-3 LGPL-3"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE=""
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DEPEND="
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dev-qt/qtcore:5
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dev-qt/qtgui:5
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dev-qt/qtwidgets:5
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dev-qt/qtxml:5
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"
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RDEPEND="${DEPEND}
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>=sci-biology/clustalw-${PV}
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"
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PATCHES=( "${FILESDIR}/${P}"-qt5.patch ) # kindly borrowed from Debian
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src_prepare() {
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default
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sed \
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-e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \
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-e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \
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-e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \
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-i ClustalQtParams.h || \
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die "Failed to patch shared files location."
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sed \
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-e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \
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-i HelpDisplayWidget.cpp || \
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die "Failed to patch help file location."
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rm -rf usr || die
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}
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src_configure() {
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eqmake5
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}
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src_install() {
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dobin clustalx
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insinto /usr/share/${PN}
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doins colprot.xml coldna.xml colprint.xml clustalx.hlp
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make_desktop_entry ${PN} ClustalX
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doicon "${WORKDIR}"/${PN}.png
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}
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295
sci-biology/clustalx/files/clustalx-2.1-qt5.patch
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295
sci-biology/clustalx/files/clustalx-2.1-qt5.patch
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@@ -0,0 +1,295 @@
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Author: Andreas Tille <tille@debian.org>
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Last-Update: Mon, 11 Sep 2017 09:30:38 +0200
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Description: Porting to Qt5 following the hints at
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https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#QtWidgets_as_a_Separate_Module
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https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#toAscii.28.29_and_fromAscii.28.29_Methods_are_deprecated
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--- a/clustalx.pro
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+++ b/clustalx.pro
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@@ -6,6 +6,7 @@ TEMPLATE = app
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TARGET = clustalx
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CONFIG += release static
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QT += xml
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+QT += widgets
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VERSION = 2.1
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win32 {
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DEFINES += OS_WINDOWS
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--- a/AlignOutputFileNames.cpp
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+++ b/AlignOutputFileNames.cpp
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@@ -20,7 +20,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <iostream>
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#include "AlignOutputFileNames.h"
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--- a/AlignmentFormatOptions.cpp
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+++ b/AlignmentFormatOptions.cpp
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@@ -5,7 +5,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include "AlignmentFormatOptions.h"
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#include "clustalW/general/userparams.h"
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--- a/AlignmentParameters.cpp
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+++ b/AlignmentParameters.cpp
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@@ -11,7 +11,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <QButtonGroup>
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#include <QLineEdit>
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--- a/AlignmentViewerWidget.cpp
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+++ b/AlignmentViewerWidget.cpp
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@@ -60,7 +60,7 @@
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*****************************************************************************/
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QFile>
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#include <QTextStream>
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#include "AlignmentViewerWidget.h"
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--- a/AlignmentWidget.cpp
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+++ b/AlignmentWidget.cpp
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@@ -45,7 +45,7 @@
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*
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****************************************************************************/
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-#include <QtGui>
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+#include <QtWidgets>
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#include "AlignmentWidget.h"
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#include "clustalW/general/userparams.h"
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#include "ClustalQtParams.h"
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--- a/BootstrapTreeDialog.cpp
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+++ b/BootstrapTreeDialog.cpp
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@@ -12,7 +12,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <iostream>
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#include "BootstrapTreeDialog.h"
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--- a/ColorFileXmlParser.cpp
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+++ b/ColorFileXmlParser.cpp
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@@ -1,4 +1,4 @@
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-#include <QtGui>
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+#include <QtWidgets>
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#include "ColorFileXmlParser.h"
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#include "ClustalQtParams.h"
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--- a/ColumnScoreParams.cpp
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+++ b/ColumnScoreParams.cpp
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@@ -11,7 +11,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <QButtonGroup>
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#include <QLineEdit>
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--- a/HelpDisplayWidget.cpp
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+++ b/HelpDisplayWidget.cpp
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@@ -16,7 +16,7 @@
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#include <QTextEdit>
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#include <iostream>
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#include <fstream>
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-#include <QtGui>
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+#include <QtWidgets>
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#include "Resources.h"
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const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp";
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--- a/HistogramWidget.cpp
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+++ b/HistogramWidget.cpp
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@@ -21,7 +21,7 @@
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****************************************************************************/
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#include "HistogramWidget.h"
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QImage>
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//#include <QPixmap>
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#include <QPoint>
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--- a/LowScoringSegParams.cpp
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+++ b/LowScoringSegParams.cpp
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@@ -12,7 +12,7 @@
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#include <QHBoxLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <QButtonGroup>
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#include <QLineEdit>
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--- a/PSPrinter.cpp
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+++ b/PSPrinter.cpp
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@@ -16,7 +16,7 @@
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#include <ctime>
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#include <iomanip>
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#include <sstream>
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-#include <QtGui>
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+#include <QtWidgets>
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#include "PSPrinter.h"
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#include "ColorFileXmlParser.h"
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#include "clustalW/general/userparams.h"
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@@ -594,7 +594,7 @@ void PSPrinter::printHeaderLine(ofstream
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{
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psX = blockLeft + (i - fr) * CHARWIDTH;
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(*psOutFile) << "(";
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- (*psOutFile) << data->seqHeader[ix][i].toAscii();
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+ (*psOutFile) << data->seqHeader[ix][i].toLatin1();
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(*psOutFile) << ") ";
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(*psOutFile) << psX << " " << psY << " " << psX << " "
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<< psY << " 1.0 1.0 1.0 color_inv\n";
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--- a/PairwiseParams.cpp
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+++ b/PairwiseParams.cpp
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@@ -18,7 +18,7 @@
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#include <QRadioButton>
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#include <QMessageBox>
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#include <QHBoxLayout>
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-#include <QtGui>
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+#include <QtWidgets>
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#include "clustalW/general/userparams.h"
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#include "clustalW/substitutionMatrix/globalmatrix.h"
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#include "FileDialog.h"
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--- a/ProteinGapParameters.cpp
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+++ b/ProteinGapParameters.cpp
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@@ -5,7 +5,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <QString>
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#include <QMessageBox>
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--- a/SaveSeqFile.cpp
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+++ b/SaveSeqFile.cpp
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@@ -18,7 +18,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include "SaveSeqFile.h"
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#include "clustalW/general/userparams.h"
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--- a/SecStructOptions.cpp
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+++ b/SecStructOptions.cpp
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@@ -5,7 +5,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <QLineEdit>
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#include "SecStructOptions.h"
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--- a/SeqNameWidget.cpp
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+++ b/SeqNameWidget.cpp
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@@ -55,7 +55,7 @@
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*
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****************************************************************************/
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-#include <QtGui>
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+#include <QtWidgets>
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#include "SeqNameWidget.h"
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#include "KeyController.h" //- nige
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#include "clustalW/alignment/Alignment.h"
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--- a/TreeFormatOptions.cpp
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+++ b/TreeFormatOptions.cpp
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@@ -4,7 +4,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <QCheckBox>
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#include "TreeFormatOptions.h"
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--- a/TreeOutputFileNames.cpp
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+++ b/TreeOutputFileNames.cpp
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@@ -11,7 +11,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <iostream>
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#include "TreeOutputFileNames.h"
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--- a/WritePostscriptFile.cpp
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+++ b/WritePostscriptFile.cpp
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@@ -18,7 +18,7 @@
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#include <QGridLayout>
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#include <QSizePolicy>
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#include <QComboBox>
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QLabel>
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#include <iostream>
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#include "WritePostscriptFile.h"
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--- a/mainwindow.cpp
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+++ b/mainwindow.cpp
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@@ -87,7 +87,7 @@
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*
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****************************************************************************/
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-#include <QtGui>
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+#include <QtWidgets>
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#include <QPixmap>
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#include <QFile>
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#include <iostream>
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--- a/ColorParameters.cpp
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+++ b/ColorParameters.cpp
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@@ -154,8 +154,8 @@ QColor ColorParameters::getResidueColor(
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{
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int i, j;
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QChar colorParRes;
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- char showRes = res.toAscii();
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- char showCon = consensus.toAscii();
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+ char showRes = res.toLatin1();
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+ char showCon = consensus.toLatin1();
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for(i = 0; i < colorPar.size(); i++)
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{
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@@ -171,7 +171,7 @@ QColor ColorParameters::getResidueColor(
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for(j = 0; j < colorPar[i].consensusConditionList.size(); j++)
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{
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- char temp = colorPar[i].consensusConditionList[j].toAscii();
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+ char temp = colorPar[i].consensusConditionList[j].toLatin1();
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if(consensus == colorPar[i].consensusConditionList[j])
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{
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return colorPar[i].color;
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@@ -191,8 +191,8 @@ int ColorParameters::getResidueColorNum(
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{
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int i, j;
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QChar colorParRes;
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- char showRes = res.toAscii();
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- char showCon = consensus.toAscii();
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+ char showRes = res.toLatin1();
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+ char showCon = consensus.toLatin1();
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for(i = 0; i < colorPar.size(); i++)
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{
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@@ -208,7 +208,7 @@ int ColorParameters::getResidueColorNum(
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for(j = 0; j < colorPar[i].consensusConditionList.size(); j++)
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{
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- char temp = colorPar[i].consensusConditionList[j].toAscii();
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+ char temp = colorPar[i].consensusConditionList[j].toLatin1();
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if(consensus == colorPar[i].consensusConditionList[j])
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{
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return getIndexOfColor(colorPar[i].color);
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