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-rw-r--r--.SRCINFO6
-rw-r--r--PKGBUILD17
-rw-r--r--qt4to5.patch214
3 files changed, 230 insertions, 7 deletions
diff --git a/.SRCINFO b/.SRCINFO
index cfd312730483..b787ec87b012 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,19 @@
pkgbase = pamlx
pkgdesc = A Graphical User Interface for PAML https://doi.org/10.1093/molbev/mst179
pkgver = 1.3.1
- pkgrel = 3
+ pkgrel = 4
url = http://abacus.gene.ucl.ac.uk/software/
arch = x86_64
license = custom
makedepends = make
- depends = qt4
+ depends = qt5-base
depends = paml
provides = pamlx
source = http://abacus.gene.ucl.ac.uk/software/pamlX1.3.1-src.tgz
source = pamlX.desktop
+ source = qt4to5.patch
sha256sums = e6abbbc715aff1d9ebcb6d9b7c2fb494f916bee53f9cf807bf38cebc7bd625bf
sha256sums = e70746b45dfdde9baa1f38db29474296fbd3cb0a8b1fb685260d6c01f373938b
+ sha256sums = f1ae154e78d95f1c6656c9d4d838de825e8ef92b9002803ceed9b2f1445b95e3
pkgname = pamlx
diff --git a/PKGBUILD b/PKGBUILD
index cda821923271..befffd6dff3d 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,20 +2,27 @@
pkgname=pamlx
_pkgname=pamlX
pkgver=1.3.1
-pkgrel=3
+pkgrel=4
pkgdesc="A Graphical User Interface for PAML https://doi.org/10.1093/molbev/mst179"
arch=('x86_64')
url="http://abacus.gene.ucl.ac.uk/software/"
license=('custom')
-depends=('qt4' 'paml')
+depends=('qt5-base' 'paml')
makedepends=('make')
provides=('pamlx')
-source=("http://abacus.gene.ucl.ac.uk/software/pamlX${pkgver}-src.tgz" "pamlX.desktop")
+source=("http://abacus.gene.ucl.ac.uk/software/pamlX${pkgver}-src.tgz" "pamlX.desktop" "qt4to5.patch")
sha256sums=('e6abbbc715aff1d9ebcb6d9b7c2fb494f916bee53f9cf807bf38cebc7bd625bf'
- 'e70746b45dfdde9baa1f38db29474296fbd3cb0a8b1fb685260d6c01f373938b')
+ 'e70746b45dfdde9baa1f38db29474296fbd3cb0a8b1fb685260d6c01f373938b'
+ 'f1ae154e78d95f1c6656c9d4d838de825e8ef92b9002803ceed9b2f1445b95e3')
+
+prepare(){
+ cd $_pkgname$pkgver-src
+ patch -p1 < $srcdir/qt4to5.patch
+}
+
build() {
cd $_pkgname$pkgver-src
- qmake-qt4
+ qmake
make
}
diff --git a/qt4to5.patch b/qt4to5.patch
new file mode 100644
index 000000000000..a0a5c5ba3767
--- /dev/null
+++ b/qt4to5.patch
@@ -0,0 +1,214 @@
+Description: upgrade pamlX from qt4 to qt5
+Author: Guoyi Zhang <guoyizhang@malacology.net>
+Last-Update: 2024-02-06
+---
+This patch header follows AGPL-3.0
+diff --git a/main.cpp b/main.cpp
+index 31edde9..6dfbad1 100644
+--- a/main.cpp
++++ b/main.cpp
+@@ -2,8 +2,8 @@
+ // Copyright (C) 2012 Bo Xu <xuxbob@gmail.com>
+ //------------------------------------------------
+
+-#include <QtGui/QApplication>
+-#include <QSplashScreen>
++#include <QtWidgets/QApplication>
++#include <QtWidgets/QSplashScreen>
+ #include "mainwindow.h"
+ #include "info.h"
+ #include "mydebug.h"
+diff --git a/mainwindow.cpp b/mainwindow.cpp
+index 42f53b6..30ace7d 100644
+--- a/mainwindow.cpp
++++ b/mainwindow.cpp
+@@ -123,7 +123,7 @@ MainWindow::MainWindow(QWidget *parent) :
+ menuRecent_Files->setIcon(icon);
+ actionSelect_All->setIcon(icon);
+
+- actionConfiguration->setText(QApplication::translate("MainWindow", "&Preferences...", 0, QApplication::UnicodeUTF8));
++ actionConfiguration->setText(QApplication::translate("MainWindow", "&Preferences..."));
+ #endif
+
+ //Toolbar
+@@ -193,7 +193,7 @@ MainWindow::MainWindow(QWidget *parent) :
+ "<p align=\"center\" style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'SimSun'; font-size:9pt;\"></p>\n"
+ "<p align=\"center\" style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\"><a href=\"http://abacus.gene.ucl.ac.uk/software/paml.html\"><span style=\" font-family:'Herculanum'; font-size:20pt; text-decoration: none; color:#000000;\">PAML Software Website</span></a></p>\n"
+ "<p align=\"center\" style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'SimSun'; font-size:20pt; font-weight:600;\"></p>\n"
+-"<p align=\"center\" style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'SimSun'; font-size:9pt;\"></p></body></html>", 0, QApplication::UnicodeUTF8));
++"<p align=\"center\" style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'SimSun'; font-size:9pt;\"></p></body></html>"));
+
+ QFont font2;
+ font2.setFamily(QString::fromUtf8("Comic Sans MS"));
+@@ -3520,7 +3520,7 @@ void MainWindow::on_comboBox_37_currentIndexChanged(int index)
+ case 1:
+ comboBox_39->setItemText(0, tr("1: b"));
+ comboBox_39->insertItems(1, QStringList()
+- << QApplication::translate("MainWindow", "2: two branch types", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "2: two branch types")
+ );
+ comboBox_39->setItemData(0, 1);
+ comboBox_39->setItemData(1, 2);
+@@ -3582,9 +3582,9 @@ void MainWindow::on_comboBox_37_currentIndexChanged(int index)
+ default:
+ comboBox_39->setItemText(0, tr("0: one"));
+ comboBox_39->insertItems(1, QStringList()
+- << QApplication::translate("MainWindow", "1: b", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "2: 2 or more dN/dS", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "3:", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "1: b")
++ << QApplication::translate("MainWindow", "2: 2 or more dN/dS")
++ << QApplication::translate("MainWindow", "3:")
+ );
+ if(!ok) currentItemData = 0;
+ comboBox_39->setCurrentIndex(currentItemData);
+@@ -3650,10 +3650,10 @@ void MainWindow::on_comboBox_31_currentIndexChanged(int index)
+ if( index == 1 && num != 4 ) {
+ if(num == 0) {
+ comboBox_39->insertItems(0, QStringList()
+- << QApplication::translate("MainWindow", "0: one", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "1: b", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "2: 2 or more dN/dS", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "3:", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "0: one")
++ << QApplication::translate("MainWindow", "1: b")
++ << QApplication::translate("MainWindow", "2: 2 or more dN/dS")
++ << QApplication::translate("MainWindow", "3:")
+ );
+ }
+ else {
+@@ -3682,14 +3682,14 @@ void MainWindow::on_comboBox_31_currentIndexChanged(int index)
+ if( (index == 2 || index == 3) && num != 8 ) {
+ if(num == 0) {
+ comboBox_39->insertItems(0, QStringList()
+- << QApplication::translate("MainWindow", "0: poisson", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "1: proportional", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "2: Empirical", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "3: Empirical+F", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "6: FromCodon", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "7: AAClasses", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "8: REVaa_0", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "9: REVaa(nr=189)", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "0: poisson")
++ << QApplication::translate("MainWindow", "1: proportional")
++ << QApplication::translate("MainWindow", "2: Empirical")
++ << QApplication::translate("MainWindow", "3: Empirical+F")
++ << QApplication::translate("MainWindow", "6: FromCodon")
++ << QApplication::translate("MainWindow", "7: AAClasses")
++ << QApplication::translate("MainWindow", "8: REVaa_0")
++ << QApplication::translate("MainWindow", "9: REVaa(nr=189)")
+ );
+ }
+ else {
+@@ -3702,10 +3702,10 @@ void MainWindow::on_comboBox_31_currentIndexChanged(int index)
+ comboBox_39->setItemText(2, tr("2: Empirical"));
+ comboBox_39->setItemText(3, tr("3: Empirical+F"));
+ comboBox_39->insertItems(4, QStringList()
+- << QApplication::translate("MainWindow", "6: FromCodon", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "7: AAClasses", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "8: REVaa_0", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "9: REVaa(nr=189)", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "6: FromCodon")
++ << QApplication::translate("MainWindow", "7: AAClasses")
++ << QApplication::translate("MainWindow", "8: REVaa_0")
++ << QApplication::translate("MainWindow", "9: REVaa(nr=189)")
+ );
+ }
+ comboBox_39->setItemData(0, 0);
+@@ -3722,20 +3722,20 @@ void MainWindow::on_comboBox_31_currentIndexChanged(int index)
+ if( index == 1 && num != 5 ) {
+ if(num == 0) {
+ comboBox_40->insertItems(0, QStringList()
+- << QApplication::translate("MainWindow", "0: rates", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "1: separate", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "2: diff pi", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "3: diff kapa", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "4: all diff", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "0: rates")
++ << QApplication::translate("MainWindow", "1: separate")
++ << QApplication::translate("MainWindow", "2: diff pi")
++ << QApplication::translate("MainWindow", "3: diff kapa")
++ << QApplication::translate("MainWindow", "4: all diff")
+ );
+ }
+ else {
+ comboBox_40->setItemData(0, QVariant::Invalid);
+ comboBox_40->setItemData(1, QVariant::Invalid);
+ comboBox_40->insertItems(2, QStringList()
+- << QApplication::translate("MainWindow", "2: diff pi", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "3: diff kapa", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "4: all diff", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "2: diff pi")
++ << QApplication::translate("MainWindow", "3: diff kapa")
++ << QApplication::translate("MainWindow", "4: all diff")
+ );
+ }
+ comboBox_40->setItemData(0, 0);
+@@ -3747,8 +3747,8 @@ void MainWindow::on_comboBox_31_currentIndexChanged(int index)
+ if( (index == 2 || index == 3) && num != 2 ) {
+ if(num == 0) {
+ comboBox_40->insertItems(0, QStringList()
+- << QApplication::translate("MainWindow", "0: rates", 0, QApplication::UnicodeUTF8)
+- << QApplication::translate("MainWindow", "1: separate", 0, QApplication::UnicodeUTF8)
++ << QApplication::translate("MainWindow", "0: rates")
++ << QApplication::translate("MainWindow", "1: separate")
+ );
+ }
+ else {
+diff --git a/mainwindow.h b/mainwindow.h
+index 303b69d..6dba937 100644
+--- a/mainwindow.h
++++ b/mainwindow.h
+@@ -5,6 +5,10 @@
+ #ifndef MAINWINDOW_H
+ #define MAINWINDOW_H
+
++#include <QPrinter>
++#include <QButtonGroup>
++#include <QMimeData>
++
+ #include "ui_mainwindow.h"
+
+ #include "engine.h"
+diff --git a/mcmctreeengine.cpp b/mcmctreeengine.cpp
+index d5891f9..ba00c56 100644
+--- a/mcmctreeengine.cpp
++++ b/mcmctreeengine.cpp
+@@ -328,8 +328,8 @@ int MCMCTreeEngine::compareVersion(const QString& versionStr) const
+ QString mRevision, revision;
+ char c;
+
+- QTextStream(mVersion.toAscii()) >> mMajor >> c >> mMinor >> mRevision;
+- QTextStream(versionStr.toAscii()) >> major >> c >> minor >> revision;
++ QTextStream(mVersion.toUtf8()) >> mMajor >> c >> mMinor >> mRevision;
++ QTextStream(versionStr.toUtf8()) >> major >> c >> minor >> revision;
+
+ int ret;
+
+diff --git a/mcmctreeengine.h b/mcmctreeengine.h
+index 4a6634a..0403b2b 100644
+--- a/mcmctreeengine.h
++++ b/mcmctreeengine.h
+@@ -5,6 +5,9 @@
+ #ifndef MCMCTREEENGINE_H
+ #define MCMCTREEENGINE_H
+
++#include <QString>
++#include <QTextStream>
++
+ #include "engine.h"
+
+ #if defined(Q_OS_WIN32) || defined(Q_OS_MAC) || defined(Q_OS_LINUX)
+diff --git a/pamlX.pro b/pamlX.pro
+index fab0064..9b5b5fc 100644
+--- a/pamlX.pro
++++ b/pamlX.pro
+@@ -6,7 +6,7 @@
+ #
+ #-------------------------------------------------
+
+-QT += core gui
++QT += core gui widgets printsupport
+
+ TARGET = pamlX
+ TEMPLATE = app