mirror of
https://github.com/BioArchLinux/Packages.git
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add clustalx
This commit is contained in:
starsareintherose
parent
c2979ebf28
commit
bf7abebea5
5 changed files with 307 additions and 0 deletions
28
clustalx/0001-fix-qt.patch
Executable file
28
clustalx/0001-fix-qt.patch
Executable file
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@ -0,0 +1,28 @@
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diff -urN clustalx-2.1/ClustalQtParams.h clustalx-2.1a/ClustalQtParams.h
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--- clustalx-2.1/ClustalQtParams.h 2010-11-17 05:12:30.000000000 -0500
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+++ clustalx-2.1a/ClustalQtParams.h 2010-11-18 12:19:42.450866697 -0500
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@@ -13,9 +13,9 @@
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#include "clustalW/alignment/Alignment.h"
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#include <vector>
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-static QString psColorFile = "colprot.xml";
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-static QString psDNAFile = "coldna.xml";
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-static QString psPrintFile = "colprint.xml";
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+static QString psColorFile = "/usr/share/clustalx/colprot.xml";
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+static QString psDNAFile = "/usr/share/clustalx/coldna.xml";
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+static QString psPrintFile = "/usr/share/clustalx/colprint.xml";
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static const int BlackAndWhite = 1;
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static const int ColorsBackGround = 2;
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diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1a/HelpDisplayWidget.cpp
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--- clustalx-2.1/HelpDisplayWidget.cpp 2010-11-17 05:12:30.000000000 -0500
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+++ clustalx-2.1a/HelpDisplayWidget.cpp 2010-11-18 12:20:34.727866697 -0500
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@@ -19,7 +19,7 @@
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#include <QtGui>
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#include "Resources.h"
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-const string HelpDisplayWidget::helpFileName = "clustalx.hlp";
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+const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp";
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HelpDisplayWidget::HelpDisplayWidget(char helpPointer)
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{
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200
clustalx/0002-fix-qt.patch
Executable file
200
clustalx/0002-fix-qt.patch
Executable file
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@ -0,0 +1,200 @@
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diff -urN clustalx-2.1/AlignOutputFileNames.cpp clustalx-2.1-bak/AlignOutputFileNames.cpp
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--- clustalx-2.1/AlignOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/AlignOutputFileNames.cpp 2015-09-18 18:59:38.582405761 +0200
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@@ -13,6 +13,7 @@
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* 18-06-07,Nigel Brown(EMBL): Made the 'ok' button in each dialogue be the
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* default instead of a Browse button.
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*/
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+#include <QtGui>
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#include <QPushButton>
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#include <QGroupBox>
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#include <QCheckBox>
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@@ -20,8 +21,8 @@
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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 <QLabel>
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+#include <QLineEdit>
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#include <iostream>
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#include "AlignOutputFileNames.h"
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#include "clustalW/general/userparams.h"
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diff -urN clustalx-2.1/AlignmentViewerWidget.cpp clustalx-2.1-bak/AlignmentViewerWidget.cpp
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--- clustalx-2.1/AlignmentViewerWidget.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/AlignmentViewerWidget.cpp 2015-09-18 18:50:09.762563103 +0200
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@@ -69,6 +69,11 @@
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#include "PSPrinter.h"
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#include "FileDialog.h"
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#include <QFontMetrics>
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+#include <QVBoxLayout>
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+#include <QScrollBar>
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+#include <QScrollArea>
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+#include <QMessageBox>
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+#include <QGroupBox>
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AlignmentViewerWidget::AlignmentViewerWidget(QWidget *parent)
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: QWidget(parent),
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diff -urN clustalx-2.1/AlignmentWidget.cpp clustalx-2.1-bak/AlignmentWidget.cpp
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--- clustalx-2.1/AlignmentWidget.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/AlignmentWidget.cpp 2015-09-18 18:58:36.656119118 +0200
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@@ -46,6 +46,7 @@
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****************************************************************************/
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#include <QtGui>
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+#include <QScrollArea>
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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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diff -urN clustalx-2.1/BootstrapTreeDialog.cpp clustalx-2.1-bak/BootstrapTreeDialog.cpp
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--- clustalx-2.1/BootstrapTreeDialog.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/BootstrapTreeDialog.cpp 2015-09-18 19:00:09.782214298 +0200
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@@ -5,6 +5,7 @@
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* 12-4-07, Mark Larkin, Removed destructor. No need to delete QObjects. Also removed
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* setAllPtrsToNull function.
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*/
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+#include <QtGui>
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#include <QPushButton>
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#include <QGroupBox>
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#include <QCheckBox>
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@@ -12,8 +13,8 @@
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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 <QLabel>
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+#include <QLineEdit>
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#include <iostream>
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#include "BootstrapTreeDialog.h"
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#include "clustalW/general/userparams.h"
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diff -urN clustalx-2.1/ColorFileXmlParser.cpp clustalx-2.1-bak/ColorFileXmlParser.cpp
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--- clustalx-2.1/ColorFileXmlParser.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/ColorFileXmlParser.cpp 2015-09-18 19:00:42.695345653 +0200
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@@ -1,4 +1,5 @@
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#include <QtGui>
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+#include <QMessageBox>
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#include "ColorFileXmlParser.h"
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#include "ClustalQtParams.h"
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@@ -202,4 +203,4 @@
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rule = rule.nextSiblingElement("resrule");
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}
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return numOfRules;
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-}
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\ No newline at end of file
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+}
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diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1-bak/HelpDisplayWidget.cpp
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--- clustalx-2.1/HelpDisplayWidget.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/HelpDisplayWidget.cpp 2015-09-18 19:34:51.692771579 +0200
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@@ -16,6 +16,8 @@
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#include <QTextEdit>
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#include <iostream>
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#include <fstream>
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+#include <QPushButton>
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+#include <QVBoxLayout>
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#include <QtGui>
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#include "Resources.h"
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diff -urN clustalx-2.1/PSPrinter.cpp clustalx-2.1-bak/PSPrinter.cpp
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--- clustalx-2.1/PSPrinter.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/PSPrinter.cpp 2015-09-18 19:20:36.528019466 +0200
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@@ -17,6 +17,7 @@
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#include <iomanip>
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#include <sstream>
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#include <QtGui>
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+#include <QMessageBox>
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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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diff -urN clustalx-2.1/ProteinGapParameters.cpp clustalx-2.1-bak/ProteinGapParameters.cpp
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--- clustalx-2.1/ProteinGapParameters.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/ProteinGapParameters.cpp 2015-09-18 19:20:07.311532091 +0200
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@@ -9,6 +9,7 @@
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#include <QLabel>
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#include <QString>
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#include <QMessageBox>
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+#include <QLineEdit>
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#include "ProteinGapParameters.h"
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#include "clustalW/general/userparams.h"
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diff -urN clustalx-2.1/SaveSeqFile.cpp clustalx-2.1-bak/SaveSeqFile.cpp
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--- clustalx-2.1/SaveSeqFile.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/SaveSeqFile.cpp 2015-09-18 19:21:28.231035513 +0200
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@@ -20,6 +20,8 @@
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#include <QComboBox>
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#include <QtGui>
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#include <QLabel>
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+#include <QMessageBox>
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+#include <QLineEdit>
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#include "SaveSeqFile.h"
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#include "clustalW/general/userparams.h"
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#include "clustalW/general/utils.h"
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diff -urN clustalx-2.1/SeqNameWidget.cpp clustalx-2.1-bak/SeqNameWidget.cpp
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--- clustalx-2.1/SeqNameWidget.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/SeqNameWidget.cpp 2015-09-18 19:22:48.903873782 +0200
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@@ -56,6 +56,7 @@
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****************************************************************************/
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#include <QtGui>
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+#include <QScrollArea>
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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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diff -urN clustalx-2.1/TreeOutputFileNames.cpp clustalx-2.1-bak/TreeOutputFileNames.cpp
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--- clustalx-2.1/TreeOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/TreeOutputFileNames.cpp 2015-09-18 19:23:37.006911921 +0200
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@@ -13,6 +13,7 @@
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#include <QComboBox>
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#include <QtGui>
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#include <QLabel>
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+#include <QLineEdit>
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#include <iostream>
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#include "TreeOutputFileNames.h"
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#include "clustalW/general/userparams.h"
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diff -urN clustalx-2.1/WritePostscriptFile.cpp clustalx-2.1-bak/WritePostscriptFile.cpp
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--- clustalx-2.1/WritePostscriptFile.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/WritePostscriptFile.cpp 2015-09-18 19:24:30.429917414 +0200
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@@ -20,6 +20,8 @@
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#include <QComboBox>
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#include <QtGui>
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#include <QLabel>
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+#include <QLineEdit>
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+#include <QMessageBox>
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#include <iostream>
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#include "WritePostscriptFile.h"
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#include "clustalW/general/userparams.h"
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Binary files clustalx-2.1/clustalx and clustalx-2.1-bak/clustalx differ
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diff -urN clustalx-2.1/clustalx.pro clustalx-2.1-bak/clustalx.pro
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--- clustalx-2.1/clustalx.pro 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/clustalx.pro 2015-09-18 19:14:42.666857671 +0200
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@@ -4,8 +4,11 @@
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TEMPLATE = app
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TARGET = clustalx
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-CONFIG += release static
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+CONFIG += release
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QT += xml
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+QT += widgets
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+DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x000000
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+
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VERSION = 2.1
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win32 {
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DEFINES += OS_WINDOWS
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diff -urN clustalx-2.1/mainwindow.cpp clustalx-2.1-bak/mainwindow.cpp
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--- clustalx-2.1/mainwindow.cpp 2010-11-17 11:12:30.000000000 +0100
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+++ clustalx-2.1-bak/mainwindow.cpp 2015-09-18 19:19:03.545256739 +0200
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@@ -94,6 +94,15 @@
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#include <cstdlib>
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#include <QCheckBox>
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#include <QStringList>
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+#include <QMenu>
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+#include <QMenuBar>
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+#include <QAction>
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+#include <QMessageBox>
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+#include <QApplication>
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+#include <QScrollBar>
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+#include <QHBoxLayout>
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+#include <QGroupBox>
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+#include <QVBoxLayout>
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#include "SecStructOptions.h"
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#include "mainwindow.h"
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#include "WritePostscriptFile.h"
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57
clustalx/PKGBUILD
Executable file
57
clustalx/PKGBUILD
Executable file
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@ -0,0 +1,57 @@
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# Maintainer: Hu Butui <hot123tea123@gmail.com>
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# Contributor: Matt Neilson <ichthyoboy at gmail dot com>
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# Contributor: Mick Elliot <micke at sfu dot ca>
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pkgname=clustalx
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pkgver=2.1
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pkgrel=2
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pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool'
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arch=('x86_64')
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url='http://www.clustal.org/clustal2'
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license=('LGPL3')
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depends=(
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qt5-base
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)
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makedepends=(
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gendesk
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)
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source=("${pkgname}-${pkgver}.tar.gz::http://www.clustal.org/download/current/clustalx-${pkgver}.tar.gz"
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"0001-fix-qt.patch"
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"0002-fix-qt.patch"
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"${pkgname}.png::http://www.clustal.org/images/clustalw_title.png"
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)
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sha256sums=('e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05'
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'5c070a5cd2e7ba5eddf984b6d5ad2bdbb1dc5fd1c50edaefd109e094ed33431c'
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'8a5bd0329015d70e2e649c33c13aaabbb88999305f83f4c0fa0c01fe1af3db72'
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'6444ab0c22ecbefba05b968558eb543dda4c7e0ad140b485832d763e9f8c2dbd')
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prepare() {
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cd "${pkgname}-${pkgver}"
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patch -p1 -i "${srcdir}/0001-fix-qt.patch"
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patch -p1 -i "${srcdir}/0002-fix-qt.patch"
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sed -i 's/static//g' clustalx.pro
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echo "Creating desktop file"
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gendesk -f -n --pkgname ${pkgname} \
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--pkgdesc "${pkgdesc}" \
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--categories "Graphics;MedicalSoftware;Science;" \
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--icon "${pkgname}" \
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--exec "${pkgname}"
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}
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build() {
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cd "${pkgname}-${pkgver}"
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qmake
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make
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}
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package() {
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cd "${pkgname}-${pkgver}"
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install -Dm755 clustalx "${pkgdir}/usr/bin/clustalx"
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install -Dm644 colprot.xml "${pkgdir}/usr/share/${pkgname}/colprot.xml"
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install -Dm644 coldna.xml "${pkgdir}/usr/share/${pkgname}/coldna.xml"
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install -Dm644 coldna.xml "${pkgdir}/usr/share/${pkgname}/colprint.xml"
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install -Dm644 clustalx.hlp "${pkgdir}/usr/share/${pkgname}/clustalx.hlp"
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install -Dm644 "${srcdir}/${pkgname}.png" "${pkgdir}/usr/share/pixmaps/${pkgname}.png"
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}
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# vim:set ts=2 sw=2 et:
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12
clustalx/lilac.py
Executable file
12
clustalx/lilac.py
Executable file
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@ -0,0 +1,12 @@
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#!/usr/bin/env python3
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from lilaclib import *
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def pre_build():
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update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
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def post_build():
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git_pkgbuild_commit()
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# vim:set ts=2 sw=2 et:
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10
clustalx/lilac.yaml
Executable file
10
clustalx/lilac.yaml
Executable file
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@ -0,0 +1,10 @@
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maintainers:
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- github: starsareintherose
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email: starsareintherose@outlook.com
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build_prefix: extra-x86_64
|
||||||
|
update_on:
|
||||||
|
- source: regex
|
||||||
|
url: "http://www.clustal.org/download/current"
|
||||||
|
regex: 'clustalx-(\d+.\d+)'
|
||||||
|
# vim:set ts=2 sw=2 et:
|
||||||
|
|
||||||
Loading…
Add table
Reference in a new issue