From 57284e7c3548cf2eb50c5218962872e508fa402e Mon Sep 17 00:00:00 2001
From: Marc Sturm <marc.sturm@med.uni-tuebingen.de>
Date: Tue, 7 Nov 2023 10:42:43 +0100
Subject: [PATCH] GSvar: added menu entry to delete IGV folder

---
 src/GSvar/MainWindow.cpp | 21 ++++++++++++++++++++-
 src/GSvar/MainWindow.h   |  2 ++
 src/GSvar/MainWindow.ui  |  9 +++++++++
 3 files changed, 31 insertions(+), 1 deletion(-)

diff --git a/src/GSvar/MainWindow.cpp b/src/GSvar/MainWindow.cpp
index 4eba2e9eb..cff877f88 100644
--- a/src/GSvar/MainWindow.cpp
+++ b/src/GSvar/MainWindow.cpp
@@ -1,6 +1,7 @@
 #include "MainWindow.h"
 #include <QFileDialog>
 #include <QMessageBox>
+#include <QStandardPaths>
 #include "Settings.h"
 #include "Exceptions.h"
 #include "ChromosomalIndex.h"
@@ -1770,7 +1771,25 @@ void MainWindow::on_actionIgvClear_triggered()
 
 void MainWindow::on_actionIgvDocumentation_triggered()
 {
-	QDesktopServices::openUrl(QUrl("https://software.broadinstitute.org/software/igv/UserGuide"));
+	QDesktopServices::openUrl(QUrl("https://igv.org/doc/desktop/#UserGuide/reference_genome/"));
+}
+
+void MainWindow::on_actionDeleteIgvFolder_triggered()
+{
+	QString title = "Delete IGV folder";
+	QString path = QStandardPaths::standardLocations(QStandardPaths::HomeLocation).at(0) + QDir::separator() + "igv" + QDir::separator();
+	QString path_canonical = QFileInfo(path).canonicalFilePath();
+	if(path_canonical.isEmpty())
+	{
+	   QMessageBox::information(this, title, "IGV folder does not exist:\n" + path);
+	   return;
+	}
+
+	int res = QMessageBox::question(this, "Delete IGV folder", "Do you want to delete the IGV folder?\nLocation: "+path_canonical+"\n\nYou will use all settings (proxy, alignment options, ...)!");
+	if (res==QMessageBox::Yes)
+	{
+		QDir(path_canonical).removeRecursively();
+	}
 }
 
 void MainWindow::on_actionSV_triggered()
diff --git a/src/GSvar/MainWindow.h b/src/GSvar/MainWindow.h
index fce765913..f33e3ea8b 100644
--- a/src/GSvar/MainWindow.h
+++ b/src/GSvar/MainWindow.h
@@ -205,6 +205,8 @@ public slots:
 	void on_actionIgvClear_triggered();
 	///Open IGV documentation in browser
 	void on_actionIgvDocumentation_triggered();
+	///Delete IGV folder
+	void on_actionDeleteIgvFolder_triggered();
 	///Open CNV dialog
 	void on_actionCNV_triggered();
 	///Open ROH dialog
diff --git a/src/GSvar/MainWindow.ui b/src/GSvar/MainWindow.ui
index 9f3d691db..30ba2b494 100644
--- a/src/GSvar/MainWindow.ui
+++ b/src/GSvar/MainWindow.ui
@@ -437,8 +437,12 @@
       <string>Open custom track</string>
      </property>
     </widget>
+    <addaction name="actionIgvDocumentation"/>
+    <addaction name="separator"/>
     <addaction name="actionIgvClear"/>
     <addaction name="menuOpenCustomTrack"/>
+    <addaction name="separator"/>
+    <addaction name="actionDeleteIgvFolder"/>
    </widget>
    <widget class="QMenu" name="menuVariants">
     <property name="title">
@@ -1458,6 +1462,11 @@
     <string>Settings</string>
    </property>
   </action>
+  <action name="actionDeleteIgvFolder">
+   <property name="text">
+    <string>Delete IGV folder</string>
+   </property>
+  </action>
  </widget>
  <layoutdefault spacing="6" margin="11"/>
  <customwidgets>