Reorganize tree to have sources in src/

phys2 · May 27, 2020 · d96d364 · d96d364
1 parent 8b15b2d
commit d96d364
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Showing 176 changed files with 125 additions and 111 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -20,11 +20,10 @@ include(flags)
 
 set(APP_NAME belki)
 
-add_executable(${APP_NAME} MACOSX_BUNDLE main.cpp)
+add_executable(${APP_NAME} MACOSX_BUNDLE src/main.cpp)
 set_target_properties(${APP_NAME} PROPERTIES
 	CXX_STANDARD 17
 	CXX_STANDARD_REQUIRED ON)
-export_version(main.cpp)
 
 ## PLATFORM SUPPORT
 if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
@@ -51,45 +50,26 @@ if (APPLE)
 	target_sources(${APP_NAME} PRIVATE resources/icon.icns)
 endif()
 
-## SOURCES
-# mean shift
-target_sources(${APP_NAME} PRIVATE
-	meanshift/fams.h meanshift/fams.cpp
-	meanshift/io.cpp meanshift/mode_pruning.cpp
-	)
+## COMPONENTS (they add to target 'belki')
+target_include_directories(${APP_NAME} PRIVATE src/core)
+add_subdirectory(src/core)
+add_subdirectory(src/compute)
+add_subdirectory(src/storage)
+add_subdirectory(src/widgets)
+add_subdirectory(src/profiles)
+add_subdirectory(src/scatterplot)
+add_subdirectory(src/heatmap)
+add_subdirectory(src/distmat)
+add_subdirectory(src/featweights)
 
-# resources
+## RESOURCES
 target_sources(${APP_NAME} PRIVATE
 	resources/index.qrc
 	resources/icons-stock/index.qrc
 	resources/icons-custom/index.qrc
 	)
-
-# main application
-target_sources(${APP_NAME} PRIVATE
-	datahub.h datahub.cpp
-	dataset.h dataset.cpp
-	fileio.h fileio.cpp
-	guistate.h guistate.cpp
-	jobregistry.h jobregistry.cpp
-	model.h
-	proteindb.h proteindb.cpp
-	utils.h
-	viewer.h viewer.cpp
-	windowstate.h windowstate.cpp
-	)
-
-# components (they add to target 'belki')
-add_subdirectory(compute)
-add_subdirectory(storage)
-add_subdirectory(widgets)
-add_subdirectory(profiles)
-add_subdirectory(scatterplot)
-add_subdirectory(heatmap)
-add_subdirectory(distmat)
-add_subdirectory(featweights)
-
-export_version(widgets/mainwindow.cpp) # for About box
+export_version(src/main.cpp)
+export_version(src/widgets/mainwindow.cpp) # for About box
 
 ## link to modules
 target_include_directories(${APP_NAME} SYSTEM PUBLIC ${DEP_INCLUDES})

diff --git a/cmake/dependencies.cmake b/cmake/dependencies.cmake
@@ -14,7 +14,7 @@ pkg_check_modules(ARPACK REQUIRED arpack)
 find_package(Eigen3 3.3 REQUIRED NO_MODULE)
 
 list(APPEND DEP_INCLUDES
-	${PROJECT_SOURCE_DIR}/include # for self-distributed Tapkee
+	${PROJECT_SOURCE_DIR}/tapkee # for self-distributed Tapkee
 	${ARPACK_INCLUDE_DIRS}
 )
 

diff --git a/compute/CMakeLists.txt → src/compute/CMakeLists.txt b/compute/CMakeLists.txt → src/compute/CMakeLists.txt
@@ -5,3 +5,10 @@ target_sources(${APP_NAME} PRIVATE
 	dimred.h dimred.cpp
 	features.h features.cpp
 	)
+
+# mean shift
+target_sources(${APP_NAME} PRIVATE
+	meanshift/fams.h meanshift/fams.cpp
+	meanshift/io.cpp meanshift/mode_pruning.cpp
+	)
+
diff --git a/compute/annotations.cpp → src/compute/annotations.cpp b/compute/annotations.cpp → src/compute/annotations.cpp
diff --git a/compute/annotations.h → src/compute/annotations.h b/compute/annotations.h → src/compute/annotations.h
diff --git a/compute/colors.cpp → src/compute/colors.cpp b/compute/colors.cpp → src/compute/colors.cpp
diff --git a/compute/colors.h → src/compute/colors.h b/compute/colors.h → src/compute/colors.h
diff --git a/compute/components.cpp → src/compute/components.cpp b/compute/components.cpp → src/compute/components.cpp
@@ -1,6 +1,6 @@
 #include "components.h"
 #include "dataset.h"
-#include "compute/features.h"
+#include "features.h"
 
 #include <tbb/parallel_for.h>
 #include <cmath>

diff --git a/compute/components.h → src/compute/components.h b/compute/components.h → src/compute/components.h
@@ -2,7 +2,7 @@
 #define COMPONENTS_H
 
 #include "model.h"
-#include "profiles/bnmsmodel.h" // TODO: awkward, see comment in that file
+#include "../profiles/bnmsmodel.h" // TODO: awkward, see comment in that file
 
 #include <QObject>
 #include <QThread>

diff --git a/compute/dimred.cpp → src/compute/dimred.cpp b/compute/dimred.cpp → src/compute/dimred.cpp
diff --git a/compute/dimred.h → src/compute/dimred.h b/compute/dimred.h → src/compute/dimred.h
diff --git a/compute/features.cpp → src/compute/features.cpp b/compute/features.cpp → src/compute/features.cpp
diff --git a/compute/features.h → src/compute/features.h b/compute/features.h → src/compute/features.h
diff --git a/meanshift/fams.cpp → src/compute/meanshift/fams.cpp b/meanshift/fams.cpp → src/compute/meanshift/fams.cpp
diff --git a/meanshift/fams.h → src/compute/meanshift/fams.h b/meanshift/fams.h → src/compute/meanshift/fams.h
diff --git a/meanshift/io.cpp → src/compute/meanshift/io.cpp b/meanshift/io.cpp → src/compute/meanshift/io.cpp
diff --git a/meanshift/mode_pruning.cpp → src/compute/meanshift/mode_pruning.cpp b/meanshift/mode_pruning.cpp → src/compute/meanshift/mode_pruning.cpp
diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
@@ -0,0 +1,13 @@
+target_sources(${APP_NAME} PRIVATE
+	datahub.h datahub.cpp
+	dataset.h dataset.cpp
+	fileio.h fileio.cpp
+	guistate.h guistate.cpp
+	jobregistry.h jobregistry.cpp
+	model.h
+	proteindb.h proteindb.cpp
+	utils.h
+	viewer.h viewer.cpp
+	windowstate.h windowstate.cpp
+	)
+
diff --git a/datahub.cpp → src/core/datahub.cpp b/datahub.cpp → src/core/datahub.cpp
@@ -2,7 +2,7 @@
 
 #include "proteindb.h"
 #include "dataset.h"
-#include "storage/storage.h"
+#include "../storage/storage.h"
 
 #include <QThread>
 #include <QVector>

diff --git a/datahub.h → src/core/datahub.h b/datahub.h → src/core/datahub.h
diff --git a/dataset.cpp → src/core/dataset.cpp b/dataset.cpp → src/core/dataset.cpp
@@ -1,6 +1,7 @@
 #include "dataset.h"
-#include "compute/features.h"
-#include "compute/dimred.h"
+#include "../compute/annotations.h"
+#include "../compute/features.h"
+#include "../compute/dimred.h"
 
 #include <QDataStream>
 #include <QTextStream>
@@ -19,6 +20,11 @@ Dataset::Dataset(ProteinDB &proteins, DatasetConfiguration conf)
 	qRegisterMetaType<ConstPtr>("ConstDataPtr");
 }
 
+Dataset::~Dataset()
+{
+	// needed for unique_ptr of incomplete type in header
+}
+
 template<>
 View<Dataset::Base> Dataset::peek() const { return View(b); }
 template<>

diff --git a/dataset.h → src/core/dataset.h b/dataset.h → src/core/dataset.h
@@ -4,7 +4,6 @@
 #include "utils.h"
 #include "model.h"
 #include "proteindb.h"
-#include "compute/annotations.h"
 
 #include <QObject>
 #include <QFlags>
@@ -15,6 +14,7 @@
 #include <map>
 #include <memory>
 
+namespace annotations {	class Meanshift; }
 class QTextStream;
 
 // a configuration that describes processing resulting in a dataset
@@ -93,6 +93,7 @@ class Dataset : public QObject
 	using Touched = QFlags<Touch>;
 
 	explicit Dataset(ProteinDB &proteins, DatasetConfiguration conf);
+	~Dataset();
 	const DatasetConfiguration& config() const { return conf; }
 	unsigned id() const { return conf.id; }
 	void setName(const QString &name) { conf.name = name; }

diff --git a/fileio.cpp → src/core/fileio.cpp b/fileio.cpp → src/core/fileio.cpp
diff --git a/fileio.h → src/core/fileio.h b/fileio.h → src/core/fileio.h
diff --git a/guistate.cpp → src/core/guistate.cpp b/guistate.cpp → src/core/guistate.cpp
@@ -1,8 +1,8 @@
 #include "guistate.h"
 #include "datahub.h"
-#include "widgets/mainwindow.h"
 #include "fileio.h"
 #include "jobregistry.h"
+#include "../widgets/mainwindow.h"
 
 #include <QAbstractProxyModel>
 #include <QTimer>

diff --git a/guistate.h → src/core/guistate.h b/guistate.h → src/core/guistate.h
diff --git a/jobregistry.cpp → src/core/jobregistry.cpp b/jobregistry.cpp → src/core/jobregistry.cpp
diff --git a/jobregistry.h → src/core/jobregistry.h b/jobregistry.h → src/core/jobregistry.h
diff --git a/model.h → src/core/model.h b/model.h → src/core/model.h
@@ -13,7 +13,9 @@
 #include <memory>
 #include <variant>
 
+#if QT_VERSION < QT_VERSION_CHECK(5, 14, 0)
 #include "utils.h" // needed with Qt<5.14 for std::map<QString,…>
+#endif
 
 using ProteinId = unsigned; // for semantic distinction
 

diff --git a/proteindb.cpp → src/core/proteindb.cpp b/proteindb.cpp → src/core/proteindb.cpp
@@ -1,6 +1,6 @@
 #include "proteindb.h"
-#include "compute/annotations.h"
-#include <compute/colors.h>
+#include "../compute/annotations.h"
+#include "../compute/colors.h"
 
 #include <QTextStream>
 #include <QRegularExpression>

diff --git a/proteindb.h → src/core/proteindb.h b/proteindb.h → src/core/proteindb.h
diff --git a/utils.h → src/core/utils.h b/utils.h → src/core/utils.h
diff --git a/viewer.cpp → src/core/viewer.cpp b/viewer.cpp → src/core/viewer.cpp
diff --git a/viewer.h → src/core/viewer.h b/viewer.h → src/core/viewer.h
diff --git a/windowstate.cpp → src/core/windowstate.cpp b/windowstate.cpp → src/core/windowstate.cpp
diff --git a/windowstate.h → src/core/windowstate.h b/windowstate.h → src/core/windowstate.h
@@ -2,7 +2,7 @@
 #define WINDOWSTATE_H
 
 #include "model.h"
-#include "compute/colors.h"
+#include "../compute/colors.h"
 
 #include <QObject>
 #include <QPointer>

diff --git a/distmat/CMakeLists.txt → src/distmat/CMakeLists.txt b/distmat/CMakeLists.txt → src/distmat/CMakeLists.txt
diff --git a/distmat/distmat.cpp → src/distmat/distmat.cpp b/distmat/distmat.cpp → src/distmat/distmat.cpp
@@ -1,5 +1,5 @@
 #include "distmat.h"
-#include "compute/colors.h"
+#include "../compute/colors.h"
 
 #include <tbb/parallel_for.h>
 

diff --git a/distmat/distmat.h → src/distmat/distmat.h b/distmat/distmat.h → src/distmat/distmat.h
@@ -1,7 +1,7 @@
 #ifndef DISTMAT_H
 #define DISTMAT_H
 
-#include "compute/features.h"
+#include "../compute/features.h"
 
 #include <QVector>
 #include <QPixmap>

diff --git a/distmat/distmatscene.cpp → src/distmat/distmatscene.cpp b/distmat/distmatscene.cpp → src/distmat/distmatscene.cpp
diff --git a/distmat/distmatscene.h → src/distmat/distmatscene.h b/distmat/distmatscene.h → src/distmat/distmatscene.h
@@ -1,7 +1,7 @@
 #ifndef DISTMATSCENE_H
 #define DISTMATSCENE_H
 
-#include "widgets/graphicsscene.h"
+#include "../widgets/graphicsscene.h"
 #include "dataset.h"
 #include "distmat.h"
 #include "utils.h"

diff --git a/distmat/distmattab.cpp → src/distmat/distmattab.cpp b/distmat/distmattab.cpp → src/distmat/distmattab.cpp
diff --git a/distmat/distmattab.h → src/distmat/distmattab.h b/distmat/distmattab.h → src/distmat/distmattab.h
diff --git a/distmat/distmattab.ui → src/distmat/distmattab.ui b/distmat/distmattab.ui → src/distmat/distmattab.ui
@@ -170,7 +170,7 @@
   <customwidget>
    <class>GraphicsView</class>
    <extends>QGraphicsView</extends>
-   <header>widgets/graphicsview.h</header>
+   <header>src/widgets/graphicsview.h</header>
   </customwidget>
  </customwidgets>
  <resources/>

diff --git a/featweights/CMakeLists.txt → src/featweights/CMakeLists.txt b/featweights/CMakeLists.txt → src/featweights/CMakeLists.txt
diff --git a/featweights/featweightsscene.cpp → src/featweights/featweightsscene.cpp b/featweights/featweightsscene.cpp → src/featweights/featweightsscene.cpp
@@ -1,6 +1,6 @@
 #include "featweightsscene.h"
-#include "compute/colors.h"
-#include "compute/features.h"
+#include "../compute/colors.h"
+#include "../compute/features.h"
 
 #include <QPainter>
 #include <QGraphicsPixmapItem>

diff --git a/featweights/featweightsscene.h → src/featweights/featweightsscene.h b/featweights/featweightsscene.h → src/featweights/featweightsscene.h
@@ -1,7 +1,7 @@
 #ifndef FEATWEIGHTSSCENE_H
 #define FEATWEIGHTSSCENE_H
 
-#include "widgets/graphicsscene.h"
+#include "../widgets/graphicsscene.h"
 #include "dataset.h"
 #include "utils.h"
 

diff --git a/featweights/featweightstab.cpp → src/featweights/featweightstab.cpp b/featweights/featweightstab.cpp → src/featweights/featweightstab.cpp
diff --git a/featweights/featweightstab.h → src/featweights/featweightstab.h b/featweights/featweightstab.h → src/featweights/featweightstab.h
diff --git a/featweights/featweightstab.ui → src/featweights/featweightstab.ui b/featweights/featweightstab.ui → src/featweights/featweightstab.ui
@@ -178,7 +178,7 @@
   <customwidget>
    <class>GraphicsView</class>
    <extends>QGraphicsView</extends>
-   <header>widgets/graphicsview.h</header>
+   <header>src/widgets/graphicsview.h</header>
   </customwidget>
  </customwidgets>
  <resources/>

diff --git a/heatmap/CMakeLists.txt → src/heatmap/CMakeLists.txt b/heatmap/CMakeLists.txt → src/heatmap/CMakeLists.txt
diff --git a/heatmap/heatmapscene.cpp → src/heatmap/heatmapscene.cpp b/heatmap/heatmapscene.cpp → src/heatmap/heatmapscene.cpp
@@ -1,7 +1,7 @@
 #include "heatmapscene.h"
 #include "windowstate.h"
-#include "compute/colors.h"
-#include "compute/features.h"
+#include "../compute/colors.h"
+#include "../compute/features.h"
 
 #include <QPainter>
 #include <QGraphicsItem>

diff --git a/heatmap/heatmapscene.h → src/heatmap/heatmapscene.h b/heatmap/heatmapscene.h → src/heatmap/heatmapscene.h
diff --git a/heatmap/heatmaptab.cpp → src/heatmap/heatmaptab.cpp b/heatmap/heatmaptab.cpp → src/heatmap/heatmaptab.cpp
diff --git a/heatmap/heatmaptab.h → src/heatmap/heatmaptab.h b/heatmap/heatmaptab.h → src/heatmap/heatmaptab.h
diff --git a/heatmap/heatmaptab.ui → src/heatmap/heatmaptab.ui b/heatmap/heatmaptab.ui → src/heatmap/heatmaptab.ui
@@ -164,7 +164,7 @@
   <customwidget>
    <class>HeatmapView</class>
    <extends>QGraphicsView</extends>
-   <header>heatmap/heatmapview.h</header>
+   <header>src/heatmap/heatmapview.h</header>
   </customwidget>
  </customwidgets>
  <resources/>

diff --git a/heatmap/heatmapview.cpp → src/heatmap/heatmapview.cpp b/heatmap/heatmapview.cpp → src/heatmap/heatmapview.cpp
diff --git a/heatmap/heatmapview.h → src/heatmap/heatmapview.h b/heatmap/heatmapview.h → src/heatmap/heatmapview.h
diff --git a/main.cpp → src/main.cpp b/main.cpp → src/main.cpp
diff --git a/profiles/CMakeLists.txt → src/profiles/CMakeLists.txt b/profiles/CMakeLists.txt → src/profiles/CMakeLists.txt
diff --git a/profiles/bnmschart.cpp → src/profiles/bnmschart.cpp b/profiles/bnmschart.cpp → src/profiles/bnmschart.cpp
@@ -1,6 +1,6 @@
 #include "bnmschart.h"
 #include "dataset.h"
-#include "compute/colors.h"
+#include "../compute/colors.h"
 
 #include <QtCharts/QLineSeries>
 #include <QtCharts/QValueAxis>

diff --git a/profiles/bnmschart.h → src/profiles/bnmschart.h b/profiles/bnmschart.h → src/profiles/bnmschart.h
@@ -3,7 +3,7 @@
 
 #include "profilechart.h"
 #include "bnmsmodel.h"
-#include "compute/components.h"
+#include "../compute/components.h"
 
 class BnmsChart : public ProfileChart
 {

diff --git a/profiles/bnmsmodel.h → src/profiles/bnmsmodel.h b/profiles/bnmsmodel.h → src/profiles/bnmsmodel.h
diff --git a/profiles/bnmstab.cpp → src/profiles/bnmstab.cpp b/profiles/bnmstab.cpp → src/profiles/bnmstab.cpp
@@ -6,7 +6,7 @@
 #include "jobregistry.h" // for splice
 
 // stuff for loading components. will most-probably be moved elsewhere!
-#include "compute/components.h"
+#include "../compute/components.h"
 #include "fileio.h"
 #include <QTextStream>
 

diff --git a/profiles/bnmstab.h → src/profiles/bnmstab.h b/profiles/bnmstab.h → src/profiles/bnmstab.h