impl layout and draw cml mode

ctlab · May 11, 2024 · 7389764 · 7389764
1 parent 92559e5
commit 7389764
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Showing 11 changed files with 176 additions and 61 deletions.
diff --git a/command_line/image.cpp b/command_line/image.cpp
@@ -41,7 +41,7 @@
 CLI::App *addImageSubcommand(CLI::App &app, ImageCmd &cmd) {
     auto *image = app.add_subcommand("image", "Generate an image file of a graph");
     image->add_option("<graph>", cmd.m_graph, "A graph file of any type supported by Bandage")
-            ->required()->check(CLI::ExistingFile);
+            ->required()->check(CLI::ExistingPath);
     image->add_option("<output_file>", cmd.m_image, "The image file to be created (must end in '.jpg', '.png' or '.svg')")
             ->required();
     image->add_option("--height", cmd.m_height, "Image height")
@@ -72,12 +72,18 @@ int handleImageCmd(QApplication *app,
         return 1;
     }
 
-    g_assemblyGraph->clear();
-    g_assemblyGraph->m_graphMap[1] = new AssemblyGraph();
-    bool loadSuccess = g_assemblyGraph->first()->loadGraphFromFile(cmd.m_graph.c_str());
-    if (!loadSuccess) {
-        outputText(("Bandage-NG error: could not load " + cmd.m_graph.native()).c_str(), &err); // FIXME
-        return 1;
+    if(std::filesystem::is_directory(cmd.m_graph.c_str())) {
+        g_settings->multyGraphMode = true;
+        g_assemblyGraph->clear();
+        g_assemblyGraph->loadGraphsFromDir(cmd.m_graph.c_str());
+    } else {
+        g_assemblyGraph->clear();
+        g_assemblyGraph->m_graphMap[1] = new AssemblyGraph();
+        bool loadSuccess = g_assemblyGraph->first()->loadGraphFromFile(cmd.m_graph.c_str());
+        if (!loadSuccess) {
+            outputText(("Bandage-NG error: could not load " + cmd.m_graph.native()).c_str(), &err); // FIXME
+            return 1;
+        }
     }
 
 
@@ -112,24 +118,20 @@ int handleImageCmd(QApplication *app,
 
     QString errorTitle;
     QString errorMessage;
-    auto scope = graph::scope(g_settings->graphScope,
-                              g_settings->startingNodes,
-                              g_settings->minDepthRange, g_settings->maxDepthRange,
-                              &g_blastSearch->queries(), "all",
-                              "", g_settings->nodeDistance);
-    std::vector<DeBruijnNode *> startingNodes = graph::getStartingNodes(&errorTitle, &errorMessage,
-                                                                        *g_assemblyGraph->first(), scope);
-    if (!errorMessage.isEmpty()) {
-        err << errorMessage << Qt::endl;
-        return 1;
-    }
 
     if (!cmd.m_color.empty()) {
         QString errormsg;
         QStringList columns;
         bool coloursLoaded = false;
+        bool isCSVLoaded = false;
+
+        for (auto graph : g_assemblyGraph->m_graphMap.values()) {
+            if (graph->loadCSV(cmd.m_color.c_str(), &columns, &errormsg, &coloursLoaded)) {
+                isCSVLoaded = true;
+            }
+        }
 
-        if (!g_assemblyGraph->first()->loadCSV(cmd.m_color.c_str(), &columns, &errormsg, &coloursLoaded)) {
+        if (!isCSVLoaded) {
             err << errormsg << Qt::endl;
             return 1;
         }
@@ -141,17 +143,43 @@ int handleImageCmd(QApplication *app,
          g_settings->initializeColorer(CUSTOM_COLOURS);
     }
 
-    g_assemblyGraph->first()->markNodesToDraw(scope, startingNodes);
+    for(auto& assemblyGraph : g_assemblyGraph->m_graphMap.values()) {
+        auto scope = graph::scope(g_settings->graphScope,
+                                      g_settings->startingNodes,
+                                      g_settings->minDepthRange, g_settings->maxDepthRange,
+                                      &g_blastSearch->queries(), "all",
+                                      "", g_settings->nodeDistance);
+            std::vector<DeBruijnNode *> startingNodes = graph::getStartingNodes(&errorTitle, &errorMessage,
+                                                                                *assemblyGraph, scope);
+
+        if (!errorMessage.isEmpty()) {
+            err << errorMessage << Qt::endl;
+            return 1;
+        }
+
+        assemblyGraph->resetEdges();
+        assemblyGraph->resetNodes();
+        assemblyGraph->markNodesToDraw(scope, startingNodes);
+    }
+
     BandageGraphicsScene scene;
     {
-        GraphLayoutStorage layout =
-                *GraphLayoutWorker(g_settings->graphLayoutQuality,
-                                  g_settings->linearLayout,
-                                  g_settings->componentSeparation).layoutGraph(g_assemblyGraph)[0];
+        GraphLayoutWorker(g_settings->graphLayoutQuality, g_settings->linearLayout, g_settings->componentSeparation).layoutGraph(g_assemblyGraph);
 
         scene.clear();
-        scene.addGraphicsItemsToScene(*g_assemblyGraph->first(), layout);
-        scene.setSceneRectangle();
+        int drawnNodeCount = 0;
+        for(AssemblyGraph* graph : g_assemblyGraph->m_graphMap.values()) {
+            GraphLayout* layout = graph->m_layout;
+            scene.addGraphicsItemsToScene(*graph, *layout);
+
+            double averageNodeWidth = g_settings->averageNodeWidth / pow(g_absoluteZoom, 0.75);
+            graph->recalculateAllNodeWidths(averageNodeWidth,
+                                            g_settings->depthPower,
+                                            g_settings->depthEffectOnWidth);
+            drawnNodeCount += (graph->getDrawnNodeCount());
+        }
+        if (drawnNodeCount > 0)
+            scene.setSceneRectangle();
     }
     double sceneRectAspectRatio = scene.sceneRect().width() / scene.sceneRect().height();
 

diff --git a/command_line/layout.cpp b/command_line/layout.cpp
@@ -37,7 +37,7 @@
 CLI::App *addLayoutSubcommand(CLI::App &app, LayoutCmd &cmd) {
     auto *layout = app.add_subcommand("layout", "Layout the graph");
     layout->add_option("<graph>", cmd.m_graph, "A graph file of any type supported by Bandage")
-            ->required()->check(CLI::ExistingFile);
+            ->required()->check(CLI::ExistingPath);
     layout->add_option("<layout>", cmd.m_layout, "The layout file to be created (must end with .tsv or .layout)")
             ->required();
 
@@ -60,10 +60,18 @@ int handleLayoutCmd(QApplication *app,
         return 1;
     }
 
-    bool loadSuccess = g_assemblyGraph->first()->loadGraphFromFile(cmd.m_graph.c_str());
-    if (!loadSuccess) {
-        outputText(("Bandage-NG error: could not load " + cmd.m_graph.native()).c_str(), &err); // FIXME
-        return 1;
+    if(std::filesystem::is_directory(cmd.m_graph.c_str())) {
+        g_settings->multyGraphMode = true;
+        g_assemblyGraph->clear();
+        g_assemblyGraph->loadGraphsFromDir(cmd.m_graph.c_str());
+    } else {
+        g_assemblyGraph->clear();
+        g_assemblyGraph->m_graphMap[1] = new AssemblyGraph();
+        bool loadSuccess = g_assemblyGraph->first()->loadGraphFromFile(cmd.m_graph.c_str());
+        if (!loadSuccess) {
+            outputText(("Bandage-NG error: could not load " + cmd.m_graph.native()).c_str(), &err); // FIXME
+            return 1;
+        }
     }
 
     if (cli.count("--query")) {
@@ -84,28 +92,44 @@ int handleLayoutCmd(QApplication *app,
 
     QString errorTitle;
     QString errorMessage;
-    auto scope = graph::scope(g_settings->graphScope,
-                              g_settings->startingNodes,
-                              g_settings->minDepthRange, g_settings->maxDepthRange,
-                              &g_blastSearch->queries(), "all",
-                              "", g_settings->nodeDistance);
-    std::vector<DeBruijnNode *> startingNodes = graph::getStartingNodes(&errorTitle, &errorMessage,
-                                                                        *g_assemblyGraph->first(), scope);
-    if (!errorMessage.isEmpty()) {
-        err << errorMessage << Qt::endl;
-        return 1;
-    }
 
-    g_assemblyGraph->first()->markNodesToDraw(scope, startingNodes);
+    for(auto& assemblyGraph : g_assemblyGraph->m_graphMap.values()) {
+        auto scope = graph::scope(g_settings->graphScope,
+                                      g_settings->startingNodes,
+                                      g_settings->minDepthRange, g_settings->maxDepthRange,
+                                      &g_blastSearch->queries(), "all",
+                                      "", g_settings->nodeDistance);
+            std::vector<DeBruijnNode *> startingNodes = graph::getStartingNodes(&errorTitle, &errorMessage,
+                                                                                *assemblyGraph, scope);
+
+        if (!errorMessage.isEmpty()) {
+            err << errorMessage << Qt::endl;
+            return 1;
+        }
 
-    GraphLayoutStorage layout =
-            *GraphLayoutWorker(g_settings->graphLayoutQuality,
-                              g_settings->linearLayout,
-                              g_settings->componentSeparation).layoutGraph(g_assemblyGraph)[0];
+        assemblyGraph->resetEdges();
+        assemblyGraph->resetNodes();
+        assemblyGraph->markNodesToDraw(scope, startingNodes);
+    }
 
-    bool success = (isTSV ?
-                    layout::io::saveTSV(cmd.m_layout.c_str(), layout) :
-                    layout::io::save(cmd.m_layout.c_str(), layout));
+    GraphLayoutWorker(g_settings->graphLayoutQuality,
+                       g_settings->linearLayout,
+                       g_settings->componentSeparation).layoutGraph(g_assemblyGraph);
+
+    bool success;
+
+    if (g_assemblyGraph->size() == 1) {
+        if (isTSV)
+            success = layout::io::saveTSV(cmd.m_layout.c_str(), *g_assemblyGraph->first()->m_layout);
+        else
+            success = layout::io::save(cmd.m_layout.c_str(), *g_assemblyGraph->first()->m_layout);
+    } else {
+        if (isTSV) {
+            success = layout::io::saveGraphListTSV(cmd.m_layout.c_str(), g_assemblyGraph, true);
+        } else {
+            success = layout::io::saveGraphList(cmd.m_layout.c_str(), g_assemblyGraph, true);
+        }
+    }
 
     if (!success) {
         out << "There was an error writing the layout to file." << Qt::endl;

diff --git a/graph/assemblygraphlist.cpp b/graph/assemblygraphlist.cpp
@@ -2,6 +2,11 @@
 #include "program/globals.h"
 #include "program/settings.h"
 
+#include <iostream>
+#include <filesystem>
+
+#include<QDebug>
+
 AssemblyGraphList::AssemblyGraphList()
 {
 }
@@ -127,3 +132,38 @@ double AssemblyGraphList::getMeanDepth(const std::vector<DeBruijnNode *> &nodes)
 
     return depthSum / totalLength;
 }
+
+bool AssemblyGraphList::loadGraphsFromDir(const QString& basePath) {
+
+    if (basePath.isEmpty()) //User did hit cancel
+        return false;
+
+    QString dirname = basePath;
+
+    clear();
+
+    loadGraphsIter(dirname, basePath);
+    return true;
+}
+
+void AssemblyGraphList::loadGraphsIter(QString fullDirName, const QString& basePath) {
+    if (fullDirName.isEmpty()) //User did hit cancel
+        return;
+    for (const auto entry : std::filesystem::directory_iterator(fullDirName.toStdString())) {
+        const std::filesystem::path path = entry.path();
+        if(std::filesystem::is_directory(path)) {
+            loadGraphsIter(QString::fromStdString(path), basePath);
+        }
+        if (std::filesystem::is_regular_file(path) && path.extension() != ".fasta") {
+            QString qpath = QString::fromStdString(path);
+
+            qInfo() << "loadGraphFromFile: " << qpath;
+            int graphId = g_assemblyGraph->m_graphMap.size() + 1;
+            g_assemblyGraph->m_graphMap[graphId] = new AssemblyGraph();
+            g_assemblyGraph->m_graphMap[graphId] -> setGraphId(graphId);
+            bool loadSuccess = g_assemblyGraph->m_graphMap[graphId]->loadGraphFromFile(qpath);
+
+            g_assemblyGraph->m_graphMap[graphId]->setGraphName(qpath.right(qpath.size() - basePath.size()));
+        }
+    }
+}
diff --git a/graph/assemblygraphlist.h b/graph/assemblygraphlist.h
@@ -76,6 +76,9 @@ class AssemblyGraphList
         return nullptr;
     }
 
+    bool loadGraphsFromDir(const QString& dirname);
+    void loadGraphsIter(QString fullDirName, const QString& basePath);
+
     QMap<int, AssemblyGraph*> m_graphMap;
 
 private:

diff --git a/layout/io.cpp b/layout/io.cpp
@@ -49,10 +49,10 @@ namespace layout::io {
         return true;
     }
 
-    bool saveGraphList(const QString &filename, QSharedPointer<AssemblyGraphList> graphList) {
+    bool saveGraphList(const QString &filename, QSharedPointer<AssemblyGraphList> graphList, bool isCliMode) {
         QJsonObject jsonLayoutGraphList;
         for (AssemblyGraph* graph : graphList->m_graphMap.values()) {
-            GraphLayout layout = layout::fromGraph(*graph, false);
+            GraphLayout layout = isCliMode ? *graph->m_layout : layout::fromGraph(*graph, false);
             QJsonObject jsonLayoutGraph;
             for (const auto &entry: layout) {
                 QJsonArray segments;
@@ -90,19 +90,17 @@ namespace layout::io {
         return true;
     }
 
-    bool saveGraphListTSV(const QString &filename, QSharedPointer<AssemblyGraphList> graphList) {
+    bool saveGraphListTSV(const QString &filename, QSharedPointer<AssemblyGraphList> graphList, bool isCliMode) {
         QFile saveFile(filename);
         if (!saveFile.open(QIODevice::WriteOnly | QIODevice::Text))
             return false;
 
         QTextStream out(&saveFile);
         for (AssemblyGraph* graph : graphList->m_graphMap.values()) {
-            GraphLayout layout = layout::fromGraph(*graph, false);
-            out << graph->getGraphName() << '\n';
+            GraphLayout layout = isCliMode ? *graph->m_layout : layout::fromGraph(*graph, false);
             for (const auto &entry: layout) {
                 const DeBruijnNode *node = entry.first;
                 QPointF pos = entry.second.front();
-                out << entry.first->getName() << '\t' << pos.x() << '\t' << pos.y() << '\n';
             }
         }
 

diff --git a/layout/io.h b/layout/io.h
@@ -28,6 +28,6 @@ namespace layout::io {
     bool saveTSV(const QString &filename,
                  const GraphLayout &layout);
 
-    bool saveGraphList(const QString &filename, QSharedPointer<AssemblyGraphList> graphList);
-    bool saveGraphListTSV(const QString &filename, QSharedPointer<AssemblyGraphList> graphList);
+    bool saveGraphList(const QString &filename, QSharedPointer<AssemblyGraphList> graphList, bool isCliMode = false);
+    bool saveGraphListTSV(const QString &filename, QSharedPointer<AssemblyGraphList> graphList, bool isCliMode = false);
 }
diff --git a/painting/commongraphicsitemnode.h b/painting/commongraphicsitemnode.h
@@ -34,7 +34,7 @@ class CommonGraphicsItemNode : public QGraphicsItem
 
     static double distance(QPointF p1, QPointF p2);
     void shiftPoints(QPointF difference);
-    void remakePath();
+    virtual void remakePath();
     void setWidth(double width) { m_width = width; }
     void updateGrabIndex(QGraphicsSceneMouseEvent* event);
     QPointF getFirst() const { return m_linePoints.front(); }

diff --git a/painting/textgraphicsitemnode.cpp b/painting/textgraphicsitemnode.cpp
@@ -42,6 +42,22 @@ QPainterPath TextGraphicsItemNode::shape() const
     return textPath;
 }
 
+void TextGraphicsItemNode::remakePath()
+{
+    QPainterPath path;
+
+    QFont font = g_settings->labelFont;
+    font.setBold(true);
+
+    QFontMetrics metrics(font);
+    double fontHeight = metrics.ascent();
+
+    int stepsUntilLast = m_text.size() - 1;
+    double shiftLeft = -metrics.boundingRect(m_text).width() / 2.0;
+    path.addText(0, -fontHeight, font, m_text);
+
+    m_path = path;
+}
 
 void TextGraphicsItemNode::paint(QPainter * painter, const QStyleOptionGraphicsItem *, QWidget *)
 {

diff --git a/painting/textgraphicsitemnode.h b/painting/textgraphicsitemnode.h
@@ -18,5 +18,6 @@ class TextGraphicsItemNode : public CommonGraphicsItemNode
     void drawTextPathAtLocation(QPainter * painter, const QPainterPath &textPath);
     void mousePressEvent(QGraphicsSceneMouseEvent * event) override;
     void mouseMoveEvent(QGraphicsSceneMouseEvent * event) override;
+    void remakePath() override;
 };
 #endif // TEXTGRAPHICSITEMNODE_H
diff --git a/program/settings.cpp b/program/settings.cpp
@@ -72,7 +72,7 @@ Settings::Settings()
     displayNodeCsvData = false;
     displayNodeCsvDataCol = 0;
     labelFont = QFont();
-    labelFont.setPixelSize(12);
+    labelFont.setPointSize(8);
     textOutline = false;
     antialiasing = true;
     positionTextNodeCentre = false;

diff --git a/ui/mainwindow.cpp b/ui/mainwindow.cpp
@@ -268,7 +268,12 @@ void MainWindow::afterMainWindowShow() {
     // If the user passed a filename as a command line argument, try to open it now.
     if (!m_fileToLoadOnStartup.isEmpty()) {
         auto start = std::chrono::system_clock::now();
-        loadGraph(m_fileToLoadOnStartup);
+        std::filesystem::path path(m_fileToLoadOnStartup.toStdString());
+        if(std::filesystem::is_directory(path)) {
+            loadGraphs(m_fileToLoadOnStartup, m_fileToLoadOnStartup);
+        } else {
+            loadGraph(m_fileToLoadOnStartup);
+        }
         auto end = std::chrono::system_clock::now();
         std::cerr << std::filesystem::path(m_fileToLoadOnStartup.toStdString()).filename().string()
                   << ", " << std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count() << std::endl;