Move graph's titles with nodes

ctlab · Jan 15, 2024 · 04c0e46 · 04c0e46
1 parent 38f8271
commit 04c0e46
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Showing 14 changed files with 113 additions and 88 deletions.
diff --git a/command_line/image.cpp b/command_line/image.cpp
@@ -73,7 +73,7 @@ int handleImageCmd(QApplication *app,
     }
 
     g_assemblyGraph->clear();
-    g_assemblyGraph->append(new AssemblyGraph());
+    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

diff --git a/graph/assemblygraphlist.cpp b/graph/assemblygraphlist.cpp
@@ -72,7 +72,7 @@ QString AssemblyGraphList::generateNodesNotFoundErrorMessage(std::vector<QString
 void AssemblyGraphList::recalculateAllNodeWidths(double averageNodeWidth,
                               double depthPower, double depthEffectOnWidth)
 {
-    for (auto assemblyGraph : m_graphList)
+    for (auto assemblyGraph : m_graphMap.values())
         assemblyGraph->recalculateAllNodeWidths(averageNodeWidth,depthPower, depthEffectOnWidth);
 }
 
@@ -88,12 +88,11 @@ void AssemblyGraphList::changeNodeDepth(const std::vector<DeBruijnNode *> &nodes
     }
 
     for (auto node : nodes) {
-        auto graphIndex = node->getGraphId() - 1;
 
         //If this graph does not already have a depthTag, give it a depthTag of KC
         //so the depth info will be saved.
-        if (m_graphList[graphIndex]->m_depthTag == "")
-            m_graphList[graphIndex]->m_depthTag = "KC";
+        if (m_graphMap[node->getGraphId()]->m_depthTag == "")
+            m_graphMap[node->getGraphId()]->m_depthTag = "KC";
     }
 }
 

diff --git a/graph/assemblygraphlist.h b/graph/assemblygraphlist.h
@@ -11,56 +11,56 @@ class AssemblyGraphList
     AssemblyGraphList();
 
     AssemblyGraph* first() {
-        if (m_graphList.isEmpty()) {
+        if (m_graphMap.isEmpty()) {
             auto assemblyGraph = new AssemblyGraph();
-            m_graphList.append(assemblyGraph);
+            m_graphMap[1] = assemblyGraph;
         }
-        return m_graphList.first();
+        return m_graphMap[1];
     }
-    AssemblyGraph* last() { return m_graphList.last(); }
-    bool isEmpty() { return m_graphList.isEmpty(); }
-    auto begin() { return m_graphList.begin(); }
-    auto begin() const { return m_graphList.begin(); }
-    auto end() { return m_graphList.end(); }
-    auto end() const { return m_graphList.end(); }
-    void append(AssemblyGraph* graph) { m_graphList.append(graph); }
-    void clear() { m_graphList.clear(); }
-    size_t size() const { return m_graphList.size(); }
+    //AssemblyGraph* last() { return m_graphList.last(); }
+    bool isEmpty() { return m_graphMap.isEmpty(); }
+    //auto begin() { return m_graphList.begin(); }
+    //auto begin() const { return m_graphList.begin(); }
+    //auto end() { return m_graphList.end(); }
+    //auto end() const { return m_graphList.end(); }
+    //void append(AssemblyGraph* graph) { m_graphList.append(graph); }
+    void clear() { m_graphMap.clear(); }
+    size_t size() const { return m_graphMap.size(); }
 
     QColor getCustomColourForDisplay(const DeBruijnNode *node) const;
     QStringList getCustomLabelForDisplay(const DeBruijnNode *node) const;
 
     int getNodeCount(){
         int count = 0;
-        for (auto graph : m_graphList) {
+        for (auto graph : m_graphMap.values()) {
             count += graph->m_nodeCount;
         }
         return count;
     }
     int getEdgeCount() {
         int count = 0;
-        for (auto graph : m_graphList) {
+        for (auto graph : m_graphMap.values()) {
             count += graph->m_edgeCount;
         }
         return count;
     }
     int getPathCount() {
         int count = 0;
-        for (auto graph : m_graphList) {
+        for (auto graph : m_graphMap.values()) {
             count += graph->m_pathCount;
         }
         return count;
     }
     int getTotalLength() {
         int count = 0;
-        for (auto graph : m_graphList) {
+        for (auto graph : m_graphMap.values()) {
             count += graph->m_totalLength;
         }
         return count;
     }
 
     void determineGraphInfo() {
-        for (auto graph : m_graphList) {
+        for (auto graph : m_graphMap.values()) {
             graph -> determineGraphInfo();
         }
     }
@@ -73,7 +73,7 @@ class AssemblyGraphList
     void changeNodeDepth(const std::vector<DeBruijnNode *> &nodes, double newDepth);
     void recalculateAllNodeWidths(double averageNodeWidth, double depthPower, double depthEffectOnWidth);
 
-    QList<AssemblyGraph*> m_graphList;
+    QMap<int, AssemblyGraph*> m_graphMap;
 
 private:
 

diff --git a/graph/graphicsitemnode.cpp b/graph/graphicsitemnode.cpp
@@ -23,6 +23,8 @@
 #include "assemblygraph.h"
 #include "annotationsmanager.h"
 
+#include "painting/textgraphicsitemnode.h"
+
 #include "program/globals.h"
 #include "program/memory.h"
 #include "program/settings.h"
@@ -394,6 +396,13 @@ void GraphicsItemNode::mouseMoveEvent(QGraphicsSceneMouseEvent * event)
 
         fixEdgePaths(&nodesToMove);
         fixHiCEdgePaths(&nodesToMove);
+        if (g_settings->multyGraphMode && g_settings->moveGraphTitle) {
+            AssemblyGraph& currrentGraph = *g_assemblyGraph->m_graphMap[m_deBruijnNode->getGraphId()];
+            if (currrentGraph.hasTextGraphicsItem()) {
+                TextGraphicsItemNode * graphTitle = currrentGraph.getTextGraphicsItemNode();
+                graphTitle->mouseMoveEvent(event);
+            }
+        }
     }
 }
 
@@ -479,7 +488,7 @@ QStringList GraphicsItemNode::getNodeText() const
     if (g_settings->displayNodeDepth)
         nodeText << formatDepthForDisplay(m_deBruijnNode->getDepth());
     if (g_settings->displayNodeCsvData) {
-        for (auto graph : g_assemblyGraph->m_graphList) {
+        for (auto graph : g_assemblyGraph->m_graphMap.values()) {
             auto data = graph->getCsvLine(m_deBruijnNode, g_settings->displayNodeCsvDataCol);
             if (data)
                 nodeText << *data;

diff --git a/graph/nodecolorer.cpp b/graph/nodecolorer.cpp
@@ -335,7 +335,7 @@ QColor GCNodeColorer::get(const GraphicsItemNode *node) {
 QColor TagValueNodeColorer::get(const GraphicsItemNode *node) {
     const DeBruijnNode *deBruijnNode = node->m_deBruijnNode;
 
-    for (auto graph : m_graphs.data()->m_graphList) {
+    for (auto graph : m_graphs.data()->m_graphMap.values()) {
         auto tags = graph->m_nodeTags.find(deBruijnNode);
         if (tags != graph->m_nodeTags.end()) {
             if (auto tag = gfa::getTag(m_tagName.c_str(), tags->second)) {
@@ -354,7 +354,7 @@ void TagValueNodeColorer::reset() {
     m_tagNames.clear();
 
     // Collect all tags and their corresponding values
-    for (auto graph : m_graphs.data()->m_graphList) {
+    for (auto graph : m_graphs.data()->m_graphMap.values()) {
         for (const auto &entry : graph->m_nodeTags) {
             for (const auto &tag: entry.second) {
                 std::stringstream stream;
@@ -386,13 +386,7 @@ void TagValueNodeColorer::reset() {
 QColor CSVNodeColorer::get(const GraphicsItemNode *node) {
     const DeBruijnNode *deBruijnNode = node->m_deBruijnNode;
 
-    AssemblyGraph* graph;
-    for(auto currentGraph : m_graphs.data()->m_graphList) {
-        if (currentGraph->getGraphId() == deBruijnNode->getGraphId()) {
-            graph = currentGraph;
-            break;
-        }
-    }
+    AssemblyGraph* graph = m_graphs.data()->m_graphMap[deBruijnNode->getGraphId()];
     auto val = graph->getCsvLine(deBruijnNode, m_colIdx);
     if (!val || m_colIdx >= m_colors.size())
         return m_graphs->getCustomColourForDisplay(deBruijnNode);
@@ -409,11 +403,11 @@ void CSVNodeColorer::reset() {
     m_colors.clear();
 
     size_t columns = 0;
-    for (auto graph : m_graphs.data()->m_graphList)
+    for (auto graph : m_graphs.data()->m_graphMap.values())
         columns = std::max(columns, size_t(graph->m_csvHeaders.size()));
     m_colors.resize(columns);
     // Store all unique values into a map
-    for(auto graph : m_graphs.data()->m_graphList) {
+    for(auto graph : m_graphs.data()->m_graphMap.values()) {
         for (const auto &entry : graph->m_nodeCSVData) {
             const auto &row = entry.second;
             for (size_t i = 0; i < row.size() && i < columns; ++i) {

diff --git a/graphsearch/blast/blastsearch.cpp b/graphsearch/blast/blastsearch.cpp
@@ -70,7 +70,7 @@ QString BlastSearch::buildDatabase(QSharedPointer<AssemblyGraphList> graphList,
 
     {
         QTextStream out(&file);
-        for (AssemblyGraph* graph: graphList->m_graphList) {
+        for (AssemblyGraph* graph: graphList->m_graphMap.values()) {
             for (const auto *node : graph->m_deBruijnGraphNodes) {
                 if (m_cancelBuildDatabase)
                     return (m_lastError = "Build cancelled.");
@@ -91,7 +91,7 @@ QString BlastSearch::buildDatabase(QSharedPointer<AssemblyGraphList> graphList,
 
     // Make sure the graph has sequences
     bool atLeastOneSequence = false;
-    for (AssemblyGraph* graph: graphList->m_graphList) {
+    for (AssemblyGraph* graph: graphList->m_graphMap.values()) {
         for (const auto *node : graph->m_deBruijnGraphNodes) {
             if (!node->sequenceIsMissing()) {
                 atLeastOneSequence = true;
@@ -341,7 +341,7 @@ buildHitsFromBlastOutput(QString blastOutput,
 
     QStringList blastHitList = blastOutput.split("\n", Qt::SkipEmptyParts);
 
-    for(auto graph : g_assemblyGraph->m_graphList) {
+    for(auto graph : g_assemblyGraph->m_graphMap.values()) {
         for (const auto &hitString : blastHitList) {
             QStringList alignmentParts = hitString.split('\t');
 

diff --git a/graphsearch/hmmer/hmmersearch.cpp b/graphsearch/hmmer/hmmersearch.cpp
@@ -73,7 +73,7 @@ QString HmmerSearch::buildDatabase(QSharedPointer<AssemblyGraphList> graphList,
         // in order to mitigate this, emit the largest (=more diverse) node first
         const DeBruijnNode *longest = nullptr;
         size_t length = 0;
-        for (AssemblyGraph* graph: graphList->m_graphList) {
+        for (AssemblyGraph* graph: graphList->m_graphMap.values()) {
             for (const auto *node : graph->m_deBruijnGraphNodes) {
                 if (!node->sequenceIsMissing() && node->getLength() > length) {
                     length = node->getLength();
@@ -115,7 +115,7 @@ QString HmmerSearch::buildDatabase(QSharedPointer<AssemblyGraphList> graphList,
 
         QTextStream out(&file);
 
-        for (AssemblyGraph* graph: graphList->m_graphList) {
+        for (AssemblyGraph* graph: graphList->m_graphMap.values()) {
             for (const auto *node : graph->m_deBruijnGraphNodes) {
                 if (m_cancelBuildDatabase)
                     return (m_lastError = "Build cancelled.");

diff --git a/graphsearch/minimap2/minimap2search.cpp b/graphsearch/minimap2/minimap2search.cpp
@@ -60,7 +60,7 @@ QString Minimap2Search::buildDatabase(QSharedPointer<AssemblyGraphList> graphLis
 
     {
         QTextStream out(&file);
-        for (AssemblyGraph* graph: graphList->m_graphList) {
+        for (AssemblyGraph* graph: graphList->m_graphMap.values()) {
         for (const auto *node : graph->m_deBruijnGraphNodes) {
             if (m_cancelBuildDatabase)
                 return (m_lastError = "Build cancelled.");
@@ -81,7 +81,7 @@ QString Minimap2Search::buildDatabase(QSharedPointer<AssemblyGraphList> graphLis
 
     // Make sure the graph has sequences
     bool atLeastOneSequence = false;
-    for (AssemblyGraph* graph: graphList->m_graphList) {
+    for (AssemblyGraph* graph: graphList->m_graphMap.values()) {
     for (const auto *node : graph->m_deBruijnGraphNodes) {
         if (!node->sequenceIsMissing()) {
             atLeastOneSequence = true;

diff --git a/layout/graphlayoutworker.cpp b/layout/graphlayoutworker.cpp
@@ -595,7 +595,7 @@ QList<GraphLayout*> GraphLayoutWorker::layoutGraph(QSharedPointer<AssemblyGraphL
     double boardWidth = 1000;
     qreal sumX = 0;
     qreal oneMaxX = 0;
-    for(AssemblyGraph* graph : graphList->m_graphList) {
+    for(AssemblyGraph* graph : graphList->m_graphMap.values()) {
         const AssemblyGraph& refGraph = std::cref(*graph);
         ogdf::Graph G;
         ogdf::EdgeArray<double> edgeLengths(G);
@@ -699,11 +699,15 @@ QList<GraphLayout*> GraphLayoutWorker::layoutGraph(QSharedPointer<AssemblyGraphL
     qreal maxY = -boardWidth;
     double textWidth = 0.0;
 
-    std::sort(graphList->m_graphList.begin(), graphList->m_graphList.end(), [](AssemblyGraph* a, AssemblyGraph* b)->bool{
-        return (layout::getMaxX(*a->m_layout) + layout::getMaxY(*a->m_layout)) > (layout::getMaxX(*b->m_layout) + layout::getMaxY(*b->m_layout));
+    QList<int> idGraphs = graphList->m_graphMap.keys();
+
+    std::sort(idGraphs.begin(), idGraphs.end(), [&](int a, int b)->bool{
+        return (layout::getMaxX(*(graphList->m_graphMap[a])->m_layout) + layout::getMaxY(*(graphList->m_graphMap[a])->m_layout)) >
+                (layout::getMaxX(*(graphList->m_graphMap[b])->m_layout) + layout::getMaxY(*(graphList->m_graphMap[b])->m_layout));
     });
 
-    for(AssemblyGraph* graph : graphList->m_graphList) {
+    for(int id : idGraphs) {
+        AssemblyGraph* graph = graphList->m_graphMap[id];
         if (maxX < boundX) {
             maxX = std::max(maxX, prevX + textWidth) + boardWidth;
             prevX = maxX;

diff --git a/painting/textgraphicsitemnode.cpp b/painting/textgraphicsitemnode.cpp
@@ -62,10 +62,6 @@ void TextGraphicsItemNode::paint(QPainter * painter, const QStyleOptionGraphicsI
     painter->scale(zoomAdjustment, zoomAdjustment);
     painter->translate(offset);
 
-//    painter->setBrush(Qt::NoBrush);
-//    painter->setPen(QPen(Qt::black, 1.0));
-//    painter->drawRect(boundingRect());
-
     drawTextPathAtLocation(painter, textPath);
     painter->translate(-offset);
     painter->scale(inverseZoomAdjustment, inverseZoomAdjustment);
@@ -97,10 +93,10 @@ void TextGraphicsItemNode::mousePressEvent(QGraphicsSceneMouseEvent * event)
 //graphics items will need to be adjusted accordingly.
 void TextGraphicsItemNode::mouseMoveEvent(QGraphicsSceneMouseEvent * event)
 {
-        QPointF difference = event->pos() - event->lastPos();
-        auto *graphicsScene = dynamic_cast<BandageGraphicsScene *>(scene());
-
+    prepareGeometryChange();
+    QPointF difference = event->pos() - event->lastPos();
+    auto *graphicsScene = dynamic_cast<BandageGraphicsScene *>(scene());
 
-        m_centre += difference;
-        graphicsScene->possiblyExpandSceneRectangle(this);
+    m_centre = m_centre + difference;
+    graphicsScene->possiblyExpandSceneRectangle(this);
 }
diff --git a/program/settings.h b/program/settings.h
@@ -247,6 +247,7 @@ class Settings
     FloatSetting hicEdgeLength;
     bool roundMode = false;
     bool multyGraphMode = false;
+    bool moveGraphTitle = true;
 };
 
 #endif // SETTINGS_H