Refactor node coloring

CMakeLists.txt

@@ -71,7 +71,7 @@ set(LIB_SOURCES
         ui/tablewidgetitemname.cpp
         ui/tablewidgetitemshown.cpp
         ui/verticallabel.cpp
-        ui/verticalscrollarea.cpp)
+        ui/verticalscrollarea.cpp graph/nodecolorer.cpp graph/nodecolorer.h graph/nodecolorers.h)
 
 set(FORMS
         ui/aboutdialog.ui

command_line/commoncommandlinefunctions.cpp

@@ -132,9 +132,8 @@ void getSettingsUsage(QStringList * text)
     *text << "";
     *text << "Depth colour scheme";
     *text << dashes;
-    *text << "These settings only apply when the depth colour scheme is used.";
-    *text << "--depcollow <col>   Colour for nodes with depth below the low depth value " + getDefaultColour(g_settings->lowDepthColour);
-    *text << "--depcolhi <col>    Colour for nodes with depth above the high depth value " + getDefaultColour(g_settings->highDepthColour);
+    *text << "These settings only apply when the depth / GC colour scheme is used.";
+    *text << "--colormap <mapname>  Color map to use " + getDefaultColorMap(g_settings->colorMap);
     *text << "--depvallow <float> Low depth value " + getRangeAndDefault(g_settings->lowDepthValue, "auto");
     *text << "--depvalhi <float>  High depth value " + getRangeAndDefault(g_settings->highDepthValue, "auto");
     *text << "";
@@ -501,7 +500,7 @@ void parseSettings(QStringList arguments)
         }
     }
 
-    g_settings->nodeColourScheme = getColourSchemeOption("--colour", &arguments);
+    g_settings->initializeColorer(getColourSchemeOption("--colour", &arguments));
 
     // For backward compatibility we allow setting blast annotation view to show from "--colour" option.
     // To be removed when we can set up annotations from CLI.
@@ -527,10 +526,8 @@ void parseSettings(QStringList arguments)
     if (isOptionPresent("--unicolspe", &arguments))
         g_settings->uniformNodeSpecialColour = getColourOption("--unicolspe", &arguments);
 
-    if (isOptionPresent("--depcollow", &arguments))
-        g_settings->lowDepthColour = getColourOption("--depcollow", &arguments);
-    if (isOptionPresent("--depcolhi", &arguments))
-        g_settings->highDepthColour = getColourOption("--depcolhi", &arguments);
+    if (isOptionPresent("--colormap", &arguments))
+        g_settings->colorMap = getColorMapOption("--colormap", &arguments);
     if (isOptionPresent("--depvallow", &arguments))
     {
         g_settings->lowDepthValue = getFloatOption("--depvallow", &arguments);
@@ -1038,9 +1035,9 @@ SciNot getSciNotOption(const QString& option, QStringList * arguments)
      return {arguments->at(sciNotIndex)};
 }
 
-NodeColourScheme getColourSchemeOption(const QString& option, QStringList * arguments)
+NodeColorScheme getColourSchemeOption(const QString& option, QStringList * arguments)
 {
-    NodeColourScheme defaultScheme = RANDOM_COLOURS;
+    NodeColorScheme defaultScheme = RANDOM_COLOURS;
 
     int optionIndex = arguments->indexOf(option);
     if (optionIndex == -1)
@@ -1122,6 +1119,19 @@ QColor getColourOption(const QString& option, QStringList * arguments)
     return {arguments->at(colIndex)};
 }
 
+ColorMap getColorMapOption(const QString& option, QStringList * arguments)
+{
+    int optionIndex = arguments->indexOf(option);
+    if (optionIndex == -1)
+        return {};
+
+    int colIndex = optionIndex + 1;
+    if (colIndex >= arguments->size())
+        return {};
+
+    return colorMapFromName(arguments->at(colIndex));
+}
+
 
 QString getStringOption(const QString& option, QStringList * arguments)
 {
@@ -1283,6 +1293,11 @@ QString getDefaultColour(QColor colour)
     return "(default: " + getColourName(colour.name()) + ")";
 }
 
+QString getDefaultColorMap(ColorMap colorMap)
+{
+    return "(default: " + getColorMapName(colorMap) + ")";
+}
+
 QString getBandageTitleAsciiArt()
 {
     return "  ____                  _                  \n |  _ \\                | |                 \n | |_) | __ _ _ __   __| | __ _  __ _  ___ \n |  _ < / _` | '_ \\ / _` |/ _` |/ _` |/ _ \\\n | |_) | (_| | | | | (_| | (_| | (_| |  __/\n |____/ \\__,_|_| |_|\\__,_|\\__,_|\\__, |\\___|\n                                 __/ |     \n                                |___/      ";

command_line/commoncommandlinefunctions.h

@@ -59,7 +59,8 @@ int getIntOption(const QString& option, QStringList * arguments);
 double getFloatOption(const QString& option, QStringList * arguments);
 SciNot getSciNotOption(const QString& option, QStringList * arguments);
 QColor getColourOption(const QString& option, QStringList * arguments);
-NodeColourScheme getColourSchemeOption(const QString& option, QStringList * arguments);
+ColorMap getColorMapOption(const QString& option, QStringList * arguments);
+NodeColorScheme getColourSchemeOption(const QString& option, QStringList * arguments);
 std::set<ViewId> getBlastAnnotationViews(const QString& option, QStringList * arguments);
 GraphScope getGraphScopeOption(const QString& option, QStringList * arguments);
 QString getStringOption(const QString& option, QStringList * arguments);
@@ -95,6 +96,7 @@ QString getRangeAndDefault(double min, double max, double defaultVal);
 QString getRangeAndDefault(double min, double max, QString defaultVal);
 QString getRangeAndDefault(const QString& min, QString max, QString defaultVal);
 QString getDefaultColour(QColor colour);
+QString getDefaultColorMap(ColorMap colorMap);
 
 QString getBandageTitleAsciiArt();
 bool isOption(QString text);

command_line/image.cpp

@@ -151,7 +151,7 @@ int bandageImage(QStringList arguments)
             err << csvPath << " didn't contain color" << Qt::endl;
             return 1;
         }
-         g_settings->nodeColourScheme = CUSTOM_COLOURS;
+         g_settings->initializeColorer(CUSTOM_COLOURS);
     }
 
     if (errorMessage != "")

graph/assemblygraph.cpp

@@ -261,7 +261,7 @@ double AssemblyGraph::getMeanDepth(bool drawnNodesOnly)
 }
 
 
-double AssemblyGraph::getMeanDepth(std::vector<DeBruijnNode *> nodes)
+double AssemblyGraph::getMeanDepth(const std::vector<DeBruijnNode *> &nodes)
 {
     if (nodes.empty())
         return 0.0;
@@ -314,22 +314,11 @@ double AssemblyGraph::getMeanDepth(const QList<DeBruijnNode *>& nodes)
 }
 
 
-void AssemblyGraph::resetNodeContiguityStatus()
-{
+void AssemblyGraph::resetNodeContiguityStatus() {
     for (auto &entry : m_deBruijnGraphNodes) {
         entry->resetContiguityStatus();
     }
     m_contiguitySearchDone = false;
-
-    resetAllNodeColours();
-}
-
-void AssemblyGraph::resetAllNodeColours()
-{
-    for (auto &entry : m_deBruijnGraphNodes) {
-        if (entry->getGraphicsItemNode() != nullptr)
-            entry->getGraphicsItemNode()->setNodeColour();
-    }
 }
 
 void AssemblyGraph::determineGraphInfo()
@@ -659,7 +648,11 @@ bool AssemblyGraph::loadGraphFromFile(const QString& filename) {
     }
 
     determineGraphInfo();
+
+    // FIXME: get rid of this!
     g_memory->clearGraphSpecificMemory();
+    g_settings->nodeColorer->reset();
+
     return true;
 }
 
@@ -790,45 +783,50 @@ void AssemblyGraph::addGraphicsItemsToScene(MyGraphicsScene * scene)
 
     double meanDrawnDepth = getMeanDepth(true);
 
-    //First make the GraphicsItemNode objects
-    for (auto &entry : m_deBruijnGraphNodes) {
-        DeBruijnNode * node = entry;
+    // First make the GraphicsItemNode objects
+    for (auto *node : m_deBruijnGraphNodes) {
+        if (!node->isDrawn())
+            continue;
 
-        if (node->isDrawn())
-        {
-            if (meanDrawnDepth == 0)
-                node->setDepthRelativeToMeanDrawnDepth(1.0);
-            else
-                node->setDepthRelativeToMeanDrawnDepth(node->getDepth() / meanDrawnDepth);
-            auto * graphicsItemNode = new GraphicsItemNode(node, m_graphAttributes);
-            node->setGraphicsItemNode(graphicsItemNode);
-            graphicsItemNode->setFlag(QGraphicsItem::ItemIsSelectable);
-            graphicsItemNode->setFlag(QGraphicsItem::ItemIsMovable);
+        node->setDepthRelativeToMeanDrawnDepth(meanDrawnDepth== 0 ?
+                                               1.0 : node->getDepth() / meanDrawnDepth);
+        auto *graphicsItemNode = new GraphicsItemNode(node, m_graphAttributes);
+        node->setGraphicsItemNode(graphicsItemNode);
+        graphicsItemNode->setFlag(QGraphicsItem::ItemIsSelectable);
+        graphicsItemNode->setFlag(QGraphicsItem::ItemIsMovable);
+
+        bool colSet = false;
+        if (auto *rcNode = node->getReverseComplement()) {
+            if (auto *revCompGraphNode = rcNode->getGraphicsItemNode()) {
+                auto colPair = g_settings->nodeColorer->get(graphicsItemNode, revCompGraphNode);
+                graphicsItemNode->setNodeColour(colPair.first);
+                revCompGraphNode->setNodeColour(colPair.second);
+                colSet = true;
+            }
         }
+        if (!colSet)
+            graphicsItemNode->setNodeColour(g_settings->nodeColorer->get(graphicsItemNode));
     }
 
-    resetAllNodeColours();
-
-    //Then make the GraphicsItemEdge objects and add them to the scene first
-    //so they are drawn underneath
+    // Then make the GraphicsItemEdge objects and add them to the scene first,
+    // so they are drawn underneath
     for (auto &entry : m_deBruijnGraphEdges) {
         DeBruijnEdge * edge = entry.second;
 
-        if (edge->isDrawn())
-        {
+        if (edge->isDrawn()) {
             auto * graphicsItemEdge = new GraphicsItemEdge(edge);
             edge->setGraphicsItemEdge(graphicsItemEdge);
             graphicsItemEdge->setFlag(QGraphicsItem::ItemIsSelectable);
             scene->addItem(graphicsItemEdge);
         }
     }
 
-    //Now add the GraphicsItemNode objects to the scene so they are drawn
-    //on top
-    for (auto &entry : m_deBruijnGraphNodes) {
-        DeBruijnNode * node = entry;
-        if (node->hasGraphicsItem())
-            scene->addItem(node->getGraphicsItemNode());
+    // Now add the GraphicsItemNode objects to the scene, so they are drawn
+    // on top
+    for (auto *node : m_deBruijnGraphNodes) {
+        if (!node->hasGraphicsItem())
+            continue;
+        scene->addItem(node->getGraphicsItemNode());
     }
 }
 
@@ -1568,8 +1566,7 @@ void AssemblyGraph::duplicateGraphicsNode(DeBruijnNode * originalNode, DeBruijnN
     newGraphicsItemNode->shiftPointsRight();
     originalGraphicsItemNode->fixEdgePaths();
 
-    originalGraphicsItemNode->setNodeColour();
-    newGraphicsItemNode->setNodeColour();
+    newGraphicsItemNode->setNodeColour(originalGraphicsItemNode->m_colour);
 
     originalGraphicsItemNode->setWidth();
 
@@ -1825,8 +1822,7 @@ bool AssemblyGraph::mergeGraphicsNodes2(QList<DeBruijnNode *> * originalNodes,
         newNode->setGraphicsItemNode(newGraphicsItemNode);
         newGraphicsItemNode->setFlag(QGraphicsItem::ItemIsSelectable);
         newGraphicsItemNode->setFlag(QGraphicsItem::ItemIsMovable);
-
-        newGraphicsItemNode->setNodeColour();
+        newGraphicsItemNode->setNodeColour(g_settings->nodeColorer->get(newGraphicsItemNode));
 
         scene->addItem(newGraphicsItemNode);
 

graph/assemblygraph.h

@@ -108,11 +108,9 @@ class AssemblyGraph : public QObject
     static QByteArray getReverseComplement(const QByteArray& forwardSequence);
     void resetEdges();
     double getMeanDepth(bool drawnNodesOnly = false);
-    static double getMeanDepth(std::vector<DeBruijnNode *> nodes);
+    static double getMeanDepth(const std::vector<DeBruijnNode *> &nodes);
     static double getMeanDepth(const QList<DeBruijnNode *>& nodes);
     void resetNodeContiguityStatus();
-    void resetAllNodeColours();
-    void clearAllBlastHitPointers();
     void determineGraphInfo();
     void clearGraphInfo();
     void recalculateAllDepthsRelativeToDrawnMean();

graph/debruijnnode.cpp

@@ -709,3 +709,13 @@ std::vector<DeBruijnNode *> DeBruijnNode::getAllConnectedPositiveNodes() const
 
     return connectedPositiveNodesVector;
 }
+
+float DeBruijnNode::getGC() const {
+    size_t gc = 0;
+    for (size_t i = 0; i < m_sequence.size(); ++i) {
+        char c = m_sequence[i];
+        gc += (c == 'G' || c == 'C');
+    }
+
+    return float(gc) / float(m_sequence.size());
+}

graph/debruijnnode.h

@@ -54,6 +54,8 @@ class DeBruijnNode
     double getDepth() const {return m_depth;}
     double getDepthRelativeToMeanDrawnDepth() const {return m_depthRelativeToMeanDrawnDepth;}
 
+    float getGC() const;
+
     const Sequence &getSequence() const;
     Sequence &getSequence();
 
@@ -67,7 +69,6 @@ class DeBruijnNode
     DeBruijnNode * getReverseComplement() const {return m_reverseComplement;}
     OgdfNode * getOgdfNode() const {return m_ogdfNode;}
     GraphicsItemNode * getGraphicsItemNode() const {return m_graphicsItemNode;}
-    bool thisOrReverseComplementHasGraphicsItemNode() const {return (m_graphicsItemNode != nullptr || getReverseComplement()->m_graphicsItemNode != nullptr);}
     bool hasGraphicsItem() const {return m_graphicsItemNode != nullptr;}
 
     auto edgeBegin() { return m_edges.begin(); }