Merge branch 'development'

graph/assemblygraph.cpp

@@ -299,6 +299,8 @@ void AssemblyGraph::resetNodeContiguityStatus()
         i.value()->resetContiguityStatus();
     }
     m_contiguitySearchDone = false;
+
+    resetAllNodeColours();
 }
 
 void AssemblyGraph::resetAllNodeColours()
@@ -1945,12 +1947,20 @@ void AssemblyGraph::duplicateNodePair(DeBruijnNode * node, MyGraphicsScene * sce
 
     double newReadDepth = node->getReadDepth() / 2.0;
 
+    //Create the new nodes.
     DeBruijnNode * newPosNode = new DeBruijnNode(newPosNodeName, newReadDepth, originalPosNode->getSequence());
     DeBruijnNode * newNegNode = new DeBruijnNode(newNegNodeName, newReadDepth, originalNegNode->getSequence());
-
     newPosNode->setReverseComplement(newNegNode);
     newNegNode->setReverseComplement(newPosNode);
 
+    //Copy over additional stuff from the original nodes.
+    newPosNode->setCustomColour(originalPosNode->getCustomColour());
+    newNegNode->setCustomColour(originalNegNode->getCustomColour());
+    newPosNode->setCustomLabel(originalPosNode->getCustomLabel());
+    newNegNode->setCustomLabel(originalNegNode->getCustomLabel());
+    newPosNode->setCsvData(originalPosNode->getAllCsvData());
+    newNegNode->setCsvData(originalNegNode->getAllCsvData());
+
     m_deBruijnGraphNodes.insert(newPosNodeName, newPosNode);
     m_deBruijnGraphNodes.insert(newNegNodeName, newNegNode);
 

ui/mainwindow.cpp

@@ -1030,7 +1030,6 @@ void MainWindow::switchColourScheme()
 void MainWindow::determineContiguityFromSelectedNode()
 {
     g_assemblyGraph->resetNodeContiguityStatus();
-    g_assemblyGraph->resetAllNodeColours();
 
     std::vector<DeBruijnNode *> selectedNodes = m_scene->getSelectedNodes();
     if (selectedNodes.size() > 0)
@@ -2228,7 +2227,11 @@ void MainWindow::removeSelection()
 
     g_assemblyGraph->determineGraphInfo();
     displayGraphDetails();
+
+    //Now that the graph has changed, we have to reset BLAST and contiguity
+    //stuff, as they may no longer apply.
     cleanUpAllBlast();
+    g_assemblyGraph->resetNodeContiguityStatus();
 }
 
 
@@ -2259,7 +2262,11 @@ void MainWindow::duplicateSelectedNodes()
 
     g_assemblyGraph->determineGraphInfo();
     displayGraphDetails();
+
+    //Now that the graph has changed, we have to reset BLAST and contiguity
+    //stuff, as they may no longer apply.
     cleanUpAllBlast();
+    g_assemblyGraph->resetNodeContiguityStatus();
 }
 
 void MainWindow::mergeSelectedNodes()
@@ -2300,7 +2307,11 @@ void MainWindow::mergeSelectedNodes()
 
     g_assemblyGraph->determineGraphInfo();
     displayGraphDetails();
+
+    //Now that the graph has changed, we have to reset BLAST and contiguity
+    //stuff, as they may no longer apply.
     cleanUpAllBlast();
+    g_assemblyGraph->resetNodeContiguityStatus();
 }
 
 void MainWindow::mergeAllPossible()
@@ -2328,7 +2339,11 @@ void MainWindow::mergeAllPossible()
     {
         g_assemblyGraph->determineGraphInfo();
         displayGraphDetails();
+
+        //Now that the graph has changed, we have to reset BLAST and contiguity
+        //stuff, as they may no longer apply.
         cleanUpAllBlast();
+        g_assemblyGraph->resetNodeContiguityStatus();
     }
     else
         QMessageBox::information(this, "No possible merges", "The graph contains no nodes that can be merged.");