Allow colors from CSV columns

.gitignore

@@ -59,6 +59,12 @@ Bandage.app
 # CLion
 .idea
 
+# clangd
+.cache
+
+# build dir
+build
+
 # Misc
 *DS_Store*
 Bandage.pro.user*

CMakeLists.txt

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

blast/blasthit.cpp

@@ -21,7 +21,7 @@
 #include "graph/debruijnnode.h"
 #include "blastquery.h"
 #include "program/globals.h"
-#include "graph/sequenceutils.hpp"
+#include "graph/sequenceutils.h"
 #include <cmath>
 
 BlastHit::BlastHit(BlastQuery * query, DeBruijnNode * node,
@@ -79,5 +79,5 @@ GraphLocation BlastHit::getHitEnd() const
 //This function returns the node sequence for this hit.
 QByteArray BlastHit::getNodeSequence() const
 {
-    return sequenceToQByteArray(m_node->getSequence().Subseq(m_nodeStart-1, m_nodeEnd));
+    return utils::sequenceToQByteArray(m_node->getSequence().Subseq(m_nodeStart-1, m_nodeEnd));
 }

blast/blastsearch.cpp

@@ -17,17 +17,20 @@
 
 
 #include "blastsearch.h"
-#include "graph/assemblygraph.h"
-#include <QDir>
-#include <QRegularExpression>
 #include "buildblastdatabaseworker.h"
 #include "runblastsearchworker.h"
+
 #include "program/settings.h"
-#include <QApplication>
-#include <utility>
+
+#include "graph/assemblygraph.h"
 #include "graph/debruijnnode.h"
+#include "graph/annotationsmanager.h"
+#include "graph/fileutils.h"
+
+#include <QDir>
+#include <QRegularExpression>
+#include <QApplication>
 #include <cmath>
-#include "graph/annotationsmanager.hpp"
 
 BlastSearch::BlastSearch() :
     m_blastQueries(), m_tempDirectory("bandage_temp/")
@@ -297,7 +300,7 @@ int BlastSearch::loadBlastQueriesFromFastaFile(QString fullFileName)
 
     std::vector<QString> queryNames;
     std::vector<QByteArray> querySequences;
-    AssemblyGraph::readFastaOrFastqFile(std::move(fullFileName), &queryNames, &querySequences);
+    utils::readFastaOrFastqFile(std::move(fullFileName), &queryNames, &querySequences);
 
     for (size_t i = 0; i < queryNames.size(); ++i)
     {

command_line/commoncommandlinefunctions.cpp

@@ -111,7 +111,7 @@ void getSettingsUsage(QStringList * text)
     *text << "";
     *text << "Node colours";
     *text << dashes;
-    *text << "--colour <scheme>   Node colouring scheme, from one of the following options: random, uniform, depth, blastsolid, blastrainbow, custom (default: random if --query option not used, blastsolid if --query option used)";
+    *text << "--colour <scheme>   Node colouring scheme, from one of the following options: random, uniform, depth, gc, blastsolid, blastrainbow, custom (default: random if --query option not used, blastsolid if --query option used)";
     *text << "";
     *text << "Random colour scheme";
     *text << dashes;
@@ -271,7 +271,7 @@ QString checkForInvalidOrExcessSettings(QStringList * arguments)
     checkOptionWithoutValue("--noaa", arguments);
     checkOptionWithoutValue("--singlearr", arguments);
     QStringList validColourOptions;
-    validColourOptions << "random" << "uniform" << "depth" << "blastsolid" << "blastrainbow" << "custom";
+    validColourOptions << "random" << "uniform" << "depth" << "blastsolid" << "blastrainbow" << "custom" << "gc" << "gfa";
     error = checkOptionForString("--colour", arguments, validColourOptions); if (error.length() > 0) return error;
     error = checkOptionForInt("--ransatpos", arguments, g_settings->randomColourPositiveSaturation, false); if (error.length() > 0) return error;
     error = checkOptionForInt("--ransatneg", arguments, g_settings->randomColourNegativeSaturation, false); if (error.length() > 0) return error;
@@ -1056,6 +1056,12 @@ NodeColorScheme getColourSchemeOption(const QString& option, QStringList * argum
         return DEPTH_COLOUR;
     else if (colourString == "custom")
         return CUSTOM_COLOURS;
+    else if (colourString == "gc")
+        return GC_CONTENT;
+    else if (colourString == "gfa")
+        return TAG_VALUE;
+    else if (colourString == "csv")
+        return CSV_COLUMN;
 
     //Random colours is the default
     return defaultScheme;

command_line/querypaths.cpp

@@ -20,6 +20,7 @@
 #include "commoncommandlinefunctions.h"
 #include "program/settings.h"
 #include "graph/assemblygraph.h"
+#include "graph/sequenceutils.h"
 #include "blast/blastsearch.h"
 #include <QDateTime>
 
@@ -229,7 +230,7 @@ int bandageQueryPaths(QStringList arguments)
         for (int i = 0; i < pathSequenceIDs.size(); ++i)
         {
             pathsOut << ">" + pathSequenceIDs[i] + "\n";
-            pathsOut << AssemblyGraph::addNewlinesToSequence(pathSequences[i]);
+            pathsOut << utils::addNewlinesToSequence(pathSequences[i]);
         }
     }
 
@@ -242,7 +243,7 @@ int bandageQueryPaths(QStringList arguments)
         for (int i = 0; i < hitSequenceIDs.size(); ++i)
         {
             hitsOut << ">" << hitSequenceIDs[i] << "\n";
-            hitsOut << AssemblyGraph::addNewlinesToSequence(hitSequences[i]);
+            hitsOut << utils::addNewlinesToSequence(hitSequences[i]);
         }
     }
 

graph/annotationsmanager.cpp

@@ -1,4 +1,4 @@
-#include "annotationsmanager.hpp"
+#include "annotationsmanager.h"
 
 AnnotationGroup &AnnotationsManager::createAnnotationGroup(QString name) {
     if (name == g_settings->blastAnnotationGroupName) {