Draft: display of Hi-C links and results of taxonomic analysis

blast/BlastFeaturesNodesMatcher.cpp

@@ -0,0 +1,54 @@
+#include "BlastFeaturesNodesMatcher.h"
+#include "BuildBlastDatabaseWorker.h"
+#include "RunBlastSearchWorker.h"
+#include "../blast/blastsearch.h"
+#include "../blast/blasthit.h"
+#include "../blast/blastquery.h"
+#include "../program/globals.h"
+#include "../program/settings.h"
+
+BlastFeaturesNodesMatcher::BlastFeaturesNodesMatcher() {
+    m_makeblastdbCommand = "makeblastdb";
+    m_blastnCommand = "blastn";
+    m_tblastnCommand = "tblastn";
+}
+
+void BlastFeaturesNodesMatcher::matchFeaturesNode(RandomForestNode* selectedNode) {
+	std::vector<QString> querySequences = selectedNode->getQuerySequences();
+	if ((querySequences.size()!= 0) && (selectedNode->getBlastColourInd() == - 1)) {
+        //build blast db
+        if (!g_blastSearch->findProgram("makeblastdb", &m_makeblastdbCommand)) {
+            return;
+        }
+
+        BuildBlastDatabaseWorker buildBlastDatabaseWorker(m_makeblastdbCommand);
+        buildBlastDatabaseWorker.buildBlastDatabase();
+
+        //add blast query
+        //g_blastSearch->cleanUp();
+        QString featureNodeName = selectedNode->getName() + "_";
+        int indexColour = g_blastSearch->m_blastQueries.m_queries.size();
+        for (size_t i = 0; i < querySequences.size(); ++i)
+        {
+            QString queryName = featureNodeName + QString::number(i);
+            g_blastSearch->m_blastQueries.addQuery(new BlastQuery(queryName, querySequences[i]), indexColour, selectedNode->getClassInd());
+
+        }
+        //run blast search
+
+        if (!g_blastSearch->findProgram("blastn", &m_blastnCommand))
+        {
+            return;
+        }
+        if (!g_blastSearch->findProgram("tblastn", &m_tblastnCommand))
+        {
+            return;
+        }
+
+        g_blastSearch->clearBlastHits();
+
+        RunBlastSearchWorker runBlastSearchWorker(m_blastnCommand, m_tblastnCommand, "");
+        runBlastSearchWorker.runBlastSearch();
+        selectedNode->setBlastColourInd(indexColour);
+	}
+}

blast/BlastFeaturesNodesMatcher.h

@@ -0,0 +1,18 @@
+#ifndef BLASTFEATURESNODESMATCHER_H
+#define BLASTFEATURESNODESMATCHER_H
+
+#include <vector>
+#include "../random_forest/RandomForestNode.h"
+
+class BlastFeaturesNodesMatcher
+{
+public:
+	BlastFeaturesNodesMatcher();
+	void matchFeaturesNode(RandomForestNode* selectedNode);
+private:
+	QString m_makeblastdbCommand;
+	QString m_blastnCommand;
+	QString m_tblastnCommand;
+};
+
+#endif //BLASTFEATURESNODESMATCHER_H

blast/blasthit.cpp

@@ -86,7 +86,12 @@ std::vector<BlastHitPart> BlastHit::getBlastHitParts(bool reverse, double scaled
             queryFraction += querySpacing;
         }
     }
-
+    else if (g_settings->nodeColourScheme == BLAST_HITS_CLASS_COLOURS) {
+        if (reverse)
+            returnVector.push_back(BlastHitPart(m_query->getFeatureClassColour(), 1.0 - m_nodeStartFraction, 1.0 - m_nodeEndFraction));
+        else
+            returnVector.push_back(BlastHitPart(m_query->getFeatureClassColour(), m_nodeStartFraction, m_nodeEndFraction));
+    }
     //If the colour scheme is Blast solid, then this function generates only one
     //BlastHitPart with a colour dependent on the Blast query.
     else
@@ -96,7 +101,6 @@ std::vector<BlastHitPart> BlastHit::getBlastHitParts(bool reverse, double scaled
         else
             returnVector.push_back(BlastHitPart(m_query->getColour(), m_nodeStartFraction, m_nodeEndFraction));
     }
-
     return returnVector;
 }
 

blast/blastqueries.cpp

@@ -66,6 +66,28 @@ void BlastQueries::addQuery(BlastQuery * newQuery)
     updateTempFiles();
 }
 
+void BlastQueries::addQuery(BlastQuery* newQuery, int colourIndex)
+{
+    newQuery->setName(getUniqueName(newQuery->getName()));
+
+    colourIndex %= m_presetColours.size();
+    newQuery->setColour(m_presetColours[colourIndex]);
+    m_queries.push_back(newQuery);
+    updateTempFiles();
+}
+
+void BlastQueries::addQuery(BlastQuery* newQuery, int colourIndex, int featureClassColour)
+{
+    newQuery->setName(getUniqueName(newQuery->getName()));
+
+    colourIndex %= m_presetColours.size();
+    newQuery->setColour(m_presetColours[colourIndex]);
+    featureClassColour %= m_presetColours.size();
+    newQuery->setFeatureClassColour(m_presetColours[featureClassColour]);
+    m_queries.push_back(newQuery);
+    updateTempFiles();
+}
+
 
 //This function renames the query.  It returns the name given, because that
 //might not be exactly the same as the name passed to the function if it

blast/blastqueries.h

@@ -55,6 +55,8 @@ class BlastQueries
     int getQueryCount(SequenceType sequenceType);
     bool isQueryPresent(BlastQuery * query);
     void findQueryPaths();
+    void addQuery(BlastQuery* newQuery, int colourIndex);
+    void addQuery(BlastQuery* newQuery, int colourIndex, int featureClassColour);
 
     std::vector<QColor> m_presetColours;
 

blast/blastquery.h

@@ -46,6 +46,7 @@ class BlastQuery : public QObject
     QList< QSharedPointer<BlastHit> > getHits() const {return m_hits;}
     bool wasSearchedFor() const {return m_searchedFor;}
     QColor getColour() const {return m_colour;}
+    QColor getFeatureClassColour() const {return m_featureClassColour;}
     SequenceType getSequenceType() const {return m_sequenceType;}
     QList<BlastQueryPath> getPaths() const {return m_paths;}
     int getPathCount() const {return m_paths.size();}
@@ -63,6 +64,7 @@ class BlastQuery : public QObject
 
 public slots:
     void setColour(QColor newColour) {m_colour = newColour;}
+    void setFeatureClassColour(QColor  newColour) { m_featureClassColour = newColour; }
     void setShown(bool newShown) {m_shown = newShown;}
 
 private:
@@ -71,6 +73,7 @@ public slots:
     QList< QSharedPointer<BlastHit> > m_hits;
     bool m_searchedFor;
     QColor m_colour;
+    QColor m_featureClassColour;
     SequenceType m_sequenceType;
     QList<BlastQueryPath> m_paths;
     bool m_shown;

build_scripts/bandage_build_windows.bat

@@ -40,4 +40,4 @@ call "%QT_PATH%\%MSVC_VERSION%\bin\windeployqt.exe" Bandage\Bandage.exe
 
 rem Zip Bandage with the sample graph and clean up.
 call "%ZIP_PATH%" a -tzip Bandage_Windows_v%VERSION%.zip Bandage\ sample_LastGraph installation.txt
-call rmdir Bandage\ /S /Q
+call rmdir Bandage\ /S /Q