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//Copyright 2017 Ryan Wick
//This file is part of Bandage
//Bandage is free software: you can redistribute it and/or modify
//it under the terms of the GNU General Public License as published by
//the Free Software Foundation, either version 3 of the License, or
//(at your option) any later version.
//Bandage is distributed in the hope that it will be useful,
//but WITHOUT ANY WARRANTY; without even the implied warranty of
//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//GNU General Public License for more details.
//You should have received a copy of the GNU General Public License
//along with Bandage. If not, see <http://www.gnu.org/licenses/>.
#ifndef DEBRUIJNNODE_H
#define DEBRUIJNNODE_H
#include <QByteArray>
#include <vector>
#include "../ogdf/basic/Graph.h"
#include "../ogdf/basic/GraphAttributes.h"
#include "../program/globals.h"
#include <QColor>
#include "../blast/blasthitpart.h"
#include "../program/settings.h"
class OgdfNode;
class DeBruijnEdge;
class GraphicsItemNode;
class BlastHit;
class DeBruijnNode
{
public:
//CREATORS
DeBruijnNode(QString name, double depth, QByteArray sequence, int length = 0);
~DeBruijnNode();
//ACCESSORS
QString getName() const {return m_name;}
QString getNameWithoutSign() const {return m_name.left(m_name.length() - 1);}
QString getSign() const {if (m_name.length() > 0) return m_name.right(1); else return "+";}
double getDepth() const {return m_depth;}
double getDepthRelativeToMeanDrawnDepth() const {return m_depthRelativeToMeanDrawnDepth;}
QByteArray getSequence() const;
int getLength() const {return m_length;}
QByteArray getSequenceForGfa() const;
int getFullLength() const;
int getLengthWithoutTrailingOverlap() const;
QByteArray getFasta(bool sign, bool newLines = true, bool evenIfEmpty = true) const;
QByteArray getGfaSegmentLine(QString depthTag) const;
char getBaseAt(int i) const {if (i >= 0 && i < m_sequence.length()) return m_sequence.at(i); else return '\0';}
ContiguityStatus getContiguityStatus() const {return m_contiguityStatus;}
DeBruijnNode * getReverseComplement() const {return m_reverseComplement;}
OgdfNode * getOgdfNode() const {return m_ogdfNode;}
GraphicsItemNode * getGraphicsItemNode() const {return m_graphicsItemNode;}
bool thisOrReverseComplementHasGraphicsItemNode() const {return (m_graphicsItemNode != 0 || getReverseComplement()->m_graphicsItemNode != 0);}
bool hasGraphicsItem() const {return m_graphicsItemNode != 0;}
const std::vector<DeBruijnEdge *> * getEdgesPointer() const {return &m_edges;}
std::vector<DeBruijnEdge *> getEnteringEdges() const;
std::vector<DeBruijnEdge *> getLeavingEdges() const;
std::vector<DeBruijnNode *> getDownstreamNodes() const;
std::vector<DeBruijnNode *> getUpstreamNodes() const;
std::vector<DeBruijnNode *> getAllConnectedPositiveNodes() const;
bool isSpecialNode() const {return m_specialNode;}
bool isDrawn() const {return m_drawn;}
bool thisNodeOrReverseComplementIsDrawn() const {return isDrawn() || getReverseComplement()->isDrawn();}
bool isNotDrawn() const {return !m_drawn;}
QColor getCustomColour() const {return m_customColour;}
QColor getCustomColourForDisplay() const;
QString getCustomLabel() const {return m_customLabel;}
QStringList getCustomLabelForDisplay() const;
bool hasCustomColour() const {return m_customColour.isValid();}
bool isPositiveNode() const;
bool isNegativeNode() const;
bool inOgdf() const {return m_ogdfNode != 0;}
bool notInOgdf() const {return m_ogdfNode == 0;}
bool thisOrReverseComplementInOgdf() const {return (inOgdf() || getReverseComplement()->inOgdf());}
bool thisOrReverseComplementNotInOgdf() const {return !thisOrReverseComplementInOgdf();}
bool isNodeConnected(DeBruijnNode * node) const;
const std::vector<BlastHit *> * getBlastHitsPointer() const {return &m_blastHits;}
bool thisNodeHasBlastHits() const {return m_blastHits.size() > 0;}
bool thisNodeOrReverseComplementHasBlastHits() const {return m_blastHits.size() > 0 || getReverseComplement()->m_blastHits.size() > 0;}
DeBruijnEdge * doesNodeLeadIn(DeBruijnNode * node) const;
DeBruijnEdge * doesNodeLeadAway(DeBruijnNode * node) const;
std::vector<BlastHitPart> getBlastHitPartsForThisNode(double scaledNodeLength) const;
std::vector<BlastHitPart> getBlastHitPartsForThisNodeOrReverseComplement(double scaledNodeLength) const;
bool hasCsvData() const {return !m_csvData.isEmpty();}
QStringList getAllCsvData() const {return m_csvData;}
QString getCsvLine(int i) const {if (i < m_csvData.length()) return m_csvData[i]; else return "";}
bool isInDepthRange(double min, double max) const;
bool sequenceIsMissing() const;
DeBruijnEdge *getSelfLoopingEdge() const;
int getDeadEndCount() const;
int getNumberOfOgdfGraphEdges(double drawnNodeLength) const;
double getDrawnNodeLength() const;
//MODIFERS
void setDepthRelativeToMeanDrawnDepth(double newVal) {m_depthRelativeToMeanDrawnDepth = newVal;}
void setSequence(QByteArray newSeq) {m_sequence = newSeq; m_length = m_sequence.length();}
void appendToSequence(QByteArray additionalSeq) {m_sequence.append(additionalSeq); m_length = m_sequence.length();}
void upgradeContiguityStatus(ContiguityStatus newStatus);
void resetContiguityStatus() {m_contiguityStatus = NOT_CONTIGUOUS;}
void setReverseComplement(DeBruijnNode * rc) {m_reverseComplement = rc;}
void setGraphicsItemNode(GraphicsItemNode * gin) {m_graphicsItemNode = gin;}
void setAsSpecial() {m_specialNode = true;}
void setAsNotSpecial() {m_specialNode = false;}
void setAsDrawn() {m_drawn = true;}
void setAsNotDrawn() {m_drawn = false;}
void setCustomColour(QColor newColour) {m_customColour = newColour;}
void setCustomLabel(QString newLabel);
void resetNode();
void addEdge(DeBruijnEdge * edge);
void removeEdge(DeBruijnEdge * edge);
void addToOgdfGraph(ogdf::Graph * ogdfGraph, ogdf::GraphAttributes * graphAttributes,
ogdf::EdgeArray<double> * edgeArray, double xPos, double yPos);
void determineContiguity();
void clearBlastHits() {m_blastHits.clear();}
void addBlastHit(BlastHit * newHit) {m_blastHits.push_back(newHit);}
void labelNeighbouringNodesAsDrawn(int nodeDistance, DeBruijnNode * callingNode);
void setCsvData(QStringList csvData) {m_csvData = csvData;}
void clearCsvData() {m_csvData.clear();}
void setDepth(double newDepth) {m_depth = newDepth;}
void setName(QString newName) {m_name = newName;}
private:
QString m_name;
double m_depth;
double m_depthRelativeToMeanDrawnDepth;
QByteArray m_sequence;
int m_length;
ContiguityStatus m_contiguityStatus;
DeBruijnNode * m_reverseComplement;
OgdfNode * m_ogdfNode;
GraphicsItemNode * m_graphicsItemNode;
std::vector<DeBruijnEdge *> m_edges;
bool m_specialNode;
bool m_drawn;
int m_highestDistanceInNeighbourSearch;
QColor m_customColour;
QString m_customLabel;
std::vector<BlastHit *> m_blastHits;
QStringList m_csvData;
QString getNodeNameForFasta(bool sign) const;
QByteArray getUpstreamSequence(int upstreamSequenceLength) const;
double getNodeLengthPerMegabase() const;
bool isOnlyPathInItsDirection(DeBruijnNode * connectedNode,
std::vector<DeBruijnNode *> * incomingNodes,
std::vector<DeBruijnNode *> * outgoingNodes) const;
bool isNotOnlyPathInItsDirection(DeBruijnNode * connectedNode,
std::vector<DeBruijnNode *> * incomingNodes,
std::vector<DeBruijnNode *> * outgoingNodes) const;
std::vector<DeBruijnNode *> getNodesCommonToAllPaths(std::vector< std::vector <DeBruijnNode *> > * paths,
bool includeReverseComplements) const;
bool doesPathLeadOnlyToNode(DeBruijnNode * node, bool includeReverseComplement);
};
#endif // DEBRUIJNNODE_H
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