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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 SETTINGS_H
#define SETTINGS_H
#include <QColor>
#include <QFont>
#include "globals.h"
#include <QString>
#include "../graph/path.h"
#include "scinot.h"
class DeBruijnNode;
class IntSetting
{
public:
IntSetting(int v, int minimum, int maximum, bool isOn = true) {val = v; min = minimum; max = maximum; on = isOn;}
IntSetting() {val = 0; min = 0; max = 0;}
int val, min, max;
bool on;
operator int() const {return val;}
IntSetting & operator=(int newVal) {val = newVal; return *this;}
bool inRange(int v) const {return v >= min && v <= max;}
};
class FloatSetting
{
public:
FloatSetting(double v, double minimum, double maximum, bool isOn = true) {val = v; min = minimum; max = maximum; on = isOn;}
FloatSetting() {val = 0.0; min = 0.0; max = 0.0;}
double val, min, max;
bool on;
operator double() const {return val;}
FloatSetting & operator=(double newVal) {val = newVal; return *this;}
bool inRange(double v) const {return v >= min && v <= max;}
};
class SciNotSetting
{
public:
SciNotSetting(SciNot v, SciNot minimum, SciNot maximum, bool isOn = true) {val = v; min = minimum; max = maximum; on = isOn;}
SciNotSetting() {val = 0.0; min = 0.0; max = 0.0;}
SciNot val, min, max;
bool on;
operator SciNot() const {return val;}
SciNotSetting & operator=(SciNot newVal) {val = newVal; return *this;}
bool inRange(SciNot v) const {return v >= min && v <= max;}
};
class Settings
{
public:
Settings();
bool doubleMode;
NodeLengthMode nodeLengthMode;
double autoNodeLengthPerMegabase;
FloatSetting manualNodeLengthPerMegabase;
double meanNodeLength;
double minTotalGraphLength;
IntSetting graphLayoutQuality;
bool linearLayout;
FloatSetting minimumNodeLength;
FloatSetting edgeLength;
FloatSetting doubleModeNodeSeparation;
FloatSetting nodeSegmentLength;
FloatSetting componentSeparation;
FloatSetting averageNodeWidth;
FloatSetting depthEffectOnWidth;
FloatSetting depthPower;
FloatSetting edgeWidth;
FloatSetting outlineThickness;
double selectionThickness;
double arrowheadSize;
double arrowheadsInSingleMode;
FloatSetting textOutlineThickness;
int blastRainbowPartsPerQuery;
GraphScope graphScope;
IntSetting nodeDistance;
bool startingNodesExactMatch;
QString startingNodes;
QString blastQueryFilename;
QString unnamedQueryDefaultName;
double minZoom;
double minZoomOnGraphDraw;
double maxZoom;
double maxAutomaticZoom;
double zoomFactor;
double textZoomScaleFactor; // 1.0 = text size constant, regardless of zoom. 0.0 = text size changes exactly with zoom.
double dragStrength;
bool displayNodeCustomLabels;
bool displayNodeNames;
bool displayNodeLengths;
bool displayNodeDepth;
bool displayNodeCsvData;
int displayNodeCsvDataCol;
bool displayBlastHits;
QFont labelFont;
bool textOutline;
bool antialiasing;
bool positionTextNodeCentre;
NodeDragging nodeDragging;
QColor edgeColour;
QColor outlineColour;
QColor selectionColour;
QColor textColour;
QColor textOutlineColour;
NodeColourScheme nodeColourScheme;
QColor uniformPositiveNodeColour;
QColor uniformNegativeNodeColour;
QColor uniformNodeSpecialColour;
IntSetting randomColourPositiveOpacity;
IntSetting randomColourNegativeOpacity;
IntSetting randomColourPositiveSaturation;
IntSetting randomColourNegativeSaturation;
IntSetting randomColourPositiveLightness;
IntSetting randomColourNegativeLightness;
IntSetting contiguitySearchSteps;
QColor contiguousStrandSpecificColour;
QColor contiguousEitherStrandColour;
QColor maybeContiguousColour;
QColor notContiguousColour;
QColor contiguityStartingColour;
QColor noBlastHitsColour;
bool autoDepthValue;
FloatSetting lowDepthValue;
QColor lowDepthColour;
FloatSetting highDepthValue;
QColor highDepthColour;
QColor pathHighlightShadingColour;
QColor pathHighlightOutlineColour;
QColor defaultCustomNodeColour;
//These specify the range of overlaps to look for when Bandage determines
//edge overlaps automatically.
int minAutoFindEdgeOverlap;
int maxAutoFindEdgeOverlap;
//These control how Bandage finds the best path in the graph to represent
//each BLAST query. Some of these settings can be turned on and off and
//therefore have a corresponding bool value.
IntSetting maxHitsForQueryPath;
IntSetting maxQueryPathNodes;
FloatSetting minQueryCoveredByPath;
FloatSetting minQueryCoveredByHits;
FloatSetting minMeanHitIdentity;
SciNotSetting maxEValueProduct;
FloatSetting minLengthPercentage;
FloatSetting maxLengthPercentage;
IntSetting minLengthBaseDiscrepancy;
IntSetting maxLengthBaseDiscrepancy;
//This holds the BLAST search parameters that a user can change before
//running a BLAST search.
QString blastSearchParameters;
//These are the optional BLAST hit filters: whether or not they are used and
//what their values are.
IntSetting blastAlignmentLengthFilter;
FloatSetting blastQueryCoverageFilter;
FloatSetting blastIdentityFilter;
SciNotSetting blastEValueFilter;
FloatSetting blastBitScoreFilter;
//These are used for the 'Depth range' graph scope.
FloatSetting minDepthRange;
FloatSetting maxDepthRange;
};
#endif // SETTINGS_H
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