#include <massspectraceplotwidget.h>

Inheritance diagram for pappso::MassSpecTracePlotWidget:

Signals
void	keyPressEventSignal (const MassSpecTracePlotContext &context)

void	massDeconvolutionSignal (const MassSpecTracePlotContext &context)

void	resolvingPowerComputationSignal (const MassSpecTracePlotContext &context)

void	mousePressEventSignal (const MassSpecTracePlotContext &context)

void	mouseReleaseEventSignal (const MassSpecTracePlotContext &context)

Signals inherited from pappso::BasePlotWidget
void	setFocusSignal ()

void	lastCursorHoveredPointSignal (const QPointF &pointf)

void	plotRangesChangedSignal (const BasePlotContext &context)

void	xAxisMeasurementSignal (const BasePlotContext &context, bool with_delta)

void	keyPressEventSignal (const BasePlotContext &context)

void	keyReleaseEventSignal (const BasePlotContext &context)

void	mousePressEventSignal (const BasePlotContext &context)

void	mouseReleaseEventSignal (const BasePlotContext &context)

void	mouseWheelEventSignal (const BasePlotContext &context)

void	plottableSelectionChangedSignal (QCPAbstractPlottable *plottable_p, bool selected)

void	integrationRequestedSignal (const BasePlotContext &context)

void	plottableDestructionRequestedSignal (BasePlotWidget base_plot_widget_p, QCPAbstractPlottable plottable_p, const BasePlotContext &context)

Public Member Functions
	MassSpecTracePlotWidget (QWidget *parent=0)

	MassSpecTracePlotWidget (QWidget *parent, const QString &x_axis_label, const QString &y_axis_label)

virtual	~MassSpecTracePlotWidget ()

void	setChargeMinimalFractionalPart (double charge_fractional_part)

double	getChargeMinimalFractionalPart () const

void	setChargeStateEnvelopePeakSpan (int interval)

int	getChargeStateEnvelopePeakSpan () const

bool	deconvolute ()
	Deconvolute the mass peaks into charge and molecular mass.

bool	deconvoluteIsotopicCluster ()
	Deconvolute the mass peaks into charge and molecular mass.

bool	deconvoluteChargedState (int span=1)
	Deconvolute the mass peaks into charge and molecular mass.

bool	computeResolvingPower ()

virtual void	keyPressEvent (QKeyEvent *event) override
	Set the `m_pressedKeyCode` to the key code in `event`.

virtual void	keyReleaseEvent (QKeyEvent *event) override
	Handle specific key codes and trigger respective actions.

virtual void	mouseMoveHandler (QMouseEvent *event) override
	Handle mouse movements, in particular record all the last visited points.

virtual void	mousePressHandler (QMouseEvent *event) override
	Record the clicks of the mouse.

virtual void	mouseReleaseHandler (QMouseEvent *event) override
	React to the release of the mouse buttons.

virtual void	mouseMoveHandlerNotDraggingCursor () override

virtual void	mouseMoveHandlerDraggingCursor () override

const MassSpecTracePlotContext &	refreshBaseContext () const

Public Member Functions inherited from pappso::BaseTracePlotWidget
	BaseTracePlotWidget (QWidget *parent=0)

	BaseTracePlotWidget (QWidget *parent, const QString &x_axis_label, const QString &y_axis_label)

virtual	~BaseTracePlotWidget ()
	Destruct `this` BaseTracePlotWidget instance.

virtual void	setGraphData (int graph_index, const std::vector< double > &keys, const std::vector< double > &values)

virtual void	setGraphData (QCPGraph *graph_p, const std::vector< double > &keys, const std::vector< double > &values)

virtual void	clearGraphData (int graph_index)

virtual void	axisDoubleClickHandler (QCPAxis axis, QCPAxis::SelectablePart part, QMouseEvent event) override

virtual void	axisRescale () override
	RANGE-related functions.

virtual void	axisReframe () override

virtual void	axisZoom () override

virtual void	axisPan () override

virtual QCPGraph *	addTrace (const pappso::Trace &trace, const QColor &color)

virtual bool	findIntegrationLowerRangeForKey (int index, double key, QCPRange &range)
	Find a minimal integration range starting at an existing data point.

std::vector< double >	getValuesX (int index) const

std::vector< double >	getValuesY (int index) const

QCPRange	getValueRangeOnKeyRange (QCPAbstractPlottable *plottable_p, bool &ok)

QCPRange	getValueRangeOnKeyRange (int index, bool &ok)

double	getYatX (double x, QCPGraph *graph_p)

double	getYatX (double x, int index=0)

pappso::Trace	toTrace (int index) const

pappso::Trace	toTrace (const QCPGraph *graph_p) const

pappso::Trace	toTrace (const QCPRange &x_axis_range, int index) const

pappso::Trace	toTrace (const QCPRange &x_axis_range, const QCPGraph *graph_p) const

Public Member Functions inherited from pappso::BasePlotWidget
	BasePlotWidget (QWidget *parent)

	BasePlotWidget (QWidget *parent, const QString &x_axis_label, const QString &y_axis_label)

virtual	~BasePlotWidget ()
	Destruct `this` BasePlotWidget instance.

virtual bool	setupWidget ()

virtual void	setPen (const QPen &pen)

virtual const QPen &	getPen () const

virtual void	setPlottingColor (QCPAbstractPlottable *plottable_p, const QColor &new_color)

virtual void	setPlottingColor (int index, const QColor &new_color)

virtual QColor	getPlottingColor (QCPAbstractPlottable *plottable_p) const

virtual QColor	getPlottingColor (int index=0) const

virtual void	setAxisLabelX (const QString &label)

virtual void	setAxisLabelY (const QString &label)

virtual void	resetAxesRangeHistory ()

virtual void	updateAxesRangeHistory ()
	Create new axis range history items and append them to the history.

virtual void	restorePreviousAxesRangeHistory ()
	Go up one history element in the axis history.

virtual void	restoreAxesRangeHistory (std::size_t index)
	Get the axis histories at index `index` and update the plot ranges.

virtual void	spaceKeyReleaseEvent (QKeyEvent *event)

virtual void	directionKeyPressEvent (QKeyEvent *event)

virtual void	directionKeyReleaseEvent (QKeyEvent *event)

virtual void	mousePseudoButtonKeyPressEvent (QKeyEvent *event)

virtual void	mousePseudoButtonKeyReleaseEvent (QKeyEvent *event)

virtual void	mouseReleaseHandlerLeftButton ()

virtual void	mouseReleaseHandlerRightButton ()

virtual void	mouseWheelHandler (QWheelEvent *event)

virtual void	mouseMoveHandlerLeftButtonDraggingCursor ()

virtual void	mouseMoveHandlerRightButtonDraggingCursor ()

bool	isClickOntoXAxis (const QPointF &mousePoint)

bool	isClickOntoYAxis (const QPointF &mousePoint)

int	dragDirection ()
	MOUSE-related EVENTS.

virtual void	moveMouseCursorGraphCoordToGlobal (QPointF plot_coordinates)

virtual void	moveMouseCursorPixelCoordToGlobal (QPointF local_coordinates)

virtual void	horizontalMoveMouseCursorCountPixels (int pixel_count)

virtual QPointF	horizontalGetGraphCoordNewPointCountPixels (int pixel_count)

virtual void	verticalMoveMouseCursorCountPixels (int pixel_count)

virtual QPointF	verticalGetGraphCoordNewPointCountPixels (int pixel_count)

virtual QCPRange	getRangeX (bool &found_range, int index) const
	MOUSE MOVEMENTS mouse/keyboard-triggered.

virtual QCPRange	getRangeY (bool &found_range, int index) const

QCPRange	getRange (Enums::Axis axis, RangeType range_type, bool &found_range) const

virtual QCPRange	getInnermostRangeX (bool &found_range) const

virtual QCPRange	getOutermostRangeX (bool &found_range) const

virtual QCPRange	getInnermostRangeY (bool &found_range) const

virtual QCPRange	getOutermostRangeY (bool &found_range) const

void	yMinMaxOnXAxisCurrentRange (double &min, double &max, QCPAbstractPlottable *plottable_p=nullptr)

void	yMinMaxOnXAxisCurrentRange (double &min, double &max, int index)

virtual void	replotWithAxesRanges (QCPRange xAxisRange, QCPRange yAxisRange, Enums::Axis axis)

virtual void	replotWithAxisRangeX (double lower, double upper)

virtual void	replotWithAxisRangeY (double lower, double upper)

virtual void	hideAllPlotItems ()
	PLOTTING / REPLOTTING functions.

virtual void	showTracers ()
	Show the traces (vertical and horizontal).

virtual void	hideTracers ()
	Hide the traces (vertical and horizontal).

virtual void	drawXScopeSpanFeatures ()

virtual void	drawYScopeSpanFeatures ()

virtual void	calculateDragDeltas ()

virtual bool	isVerticalDisplacementAboveThreshold ()

virtual void	drawSelectionRectangleAndPrepareZoom (bool as_line_segment=false, bool for_integration=false)

virtual void	updateIntegrationScopeDrawing (bool as_line_segment=false, bool for_integration=false)

virtual void	resetSelectionRectangle ()

virtual void	hideSelectionRectangle (bool reset_values=false)

virtual bool	isSelectionRectangleVisible ()

virtual SelectionDrawingLines	whatIsVisibleOfTheSelectionRectangle ()

virtual void	setFocus ()
	PLOT ITEMS : TRACER TEXT ITEMS...

virtual void	redrawPlotBackground (QWidget *focusedPlotWidget)
	Redraw the background of the `focusedPlotWidget` plot widget.

virtual void	updateContextXandYAxisRanges ()

virtual const BasePlotContext &	getContext () const

Protected Attributes
MassSpecTracePlotContext	m_context

double	m_chargeMinimalFractionalPart = 0.990

int	m_chargeStateEnvelopePeakSpan = 1

Protected Attributes inherited from pappso::BasePlotWidget
QString	m_name = "NOT_SET"
	Name of the plot widget.

QString	m_desc = "NOT_SET"
	Description of the plot widget.

QString	m_fileName
	The name of the data file from which the mass data were read.

QString	m_axisLabelX

QString	m_axisLabelY

BasePlotContext	m_context

int	m_leftMousePseudoButtonKey = Qt::Key_Less

int	m_rightMousePseudoButtonKey = Qt::Key_Greater

QCPItemLine *	mp_selectionRectangeLine1 = nullptr
	Rectangle defining the borders of zoomed-in/out data.

QCPItemLine *	mp_selectionRectangeLine2 = nullptr

QCPItemLine *	mp_selectionRectangeLine3 = nullptr

QCPItemLine *	mp_selectionRectangeLine4 = nullptr

QCPItemText *	mp_xDeltaTextItem = nullptr
	Text describing the x-axis delta value during a drag operation.

QCPItemText *	mp_yDeltaTextItem = nullptr

bool	m_shouldTracersBeVisible = true
	Tells if the tracers should be visible.

QCPItemLine *	mp_hPosTracerItem = nullptr
	Horizontal position tracer.

QCPItemLine *	mp_vPosTracerItem = nullptr
	Vertical position tracer.

QCPItemLine *	mp_vStartTracerItem = nullptr
	Vertical selection start tracer (typically in green).

QCPItemLine *	mp_vEndTracerItem = nullptr
	Vertical selection end tracer (typically in red).

std::size_t	m_lastAxisRangeHistoryIndex = 0
	Index of the last axis range history item.

std::vector< QCPRange * >	m_xAxisRangeHistory
	List of x axis ranges occurring during the panning zooming actions.

std::vector< QCPRange * >	m_yAxisRangeHistory
	List of y axis ranges occurring during the panning zooming actions.

int	m_mouseMoveHandlerSkipAmount = 10
	How many mouse move events must be skipped *‍/.

int	m_mouseMoveHandlerSkipCount = 0
	Counter to handle the "fat data" mouse move event handling.

QColor	m_unfocusedColor = QColor("lightgray")
	Color used for the background of unfocused plot.

QBrush	m_unfocusedBrush = QBrush(m_unfocusedColor)
	Color used for the background of unfocused plot.

QColor	m_focusedColor = QColor(Qt::transparent)
	Color used for the background of focused plot.

QBrush	m_focusedBrush = QBrush(m_focusedColor)
	Color used for the background of focused plot.

QPen	m_pen
	Pen used to draw the graph and textual elements in the plot widget.

Additional Inherited Members
Protected Member Functions inherited from pappso::BasePlotWidget
virtual void	createAllAncillaryItems ()

virtual void	updateIntegrationScope (bool for_integration=false)

virtual void	updateIntegrationScopeRect (bool for_integration=false)

virtual void	updateIntegrationScopeHorizontalRhomb (bool for_integration=false)

virtual void	updateIntegrationScopeVerticalRhomb (bool for_integration=false)

virtual void	updateIntegrationScopeRhomb (bool for_integration=false)

virtual QString	allLayerNamesToString () const

virtual QString	layerableLayerName (QCPLayerable *layerable_p) const

virtual int	layerableLayerIndex (QCPLayerable *layerable_p) const

Detailed Description

Definition at line 57 of file massspectraceplotwidget.h.

Constructor & Destructor Documentation

◆ MassSpecTracePlotWidget() [1/2]

pappso::MassSpecTracePlotWidget::MassSpecTracePlotWidget ( QWidget * parent = 0 )

explicit

Definition at line 53 of file massspectraceplotwidget.cpp.

                                                                : BaseTracePlotWidget(parent)
{
  BasePlotWidget::m_context.m_dataKind = Enums::DataKind::mz;
  m_context.m_dataKind                 = Enums::DataKind::mz;
 
  // qDebug() << "Data kind:" << static_cast<int>(m_context.m_dataKind);
}

References pappso::BasePlotWidget::m_context, m_context, pappso::BasePlotContext::m_dataKind, and pappso::Enums::mz.

◆ MassSpecTracePlotWidget() [2/2]

pappso::MassSpecTracePlotWidget::MassSpecTracePlotWidget	(	QWidget *	parent,
		const QString &	x_axis_label,
		const QString &	y_axis_label
	)

explicit

Definition at line 61 of file massspectraceplotwidget.cpp.

  : BaseTracePlotWidget(parent, x_axis_label, y_axis_label)
{
  // Set the base context to be of kind Enums::DataKind::mz;
 
  BasePlotWidget::m_context.m_dataKind = Enums::DataKind::mz;
  m_context.m_dataKind                 = Enums::DataKind::mz;
 
  // qDebug() << "Data kind:" << static_cast<int>(m_context.m_dataKind);
}

References pappso::BasePlotWidget::m_context, m_context, pappso::BasePlotContext::m_dataKind, and pappso::Enums::mz.

◆ ~MassSpecTracePlotWidget()

pappso::MassSpecTracePlotWidget::~MassSpecTracePlotWidget ( )

virtual

Definition at line 75 of file massspectraceplotwidget.cpp.

76{

77}

Member Function Documentation

◆ computeResolvingPower()

bool pappso::MassSpecTracePlotWidget::computeResolvingPower ( )

Definition at line 574 of file massspectraceplotwidget.cpp.

{
 
  // m_xRangeLower and m_xRangeUpper and m_xDelta (in fabs() form) have been set
  // during mouve movement handling. Note that the range values *are
  // sorted*.
 
  if(!m_context.m_xDelta || m_context.m_xDelta > 1)
    {
      m_context.m_lastResolvingPower = std::numeric_limits<double>::min();
 
      return false;
    }
 
  // Resolving power is m/z / Delta(m/z), for singly-charged species.
 
  // qDebug() << "Calculating the resolving power with these data:"
  //<< "m_context.m_xRegionRangeStart: " << m_context.m_xRegionRangeStart
  //<< "m_context.m_xRegionRangeEnd: " << m_context.m_xRegionRangeEnd
  //<< "m_context.m_xDelta / 2: " << m_context.m_xDelta / 2;
 
  m_context.m_lastResolvingPower =
    (std::min<double>(m_context.m_xRegionRangeStart, m_context.m_xRegionRangeEnd) +
     (m_context.m_xDelta / 2)) /
    m_context.m_xDelta;
 
  // The m_context was refreshed with the base class context in the calling
  // chain.
  emit resolvingPowerComputationSignal(m_context);
 
  return true;
}

References m_context, pappso::MassSpecTracePlotContext::m_lastResolvingPower, pappso::BasePlotContext::m_xDelta, pappso::BasePlotContext::m_xRegionRangeEnd, pappso::BasePlotContext::m_xRegionRangeStart, and resolvingPowerComputationSignal().

Referenced by mouseMoveHandlerDraggingCursor().

◆ deconvolute()

bool pappso::MassSpecTracePlotWidget::deconvolute ( )

Deconvolute the mass peaks into charge and molecular mass.

Definition at line 285 of file massspectraceplotwidget.cpp.

{
 
  // qDebug() << "The current m_lastZ value:" << m_context.m_lastZ;
 
  // There are two situations: when the user is deconvoluting on the
  // basis of the distance between two consecutive peaks of a same
  // isotopic cluster or when the user deconvolutes on the basis of two
  // different charged-stated peaks that belong to the same envelope.
 
  // We can tell the difference because in the first case the xDelta
  // should be less than 1. In the other case, of course the difference
  // is much greater than 1.
 
  // In order to do the deconvolutions, we need to know what is the tolerance
  // on the fractional part of the deconvoluted charge value. This value is set
  // in the parent window's double spin box.
 
  if(fabs(m_context.m_xDelta) >= 0 && fabs(m_context.m_xDelta) <= 1.1)
    {
      // qDebug() << "m_xDelta:" << m_context.m_xDelta
      //<< "trying isotope-based deconvolution.";
 
      return deconvoluteIsotopicCluster();
    }
 
  // If not deconvoluting on the basis of the isotopic cluster, then:
 
  return deconvoluteChargedState(m_chargeStateEnvelopePeakSpan);
}

References deconvoluteChargedState(), deconvoluteIsotopicCluster(), m_chargeStateEnvelopePeakSpan, m_context, and pappso::BasePlotContext::m_xDelta.

Referenced by mouseMoveHandlerDraggingCursor().

◆ deconvoluteChargedState()

bool pappso::MassSpecTracePlotWidget::deconvoluteChargedState ( int span = 1 )

Deconvolute the mass peaks into charge and molecular mass.

This is one of two methods to deconvolute mass data into a charge value and a Mr value. The method implemented in this function is based on the charge state envelope offered by the mass spectrum (most often for polymers of a reasonable size).

Parameters

span	value representing the number of peaks of the charge state envelope that are spanned by the user selection. Defaults to 1, that is, the span encompasses two consecutive mass peaks of a given charge state envelope.

Set m_lastMz, m_lastZ and m_lastMass.

Returns: true if the deconvolution could be performed, false otherwise.

Definition at line 335 of file massspectraceplotwidget.cpp.

{
  // We assume that we are dealing with two successive (if span is 1) mass
  // peaks belonging to a given charge state family.
 
  // We call span the number of intervals in a given charge state envelope
  // that separate the initial peak (lowerMz) from the last peak (upperMz).
  // That parameter defaults to 1, that is the two peaks are immediately
  // consecutive, that is, there is only one interval.
 
  qDebug() << "The span is:" << span;
 
  // The m_context ranges are inherently sorted. This is not something that
  // is favorable to us because we need to know what is the direction of the
  // drag. That should be configurable, but we can establish that by
  // default, the z value will be calculated for the mass peak at which
  // the mouse drag movement started.
 
  // These two values reflect a m/z range:
  // startMz and curMz are always sorted (startMz < curMz)
  double startMz = m_context.m_xRegionRangeStart;
  double curMz   = m_context.m_xRegionRangeEnd;
 
  qDebug() << "startMz:" << startMz << "curMz:" << curMz;
 
  if(startMz == curMz)
    {
      m_context.m_lastZ            = std::numeric_limits<quint16>::max();
      m_context.m_lastMz           = qQNaN();
      m_context.m_lastTicIntensity = qQNaN();
      m_context.m_lastMr           = qQNaN();
 
      qDebug() << "Start and Cur are the same, no deconvolution possible.";
      return false;
    }
 
  // After much discussing, the agreement we reached with users is that the
  // m/z value that is reported has to be that of the clicked peak, that is
  // the start point of the mouse cursor drag operation. The z charge value
  // has to be related to that m/z value.
 
  double chargeTemp = ((startMz * span) - span) / (curMz - startMz);
  // This is the charge of the least charged peak, that is, by necessity
  // the charge of the peak on the right (curMz, because the values
  // are sorted).
 
  // Make a judicious roundup.
 
  double chargeIntPart;
  double chargeFracPart = modf(chargeTemp, &chargeIntPart);
 
  // When calculating the charge of the ion, very rarely does it provide a
  // perfect integer value. Most often (if deconvolution is for bona fide
  // peaks belonging to the same charge state envelope) that value is with
  // either a large fractional part or a very small fractional part. What we
  // test here, it that fractional part. If it is greater than
  // m_chargeMinimalFractionalPart, then we simply round up to the next integer
  // value (that is, chargeIntPart = 27 and chargeFracPart 0.995, then we
  // set charge to 28). If it is lesser or equal to (1 -
  // m_chargeMinimalFractionalPart /* that is >= 0.01 */, then we let
  // chargeIntPart unmodified (that is, chargeIntPart = 29 and
  // chargeFracPart 0.01, then we set charge to 29). If chargeFracPart is in
  // between (1 - m_chargeMinimalFractionalPart) and
  // m_chargeMinimalFractionalPart, then we consider that the peaks do not
  // belong to the same charge state envelope.
 
  // qDebug() << "Charge:" << chargeIntPart << "Charge fractional part: " << chargeFracPart;
 
 
  if(chargeFracPart >= (1 - m_chargeMinimalFractionalPart /* that is >= 0.01 */) &&
     chargeFracPart <= m_chargeMinimalFractionalPart /* that is <= 0.99 */)
    {
      m_context.m_lastZ            = std::numeric_limits<quint16>::max();
      m_context.m_lastMz           = qQNaN();
      m_context.m_lastTicIntensity = qQNaN();
      m_context.m_lastMr           = qQNaN();
 
      // qDebug() << "Not a charge state family peak,"
      //          << "returning from deconvoluteChargeState";
 
      return false;
    }
 
  if(chargeFracPart > m_chargeMinimalFractionalPart)
    m_context.m_lastZ = chargeIntPart + 1;
  else
    m_context.m_lastZ = chargeIntPart;
 
  qDebug() << "Initially computed m_lastZ as " << m_context.m_lastZ;
 
  // We know the that formula above computed the charge of the least charged
  // ion, that corresponds to the greater m/z value of the range: curMz.
 
  // Now, if the user did click on that least-charged peak, nothing is
  // to be modified. But, if the user did click on the most-charged
  // peak, that is on startMz, the we need to fix the values:
 
  if(static_cast<int>(m_context.m_dragDirections) & static_cast<int>(DragDirections::RIGHT_TO_LEFT))
    {
      qDebug() << "Dragging from right to left, that is from higher m/z value.";
      m_context.m_lastMz = curMz;
    }
  else if(static_cast<int>(m_context.m_dragDirections) &
          static_cast<int>(DragDirections::LEFT_TO_RIGHT))
    {
      qDebug() << "Dragging from left to right, we need to report"
               << "the mass for the left peak, that is for z+span and lower m/z value.";
      m_context.m_lastZ += span;
      m_context.m_lastMz = startMz;
    }
 
  qDebug() << "Final m_lastZ is " << m_context.m_lastZ << "m/z: m_context.m_lastMz";
 
  m_context.m_lastMr = (m_context.m_lastMz * m_context.m_lastZ) - (m_context.m_lastZ * MPROTON);
 
  qDebug() << "startMz:" << QString("%1").arg(startMz, 0, 'f', 6)
           << "curMz:" << QString("%1").arg(curMz, 0, 'f', 6)
           << "m_lastMz (make computation for this startMz):"
           << QString("%1").arg(m_context.m_lastMz, 0, 'f', 6)
           << "m_lastZ:" << QString("%1").arg(m_context.m_lastZ)
           << "m_lastMass:" << QString("%1").arg(m_context.m_lastMr, 0, 'f', 6);
 
  // The m_context was refreshed with the base class context in the calling
  // chain.
  emit massDeconvolutionSignal(m_context);
 
  return true;
}

References pappso::LEFT_TO_RIGHT, m_chargeMinimalFractionalPart, m_context, pappso::BasePlotContext::m_dragDirections, pappso::MassSpecTracePlotContext::m_lastMr, pappso::MassSpecTracePlotContext::m_lastMz, pappso::MassSpecTracePlotContext::m_lastTicIntensity, pappso::MassSpecTracePlotContext::m_lastZ, pappso::BasePlotContext::m_xRegionRangeEnd, pappso::BasePlotContext::m_xRegionRangeStart, massDeconvolutionSignal(), pappso::MPROTON(), and pappso::RIGHT_TO_LEFT.

Referenced by deconvolute().

◆ deconvoluteIsotopicCluster()

bool pappso::MassSpecTracePlotWidget::deconvoluteIsotopicCluster ( )

Deconvolute the mass peaks into charge and molecular mass.

This is one of two methods to deconvolute mass data into a charge value and a Mr value. The method implemented in this function is based on the distance that separates two immediately consecutive peaks of an isotopic cluster. This method can be used as long as the instrument produced data with a resolution sufficient to separate reasonably well the different peaks of an isotopic cluster.

Set m_lastMz, m_lastZ and m_lastMass.

Returns: true if the deconvolution could be performed, false otherwise.

Definition at line 480 of file massspectraceplotwidget.cpp.

{
 
  double startMz = m_context.m_xRegionRangeStart;
  double curMz   = m_context.m_xRegionRangeEnd;
 
  qDebug() << "startMz:" << startMz << "curMz:" << curMz;
 
  if(startMz == curMz)
    {
      m_context.m_lastZ            = std::numeric_limits<quint16>::max();
      m_context.m_lastMz           = qQNaN();
      m_context.m_lastTicIntensity = qQNaN();
      m_context.m_lastMr           = qQNaN();
 
      return false;
    }
 
  double chargeTemp = 1 / fabs(m_context.m_xDelta);
 
  qDebug() << qSetRealNumberPrecision(6) << "curMz - startMz = " << fabs(curMz - startMz)
           << "while m_context.m_xDelta = " << m_context.m_xDelta;
 
  // Sanity check
  if(fabs(m_context.m_xDelta) != fabs(curMz - startMz))
    qFatal() << "Programming error.";
 
  // Make a judicious roundup.
  double chargeIntPart;
  double chargeFracPart = modf(chargeTemp, &chargeIntPart);
 
  // qDebug() << "m_xDelta:" << m_context.m_xDelta
  //          << "chargeTemp:" << QString("%1").arg(chargeTemp, 0, 'f', 6)
  //          << "chargeIntPart:" << chargeIntPart
  //          << "chargeFracPart:" << QString("%1").arg(chargeFracPart, 0, 'f', 6)
  //          << "m_chargeMinimalFractionalPart:" << m_chargeMinimalFractionalPart;
 
  if(chargeFracPart >= (1 - m_chargeMinimalFractionalPart /* that is >= 0.01 */) &&
     chargeFracPart <= m_chargeMinimalFractionalPart /* that is <= 0.99 */)
    {
      m_context.m_lastZ            = std::numeric_limits<quint16>::max();
      m_context.m_lastMz           = qQNaN();
      m_context.m_lastTicIntensity = qQNaN();
      m_context.m_lastMr           = qQNaN();
 
      // qDebug() << "Not in a isotopic cluster peak:"
      //          << "returning from deconvoluteIsotopicCluster";
 
      return false;
    }
 
  if(chargeFracPart > m_chargeMinimalFractionalPart)
    {
      m_context.m_lastZ = chargeIntPart + 1;
 
      // qDebug() << "chargeFracPart > m_chargeMinimalFractionalPart -> m_lastZ
      // = "
      //<< m_context.m_lastZ;
    }
  else
    {
      m_context.m_lastZ = chargeIntPart;
 
      // qDebug()
      //<< "chargeFracPart <=  m_chargeMinimalFractionalPart -> m_lastZ = "
      //<< m_context.m_lastZ;
    }
 
  // qDebug() << "Settled on m_lastZ: " << m_context.m_lastZ;
 
  // Now that we have the charge in the form of an int, we can compute the
  // Mr of the lightest isotopic cluster peak (the one that has the lowest x
  // value). That value is stored in m_xRangeLower.
 
  // We need to sort the xRegionRange before being certain that lower is indeed
  // the left value of the drag span.
 
  m_context.m_lastMz = std::min<double>(m_context.m_xRegionRangeStart, m_context.m_xRegionRangeEnd);
 
  m_context.m_lastMr = (m_context.m_lastMz * m_context.m_lastZ) - (m_context.m_lastZ * MPROTON);
 
  // qDebug() << "m_lastMz :" << QString("%1").arg(m_context.m_lastMz, 0, 'f', 6)
  //          << "m_lastZ:" << QString("%1").arg(m_context.m_lastZ)
  //          << "m_lastMr:" << QString("%1").arg(m_context.m_lastMr, 0, 'f', 6);
 
  // The m_context was refreshed with the base class context in the calling
  // chain.
  emit massDeconvolutionSignal(m_context);
 
  return true;
}

References m_chargeMinimalFractionalPart, m_context, pappso::MassSpecTracePlotContext::m_lastMr, pappso::MassSpecTracePlotContext::m_lastMz, pappso::MassSpecTracePlotContext::m_lastTicIntensity, pappso::MassSpecTracePlotContext::m_lastZ, pappso::BasePlotContext::m_xDelta, pappso::BasePlotContext::m_xRegionRangeEnd, pappso::BasePlotContext::m_xRegionRangeStart, massDeconvolutionSignal(), and pappso::MPROTON().

Referenced by deconvolute().

◆ getChargeMinimalFractionalPart()

double pappso::MassSpecTracePlotWidget::getChargeMinimalFractionalPart ( ) const

Definition at line 263 of file massspectraceplotwidget.cpp.

{
  return m_chargeMinimalFractionalPart;
}

References m_chargeMinimalFractionalPart.

◆ getChargeStateEnvelopePeakSpan()

int pappso::MassSpecTracePlotWidget::getChargeStateEnvelopePeakSpan ( ) const

Definition at line 277 of file massspectraceplotwidget.cpp.

{
  return m_chargeStateEnvelopePeakSpan;
}

References m_chargeStateEnvelopePeakSpan.

◆ keyPressEvent()

void pappso::MassSpecTracePlotWidget::keyPressEvent ( QKeyEvent * event )

overridevirtual

Set the m_pressedKeyCode to the key code in event.

Reimplemented from pappso::BasePlotWidget.

Definition at line 82 of file massspectraceplotwidget.cpp.

{
  // qDebug() << "ENTER";
  BasePlotWidget::keyPressEvent(event);
 
  // Before working on the various data belonging to the base context, we need
  // to get it from the base class and refresh our local context with it.
  refreshBaseContext();
 
  // qDebug() << "Going to emit keyPressEventSignal(m_context);";
 
  emit keyPressEventSignal(m_context);
}

References pappso::BasePlotWidget::keyPressEvent(), keyPressEventSignal(), m_context, and refreshBaseContext().

◆ keyPressEventSignal

void pappso::MassSpecTracePlotWidget::keyPressEventSignal ( const MassSpecTracePlotContext & context )

signal

Referenced by keyPressEvent().

◆ keyReleaseEvent()

void pappso::MassSpecTracePlotWidget::keyReleaseEvent ( QKeyEvent * event )

overridevirtual

Handle specific key codes and trigger respective actions.

Reimplemented from pappso::BasePlotWidget.

Definition at line 99 of file massspectraceplotwidget.cpp.

{
  // Before working on the various data belonging to the base context, we need
  // to get it from the base class and refresh our local context with it.
  refreshBaseContext();
 
  BasePlotWidget::keyReleaseEvent(event);
}

References pappso::BasePlotWidget::keyReleaseEvent(), and refreshBaseContext().

◆ massDeconvolutionSignal

void pappso::MassSpecTracePlotWidget::massDeconvolutionSignal ( const MassSpecTracePlotContext & context )

signal

Referenced by deconvoluteChargedState(), and deconvoluteIsotopicCluster().

◆ mouseMoveHandler()

void pappso::MassSpecTracePlotWidget::mouseMoveHandler ( QMouseEvent * event )

overridevirtual

Handle mouse movements, in particular record all the last visited points.

This function is reponsible for storing at each time the last visited point in the graph. Here, point is intended as any x/y coordinate in the plot widget viewport, not a graph point.

The stored values are then the basis for a large set of calculations throughout all the plot widget.

Parameters

pointer to QMouseEvent from which to retrieve the coordinates of the visited viewport points.

Reimplemented from pappso::BasePlotWidget.

Definition at line 123 of file massspectraceplotwidget.cpp.

{
  // Before working on the various data belonging to the base context, we need
  // to get it from the base class and refresh our local context with it.
  refreshBaseContext();
 
  BasePlotWidget::mouseMoveHandler(event);
}

References pappso::BasePlotWidget::mouseMoveHandler(), and refreshBaseContext().

◆ mouseMoveHandlerDraggingCursor()

void pappso::MassSpecTracePlotWidget::mouseMoveHandlerDraggingCursor ( )

overridevirtual

Reimplemented from pappso::BasePlotWidget.

Definition at line 147 of file massspectraceplotwidget.cpp.

{
  BasePlotWidget::mouseMoveHandlerDraggingCursor();
 
  // Before working on the various data belonging to the base context, we need
  // to get it from the base class and refresh our local context with it.
  refreshBaseContext();
 
  if(m_context.m_mouseButtonsAtMousePress & Qt::LeftButton)
    {
      if(!m_context.m_isMeasuringDistance)
        return;
 
      // qDebug() << "Mouse Buttons at Mouse press:" << m_context.m_mouseButtonsAtMousePress;
 
      // qDebug() << "The current m_lastZ value:" << m_context.m_lastZ;
 
      deconvolute();
      computeResolvingPower();
    }
}

References computeResolvingPower(), deconvolute(), m_context, pappso::BasePlotContext::m_isMeasuringDistance, pappso::BasePlotContext::m_mouseButtonsAtMousePress, pappso::BasePlotWidget::mouseMoveHandlerDraggingCursor(), and refreshBaseContext().

◆ mouseMoveHandlerNotDraggingCursor()

void pappso::MassSpecTracePlotWidget::mouseMoveHandlerNotDraggingCursor ( )

overridevirtual

Reimplemented from pappso::BasePlotWidget.

Definition at line 134 of file massspectraceplotwidget.cpp.

{
  // Before working on the various data belonging to the base context, we need
  // to get it from the base class and refresh our local context with it.
  refreshBaseContext();
 
  BasePlotWidget::mouseMoveHandlerNotDraggingCursor();
 
  // qDebug() << "The current m_lastZ value:" << m_context.m_lastZ;
}

References pappso::BasePlotWidget::mouseMoveHandlerNotDraggingCursor(), and refreshBaseContext().

◆ mousePressEventSignal

void pappso::MassSpecTracePlotWidget::mousePressEventSignal ( const MassSpecTracePlotContext & context )

signal

Referenced by mousePressHandler().

◆ mousePressHandler()

void pappso::MassSpecTracePlotWidget::mousePressHandler ( QMouseEvent * event )

overridevirtual

Record the clicks of the mouse.

Reimplemented from pappso::BasePlotWidget.

Definition at line 172 of file massspectraceplotwidget.cpp.

{
  // qDebug() << "Entering";
 
  // Before working on the various data belonging to the base context, we need
  // to get it from the base class and refresh our local context with it.
  refreshBaseContext();
 
  BasePlotWidget::mousePressHandler(event);
 
  // qDebug() << "The current m_lastZ value:" << m_context.m_lastZ;
 
  emit mousePressEventSignal(m_context);
 
  // qDebug() << "Exiting after having emitted mousePressEventSignal with context:"
  // << m_context.toString();
}

References m_context, mousePressEventSignal(), pappso::BasePlotWidget::mousePressHandler(), and refreshBaseContext().

◆ mouseReleaseEventSignal

void pappso::MassSpecTracePlotWidget::mouseReleaseEventSignal ( const MassSpecTracePlotContext & context )

signal

Referenced by mouseReleaseHandler().

◆ mouseReleaseHandler()

void pappso::MassSpecTracePlotWidget::mouseReleaseHandler ( QMouseEvent * event )

overridevirtual

React to the release of the mouse buttons.

Reimplemented from pappso::BasePlotWidget.

Definition at line 193 of file massspectraceplotwidget.cpp.

{
  // qDebug() << "Entering";
 
  // Before working on the various data belonging to the base context, we need
  // to get it from the base class and refresh our local context with it.
  refreshBaseContext();
 
  BasePlotWidget::mouseReleaseHandler(event);
 
  // qDebug() << "The current m_lastZ value:" << m_context.m_lastZ;
 
  if(!m_context.m_isMouseDragging)
    {
      // Since we were not dragging, by essence we were not measuring
      // distances and _a fortiori_ we were not deconvoluting. So
      // reset deconvolution data in the context.
 
      m_context.resetDeconvolutionData();
    }
 
  emit mouseReleaseEventSignal(m_context);
 
  // qDebug() << "Exiting after having emitted mouseReleaseEventSignal with context:"
  // << m_context.toString();
}

References m_context, pappso::BasePlotContext::m_isMouseDragging, mouseReleaseEventSignal(), pappso::BasePlotWidget::mouseReleaseHandler(), refreshBaseContext(), and pappso::MassSpecTracePlotContext::resetDeconvolutionData().

◆ refreshBaseContext()

const MassSpecTracePlotContext & pappso::MassSpecTracePlotWidget::refreshBaseContext ( ) const

Definition at line 222 of file massspectraceplotwidget.cpp.

{
  // BasePlotWidget has a member m_context of type BasePlotContext.
  // Here we also have a m_context *distinct* member that is of type
  // MassSpecTracePlotContext.
 
  // While MassSpecTracePlotContext is derived from BasePlotContext, the two
  // m_context members are distinct and there are lots of housekeeping data that
  // are managed by the parent BasePlotWidget class in its m_context member
  // *independently* of what we have in the ::BasePlotContext part of our
  // m_context member that is of type MassSpecTracePlotContext. We thus need to
  // resynchronize the data from BasePlotWidget::m_context to our m_context.
 
  // qDebug().noquote() << "The base plot context:" <<
  // BasePlotWidget::m_context.toString();
 
 
  // qDebug() << "Right before refreshing the context, the current m_lastZ value:"
  //          << m_context.m_lastZ;
 
  m_context.initialize(BasePlotWidget::m_context);
 
 
  // qDebug() << "Right after refreshing the context, the current m_lastZ value:"
  //          << m_context.m_lastZ;
 
  // qDebug().noquote() << "After refreshing the base context, base context:"
  //                    << m_context.toString();
 
  return m_context;
}

References pappso::MassSpecTracePlotContext::initialize(), pappso::BasePlotWidget::m_context, and m_context.

Referenced by keyPressEvent(), keyReleaseEvent(), mouseMoveHandler(), mouseMoveHandlerDraggingCursor(), mouseMoveHandlerNotDraggingCursor(), mousePressHandler(), and mouseReleaseHandler().

◆ resolvingPowerComputationSignal

void pappso::MassSpecTracePlotWidget::resolvingPowerComputationSignal ( const MassSpecTracePlotContext & context )

signal

Referenced by computeResolvingPower().

◆ setChargeMinimalFractionalPart()

void pappso::MassSpecTracePlotWidget::setChargeMinimalFractionalPart ( double charge_fractional_part )

Definition at line 256 of file massspectraceplotwidget.cpp.

{
  m_chargeMinimalFractionalPart = charge_fractional_part;
}

References m_chargeMinimalFractionalPart.

◆ setChargeStateEnvelopePeakSpan()

void pappso::MassSpecTracePlotWidget::setChargeStateEnvelopePeakSpan ( int interval )

Definition at line 270 of file massspectraceplotwidget.cpp.

{
  m_chargeStateEnvelopePeakSpan = interval;
}

References m_chargeStateEnvelopePeakSpan.

Member Data Documentation

◆ m_chargeMinimalFractionalPart

double pappso::MassSpecTracePlotWidget::m_chargeMinimalFractionalPart = 0.990

protected

Definition at line 121 of file massspectraceplotwidget.h.

Referenced by deconvoluteChargedState(), deconvoluteIsotopicCluster(), getChargeMinimalFractionalPart(), and setChargeMinimalFractionalPart().

◆ m_chargeStateEnvelopePeakSpan

int pappso::MassSpecTracePlotWidget::m_chargeStateEnvelopePeakSpan = 1

protected

Definition at line 128 of file massspectraceplotwidget.h.

Referenced by deconvolute(), getChargeStateEnvelopePeakSpan(), and setChargeStateEnvelopePeakSpan().

◆ m_context

MassSpecTracePlotContext pappso::MassSpecTracePlotWidget::m_context

mutableprotected

Definition at line 114 of file massspectraceplotwidget.h.

Referenced by MassSpecTracePlotWidget(), MassSpecTracePlotWidget(), computeResolvingPower(), deconvolute(), deconvoluteChargedState(), deconvoluteIsotopicCluster(), keyPressEvent(), mouseMoveHandlerDraggingCursor(), mousePressHandler(), mouseReleaseHandler(), and refreshBaseContext().

The documentation for this class was generated from the following files:

pappsomspp/gui/plotwidget/massspectraceplotwidget.h
pappsomspp/gui/plotwidget/massspectraceplotwidget.cpp

Signals

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MassSpecTracePlotWidget() [1/2]

◆ MassSpecTracePlotWidget() [2/2]

◆ ~MassSpecTracePlotWidget()

Member Function Documentation

◆ computeResolvingPower()

◆ deconvolute()

◆ deconvoluteChargedState()

◆ deconvoluteIsotopicCluster()

◆ getChargeMinimalFractionalPart()

◆ getChargeStateEnvelopePeakSpan()

◆ keyPressEvent()

◆ keyPressEventSignal

◆ keyReleaseEvent()

◆ massDeconvolutionSignal

◆ mouseMoveHandler()

◆ mouseMoveHandlerDraggingCursor()

◆ mouseMoveHandlerNotDraggingCursor()

◆ mousePressEventSignal

◆ mousePressHandler()

◆ mouseReleaseEventSignal

◆ mouseReleaseHandler()

◆ refreshBaseContext()

◆ resolvingPowerComputationSignal

◆ setChargeMinimalFractionalPart()

◆ setChargeStateEnvelopePeakSpan()

Member Data Documentation

◆ m_chargeMinimalFractionalPart

◆ m_chargeStateEnvelopePeakSpan

◆ m_context