libpappsomspp
Library for mass spectrometry
pappso::MassSpecTracePlotWidget Class Reference

#include <massspectraceplotwidget.h>

Inheritance diagram for pappso::MassSpecTracePlotWidget:
pappso::BaseTracePlotWidget pappso::BasePlotWidget

Signals

void keyPressEventSignal (const MassSpecTracePlotContext &context)
 
void massDeconvolutionSignal (const MassSpecTracePlotContext &context)
 
void resolvingPowerComputationSignal (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 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. More...
 
bool deconvoluteIsotopicCluster ()
 Deconvolute the mass peaks into charge and molecular mass. More...
 
bool deconvoluteChargedState (int span=1)
 Deconvolute the mass peaks into charge and molecular mass. More...
 
bool computeResolvingPower ()
 
virtual void keyPressEvent (QKeyEvent *event) override
 Set the m_pressedKeyCode to the key code in event. More...
 
virtual void keyReleaseEvent (QKeyEvent *event) override
 Handle specific key codes and trigger respective actions. More...
 
virtual void mouseMoveHandler (QMouseEvent *event) override
 Handle mouse movements, in particular record all the last visited points. More...
 
virtual void mousePressHandler (QMouseEvent *event) override
 Record the clicks of the mouse. More...
 
virtual void mouseReleaseHandler (QMouseEvent *event) override
 React to the release of the mouse buttons. More...
 
virtual void mouseMoveHandlerNotDraggingCursor () override
 
virtual void mouseMoveHandlerDraggingCursor () override
 
const MassSpecTracePlotContextrefreshBaseContext () 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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
virtual void restorePreviousAxesRangeHistory ()
 Go up one history element in the axis history. More...
 
virtual void restoreAxesRangeHistory (std::size_t index)
 Get the axis histories at index index and update the plot ranges. More...
 
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. More...
 
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. More...
 
virtual QCPRange getRangeY (bool &found_range, int index) const
 
QCPRange getRange (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, Axis axis)
 
virtual void replotWithAxisRangeX (double lower, double upper)
 
virtual void replotWithAxisRangeY (double lower, double upper)
 
virtual void hideAllPlotItems ()
 PLOTTING / REPLOTTING functions. More...
 
virtual void showTracers ()
 Show the traces (vertical and horizontal). More...
 
virtual void hideTracers ()
 Hide the traces (vertical and horizontal). More...
 
virtual void drawXDeltaFeatures ()
 
virtual void drawYDeltaFeatures ()
 
virtual void calculateDragDeltas ()
 
virtual bool isVerticalDisplacementAboveThreshold ()
 
virtual void drawSelectionRectangleAndPrepareZoom (bool as_line_segment=false, bool for_integration=false)
 
virtual void updateSelectionRectangle (bool as_line_segment=false, bool for_integration=false)
 
virtual void resetSelectionRectangle ()
 
virtual void hideSelectionRectangle (bool reset_values=false)
 
virtual bool isSelectionRectangleVisible ()
 
virtual PolygonType whatIsVisibleOfTheSelectionRectangle ()
 
virtual void setFocus ()
 PLOT ITEMS : TRACER TEXT ITEMS... More...
 
virtual void redrawPlotBackground (QWidget *focusedPlotWidget)
 Redraw the background of the focusedPlotWidget plot widget. More...
 
virtual void updateContextXandYAxisRanges ()
 
virtual const BasePlotContextgetContext () 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. More...
 
QString m_desc = "NOT_SET"
 Description of the plot widget. More...
 
QString m_fileName
 The name of the data file from which the mass data were read. More...
 
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. More...
 
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. More...
 
QCPItemText * mp_yDeltaTextItem = nullptr
 
bool m_shouldTracersBeVisible = true
 Tells if the tracers should be visible. More...
 
QCPItemLine * mp_hPosTracerItem = nullptr
 Horizontal position tracer. More...
 
QCPItemLine * mp_vPosTracerItem = nullptr
 Vertical position tracer. More...
 
QCPItemLine * mp_vStartTracerItem = nullptr
 Vertical selection start tracer (typically in green). More...
 
QCPItemLine * mp_vEndTracerItem = nullptr
 Vertical selection end tracer (typically in red). More...
 
std::size_t m_lastAxisRangeHistoryIndex = 0
 Index of the last axis range history item. More...
 
std::vector< QCPRange * > m_xAxisRangeHistory
 List of x axis ranges occurring during the panning zooming actions. More...
 
std::vector< QCPRange * > m_yAxisRangeHistory
 List of y axis ranges occurring during the panning zooming actions. More...
 
int m_mouseMoveHandlerSkipAmount = 10
 How many mouse move events must be skipped *‍/. More...
 
int m_mouseMoveHandlerSkipCount = 0
 Counter to handle the "fat data" mouse move event handling. More...
 
QColor m_unfocusedColor = QColor("lightgray")
 Color used for the background of unfocused plot. More...
 
QBrush m_unfocusedBrush = QBrush(m_unfocusedColor)
 Color used for the background of unfocused plot. More...
 
QColor m_focusedColor = QColor(Qt::transparent)
 Color used for the background of focused plot. More...
 
QBrush m_focusedBrush = QBrush(m_focusedColor)
 Color used for the background of focused plot. More...
 
QPen m_pen
 Pen used to draw the graph and textual elements in the plot widget. More...
 

Additional Inherited Members

- Protected Member Functions inherited from pappso::BasePlotWidget
virtual void createAllAncillaryItems ()
 
virtual void update1DSelectionRectangle (bool for_integration=false)
 
virtual void update2DSelectionRectangleSquare (bool for_integration=false)
 
virtual void update2DSelectionRectangleSkewed (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 55 of file massspectraceplotwidget.cpp.

56  : BaseTracePlotWidget(parent)
57 {
59 
60  // qDebug() << "Data kind:" <<
61  // static_cast<int>(m_context.m_baseContext.m_dataKind);
62 }
BaseTracePlotWidget(QWidget *parent=0)

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

◆ MassSpecTracePlotWidget() [2/2]

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

Definition at line 64 of file massspectraceplotwidget.cpp.

67  : BaseTracePlotWidget(parent, x_axis_label, y_axis_label)
68 {
69  // Set the base context to be of kind DataKind::mz;
70 
72 
73  // qDebug() << "Data kind:" <<
74  // static_cast<int>(m_context.m_baseContext.m_dataKind);
75 }

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

◆ ~MassSpecTracePlotWidget()

pappso::MassSpecTracePlotWidget::~MassSpecTracePlotWidget ( )
virtual

Definition at line 78 of file massspectraceplotwidget.cpp.

79 {
80 }

Member Function Documentation

◆ computeResolvingPower()

bool pappso::MassSpecTracePlotWidget::computeResolvingPower ( )

Definition at line 536 of file massspectraceplotwidget.cpp.

537 {
538 
539  // m_xRangeLower and m_xRangeUpper and m_xDelta (in fabs() form) have been set
540  // during mouve movement handling. Note that the range values *are
541  // sorted*.
542 
544  {
545  m_context.m_lastResolvingPower = std::numeric_limits<double>::min();
546 
547  return false;
548  }
549 
550  // Resolving power is m/z / Delta(m/z), for singly-charged species.
551 
553  (std::min<double>(m_context.m_xRegionRangeStart,
555  (m_context.m_xDelta / 2)) /
557 
558  // The m_context was refreshed with the base class context in the calling
559  // chain.
561 
562  return true;
563 }
void resolvingPowerComputationSignal(const MassSpecTracePlotContext &context)

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 245 of file massspectraceplotwidget.cpp.

246 {
247 
248  // There are two situations: when the user is deconvoluting on the
249  // basis of the distance between two consecutive peaks of a same
250  // isotopic cluster or when the user deconvolutes on the basis of two
251  // different charged-stated peaks that belong to the same envelope.
252 
253  // We can tell the difference because in the first case the xDelta
254  // should be less than 1. In the other case, of course the difference
255  // is much greater than 1.
256 
257  // In order to do the deconvolutions, we need to know what is the tolerance
258  // on the fractional part of the deconvoluted charge value. This value is set
259  // in the parent window's double spin box.
260 
261  if(fabs(m_context.m_xDelta) >= 0 && fabs(m_context.m_xDelta) <= 1.1)
262  {
263  // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()"
264  //<< "m_xDelta:" << m_context.m_baseContext.m_xDelta
265  //<< "trying isotope-based deconvolution.";
266 
268  }
269 
270  // If not deconvoluting on the basis of the isotopic cluster, then:
271 
273 }
bool deconvoluteChargedState(int span=1)
Deconvolute the mass peaks into charge and molecular mass.
bool deconvoluteIsotopicCluster()
Deconvolute the mass peaks into charge and molecular mass.

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
spanvalue 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 294 of file massspectraceplotwidget.cpp.

295 {
296  // We assume that we are dealing with two successive (if span is 1) mass
297  // peaks belonging to a given charge state family.
298 
299  // We call span the number of intervals in a given charge state envelope
300  // that separate the initial peak (lowerMz) from the last peak (upperMz).
301  // That parameter defaults to 1, that is the two peaks are immediately
302  // consecutive, that is, there is only one interval.
303 
304  // We use the m_contex.basecontext.m_xRegionRange structure that is unsorted.
305  // That is, lower is the start drag point.x and upper is the current drag
306  // point.x. If dragging occurs from left to right, start.x < cur.x.
307  // We use the unsorted values, because we need to know in which direction
308  // the user has drug the mouse, because we want to provide the Mr value
309  // for the peak currently under the mouse cursor, that is under
310  // currentDragPoint, that is the value in
311  // m_context.m_baseContext.m_xRegionRange.upper.
312 
313  double startMz = m_context.m_xRegionRangeStart;
314  double curMz = m_context.m_xRegionRangeEnd;
315 
316  // qDebug() << "startMz:" << startMz << "curMz:" << curMz;
317 
318  if(startMz == curMz)
319  {
320  m_context.m_lastZ = -1;
321  m_context.m_lastMz = std::numeric_limits<double>::min();
322  m_context.m_lastTicIntensity = std::numeric_limits<double>::min();
323  m_context.m_lastMr = std::numeric_limits<double>::min();
324 
325  return false;
326  }
327 
328  // We need to be aware that the status bar of the window that contains
329  // this plot widget shows the cursor position realtime, and that cursor
330  // position is the m_currentDragPoint.x value, that is, curMz. Thus, we need
331  // to make the calculations with the charge being the one of the polymer under
332  // the cursor position. This is tricky because it changes when the user
333  // switches drag senses: from left to right and right to left.
334  // The way z is calculated always makes it the charge of the highest mz
335  // value. So knowing this, depending on the drag direction we'll have to take
336  // curMz and apply to it either z charge (left to right drag) or (z+span)
337  // charge (right to left).
338 
339  // Make sure lower is actually lower, even if drag is from right to left.
340  // This is only to have a single charge calculation.
341  double lowerMz;
342  double upperMz;
343 
344  if(startMz < curMz)
345  {
346  lowerMz = startMz;
347  upperMz = curMz;
348  }
349  else
350  {
351  lowerMz = curMz;
352  upperMz = startMz;
353  }
354 
355  double chargeTemp = ((lowerMz * span) - span) / (upperMz - lowerMz);
356 
357  // Make a judicious roundup.
358 
359  double chargeIntPart;
360  double chargeFracPart = modf(chargeTemp, &chargeIntPart);
361 
362  // When calculating the charge of the ion, very rarely does it provide a
363  // perfect integer value. Most often (if deconvolution is for bona fide
364  // peaks belonging to the same charge state envelope) that value is with
365  // either a large fractional part or a very small fractional part. What we
366  // test here, it that fractional part. If it is greater than
367  // m_chargeMinimalFractionalPart, then we simply round up to the next integer
368  // value (that is, chargeIntPart = 27 and chargeFracPart 0.995, then we
369  // set charge to 28). If it is lesser or equal to (1 -
370  // m_chargeMinimalFractionalPart /* that is >= 0.01 */, then we let
371  // chargeIntPart unmodified (that is, chargeIntPart = 29 and
372  // chargeFracPart 0.01, then we set charge to 29). If chargeFracPart is in
373  // between (1 - m_chargeMinimalFractionalPart) and
374  // m_chargeMinimalFractionalPart, then we consider that the peaks do not
375  // belong to the same charge state envelope.
376 
377  // qDebug() << __FILE__ << __LINE__ << __FUNCTION__
378  //<< "Charge:" << chargeIntPart
379  //<< "Charge fractional part: " << chargeFracPart;
380 
381 
382  if(chargeFracPart >=
383  (1 - m_chargeMinimalFractionalPart /* that is >= 0.01 */) &&
384  chargeFracPart <= m_chargeMinimalFractionalPart /* that is <= 0.99 */)
385  {
386  m_context.m_lastZ = -1;
387  m_context.m_lastMz = std::numeric_limits<double>::min();
388  m_context.m_lastTicIntensity = std::numeric_limits<double>::min();
389  m_context.m_lastMr = std::numeric_limits<double>::min();
390 
391  // qDebug() << __FILE__ << __LINE__
392  //<< "Not a charge state family peak,"
393  //<< "returning from deconvoluteChargeState";
394 
395  return false;
396  }
397 
398  if(chargeFracPart > m_chargeMinimalFractionalPart)
399  m_context.m_lastZ = chargeIntPart + 1;
400  else
401  m_context.m_lastZ = chargeIntPart;
402 
403  // Now, to actually compute the molecular mass based on the charge and on
404  // the currently displayed m/z value, we need to have some thinking:
405 
406  if(startMz < curMz)
407  {
408  // The drag was from left to right, that is curMz is greater than
409  // startMz. Fine, the z value is effectively the charge of the ion at
410  // curMz. Easy, no charge value modification here.
411  }
412  else
413  {
414  // The drag was from right to left, that is curMz is less than startMz.
415  // So we want to show the charge of the curMz, that is, z + span.
417  }
418 
419  m_context.m_lastMz = curMz;
422 
423  // qDebug() << __FILE__ << __LINE__
424  //<< "startMz:" << QString("%1").arg(startMz, 0, 'f', 6)
425  //<< "m_lastMz (curMz):"
426  //<< QString("%1").arg(m_context.m_lastMz, 0, 'f', 6)
427  //<< "m_lastMass:" << QString("%1").arg(m_context.m_lastMr, 0, 'f', 6)
428  //<< "m_lastZ:" << QString("%1").arg(m_context.m_lastZ);
429 
430  // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()"
431  //<< "returning true";
432 
433  // The m_context was refreshed with the base class context in the calling
434  // chain.
436 
437  return true;
438 }
void massDeconvolutionSignal(const MassSpecTracePlotContext &context)
const pappso_double MPROTON(1.007276466879)

References m_chargeMinimalFractionalPart, m_context, 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(), and pappso::MPROTON().

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 456 of file massspectraceplotwidget.cpp.

457 {
458 
460  {
461  // qDebug() << __FILE__ << __LINE__
462  //<< "Same xRegionRange.upper and xRegionRange.lower:"
463  //<< "returning from deconvoluteIsotopicCluster";
464 
465  return false;
466  }
467 
468  double chargeTemp = 1 / fabs(m_context.m_xDelta);
469 
470  // Make a judicious roundup.
471  double chargeIntPart;
472  double chargeFracPart = modf(chargeTemp, &chargeIntPart);
473 
474  // qDebug() << "m_xDelta:" << m_context.m_baseContext.m_xDelta
475  //<< "chargeTemp:" << QString("%1").arg(chargeTemp, 0, 'f', 6)
476  //<< "chargeIntPart:" << chargeIntPart
477  //<< "chargeFracPart:" << QString("%1").arg(chargeFracPart, 0, 'f', 6)
478  //<< "m_chargeMinimalFractionalPart:" << m_chargeMinimalFractionalPart;
479 
480  if(chargeFracPart >= (1 - m_chargeMinimalFractionalPart) &&
481  chargeFracPart <= m_chargeMinimalFractionalPart)
482  {
483  m_context.m_lastZ = -1;
484  m_context.m_lastMz = std::numeric_limits<double>::min();
485  m_context.m_lastTicIntensity = std::numeric_limits<double>::min();
486  m_context.m_lastMr = std::numeric_limits<double>::min();
487 
488  // qDebug() << "Not in a isotopic cluster peak:"
489  //<< "returning from deconvoluteIsotopicCluster";
490 
491  return false;
492  }
493 
494  if(chargeFracPart > m_chargeMinimalFractionalPart)
495  {
496  m_context.m_lastZ = chargeIntPart + 1;
497 
498  // qDebug() << "chargeFracPart > m_chargeMinimalFractionalPart -> m_lastZ
499  // = "
500  //<< m_context.m_lastZ;
501  }
502  else
503  {
504  m_context.m_lastZ = chargeIntPart;
505 
506  // qDebug()
507  //<< "chargeFracPart <= m_chargeMinimalFractionalPart -> m_lastZ = "
508  //<< m_context.m_lastZ;
509  }
510 
511  // Now that we have the charge in the form of an int, we can compute the
512  // Mr of the lightest isotopic cluster peak (the one that has the lowest x
513  // value). That value is stored in m_xRangeLower.
514 
515  // We need to sort the xRegionRange before being certain that lower is indeed
516  // the left value of the drag span.
517 
518  m_context.m_lastMz = std::min<double>(m_context.m_xRegionRangeStart,
520 
523 
524  // qDebug() << __FILE__ << __LINE__ << __FUNCTION__ << "()"
525  //<< "returning true";
526 
527  // The m_context was refreshed with the base class context in the calling
528  // chain.
530 
531  return true;
532 }

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 223 of file massspectraceplotwidget.cpp.

224 {
226 }

References m_chargeMinimalFractionalPart.

◆ getChargeStateEnvelopePeakSpan()

int pappso::MassSpecTracePlotWidget::getChargeStateEnvelopePeakSpan ( ) const

Definition at line 237 of file massspectraceplotwidget.cpp.

238 {
240 }

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 85 of file massspectraceplotwidget.cpp.

86 {
87  // qDebug() << "ENTER";
89 
90  // Before working on the various data belonging to the base context, we need
91  // to get it from the base class and refresh our local context with it.
93 
94  // qDebug() << "Going to emit keyPressEventSignal(m_context);";
95 
97 }
virtual void keyPressEvent(QKeyEvent *event)
KEYBOARD-related EVENTS.
const MassSpecTracePlotContext & refreshBaseContext() const
void keyPressEventSignal(const MassSpecTracePlotContext &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 102 of file massspectraceplotwidget.cpp.

103 {
105 
106  // Before working on the various data belonging to the base context, we need
107  // to get it from the base class and refresh our local context with it.
109 }
virtual void keyReleaseEvent(QKeyEvent *event)
Handle specific key codes and trigger respective actions.

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

◆ massDeconvolutionSignal

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

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

Reimplemented from pappso::BasePlotWidget.

Definition at line 126 of file massspectraceplotwidget.cpp.

127 {
129 
130  // Before working on the various data belonging to the base context, we need
131  // to get it from the base class and refresh our local context with it.
133 }
virtual void mouseMoveHandler(QMouseEvent *event)
KEYBOARD-related EVENTS.

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

◆ mouseMoveHandlerDraggingCursor()

void pappso::MassSpecTracePlotWidget::mouseMoveHandlerDraggingCursor ( )
overridevirtual

Reimplemented from pappso::BasePlotWidget.

Definition at line 148 of file massspectraceplotwidget.cpp.

149 {
151 
152  // Before working on the various data belonging to the base context, we need
153  // to get it from the base class and refresh our local context with it.
155 
156  if(m_context.m_mouseButtonsAtMousePress & Qt::LeftButton)
157  {
159  return;
160 
161  // qDebug() << "lastMovingMouseButtons:"
162  //<< m_context.m_baseContext.m_lastMovingMouseButtons;
163 
164  deconvolute();
166  }
167 }
Qt::MouseButtons m_mouseButtonsAtMousePress
virtual void mouseMoveHandlerDraggingCursor()
bool deconvolute()
Deconvolute the mass peaks into charge and molecular mass.

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 137 of file massspectraceplotwidget.cpp.

138 {
140 
141  // Before working on the various data belonging to the base context, we need
142  // to get it from the base class and refresh our local context with it.
144 }
virtual void mouseMoveHandlerNotDraggingCursor()

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

◆ 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.

173 {
175 
176  // Before working on the various data belonging to the base context, we need
177  // to get it from the base class and refresh our local context with it.
179 }
virtual void mousePressHandler(QMouseEvent *event)
KEYBOARD-related EVENTS.

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

◆ mouseReleaseEventSignal

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

◆ mouseReleaseHandler()

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

React to the release of the mouse buttons.

Reimplemented from pappso::BasePlotWidget.

Definition at line 184 of file massspectraceplotwidget.cpp.

185 {
187 
188  // Before working on the various data belonging to the base context, we need
189  // to get it from the base class and refresh our local context with it.
191 }
virtual void mouseReleaseHandler(QMouseEvent *event)

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

◆ refreshBaseContext()

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

Definition at line 195 of file massspectraceplotwidget.cpp.

196 {
197  // BasePlotWidget has a member m_context of type BasePlotContext.
198  // Here we also have a m_context *distinct* member that is of type
199  // MassSpecTracePlotContext.
200 
201  // While MassSpecTracePlotContext is derived from BasePlotContext, the two
202  // m_context members are distinct and there are lots of housekeeping data that
203  // are managed by the parent BasePlotWidget class in its m_context member
204  // *independently* of what we have in the ::BasePlotContext part of our
205  // m_context member that is of type MassSpecTracePlotContext. We thus need to
206  // resynchronize the data from BasePlotWidget::m_context to our m_context.
207 
209 
210  return m_context;
211 }
BasePlotContext m_context

References 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 215 of file massspectraceplotwidget.cpp.

217 {
218  m_chargeMinimalFractionalPart = charge_fractional_part;
219 }

References m_chargeMinimalFractionalPart.

◆ setChargeStateEnvelopePeakSpan()

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

Definition at line 230 of file massspectraceplotwidget.cpp.

231 {
233 }

References m_chargeStateEnvelopePeakSpan.

Member Data Documentation

◆ m_chargeMinimalFractionalPart

double pappso::MassSpecTracePlotWidget::m_chargeMinimalFractionalPart = 0.990
protected

◆ m_chargeStateEnvelopePeakSpan

int pappso::MassSpecTracePlotWidget::m_chargeStateEnvelopePeakSpan = 1
protected

◆ m_context


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