xicPlot continued

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2246 e4b6dbb4-9209-464b-83f7-6257456c460c

masschroq/debian/masschroq.substvars

-shlibs:Depends=libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libqt4-network (>= 4:4.5.3), libqt4-xml (>= 4:4.5.3), libqt4-xmlpatterns (>= 4:4.5.3), libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.4.0)
+shlibs:Depends=libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libqt4-network (>= 4:4.5.3), libqt4-xml (>= 4:4.5.3), libqt4-xmlpatterns (>= 4:4.5.3), libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.4.0), masschroq
 misc:Depends=

masschroq/src/gui/gui_utilities.h

+/*
+*
+* MassChroQ: Mass Chromatogram Quantification software.
+* Copyright (C) 2010 Olivier Langella, Edlira Nano, Benoit Valot, Michel Zivy.
+*
+* This program 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.
+*
+* This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+*
+*/
+
+/**
+ * \file gui_utilities.h
+ * \date November 22, 2011
+ * \author Edlira Nano
+ */
+
+#ifndef GUI_UTILITIES_H_
+#define GUI_UTILITIES_H_ 1
+
+typedef struct {
+  QPen pen;
+  QwtPlotCurve::CurveStyle style; // setStyle(QwtPlotCurve::Lines)
+  QwtPlotCurve::RenderHint render; // setRenderHint(QwtPlotItem::RenderAntialiased)
+  QwtPlotCurve::LegendAttribute legend; // setLegendAttribute(QwtPlotCurve::LegendShowLine, on)
+  
+  PlotStyle(QPen p, 
+	    QwtPlotCurve::CurveStyle s = QwtPlotCurve::Lines, 
+	    QwtPlotCurve::RenderHint r = QwtPlotItem::RenderAntialiased,
+	    QwtPlotCurve::LegendAttribute l = QwtPlotCurve::LegendShowLine) 
+  : pen(p), 
+    style(s), 
+    render(r), 
+    legend(l)
+  {
+  }
+  
+} PlotStyle;
+
+
+const PlotStyle OriginalXicStyle(QPen(Qt::black));
+
+const PlotStyle FilterBackgroundStyle(QPen(Qt::green));
+
+const PlotStyle FilterSpikeStyle(QPen(Qt::blue));
+
+
+/**
+   \class GuiUtilities
+   \brief This class implements some calculation algorithms needed by 
+   the MassChroQ Gui
+*/
+
+class GuiUtilities {
+ private :
+ 
+  GuiUtilities();
+  
+  virtual ~GuiUtilities();
+  
+ public :
+
+};
+
+#endif /* GUI_UTILITIES_H_ */

masschroq/src/gui/mainwindow.cpp

@@ -105,7 +105,8 @@ MainWindow::extractXicWidget() {
 
 void
 MainWindow::extractXic(XicSelectionWidget * xic) {
-  _masschroq_gui->extractXicProfile(_current_msrun_file, xic);
+  XicProfile * original_xic = _masschroq_gui->extractXicProfile(_current_msrun_file, xic);
+  _xic_profiles->push_back[original_xic];
 }
 
 void

masschroq/src/gui/mainwindow.h

@@ -57,4 +57,6 @@ private:
 
   QString _current_msrun_file;
 
+  std::vector<XicProfile *> _xic_profiles;
+
 };

masschroq/src/gui/xicPlot.cpp

+#include "xicPlot.h"
+
+XicPlot::XicPlot(QWidget * parent, XicProfile * xic_profile) :
+  QwtPlot(parent), 
+  _xic_profile(xic_profile) 
+{
+  setAutoReplot(false);
+  connect(_xic_profile, SIGNAL(changed()), this, SLOT(plotXic()));
+}
+
+XicPlot::~XicPlot() {
+}
+
+void
+XicPlot::setStyle(const PlotStyle * style) {
+  _plot_style = style;
+}
+
+
+void
+XicPlot::plotXic() {
+  this->setStyle(_xic_profile->getStyle());
+  _curve = new QwtPlotCurve(_plot_style->legend);
+  // setSamples()
+  // attach/add à main_window
+}

masschroq/src/gui/xicPlots.h → masschroq/src/gui/xicPlot.h

@@ -19,62 +19,37 @@
 */
 
 /**
- * \file xicPlots.h
+ * \file xicPlot.h
  * \date November 08, 2011
  * \author Edlira Nano
  */
 
-#ifndef _XICPLOTS_H_
-#define _XICPLOTS_H_ 1
+#ifndef _XICPLOT_H_
+#define _XICPLOT_H_ 1
 
+#include <QwtPlot>
 
 class QwtPlotCurve;
 
-class CurveData {
-	// A container class for growing data
-public:
-
-	CurveData();
-
-	void append(double * x, double * y, int count);
-
-	//	int count() const;
-	int size() const;
-	const double *x() const;
-	const double *y() const;
+class XicPlot : public QwtPlot {
+  Q_OBJECT
 
-private:
-	int d_count;
-	QwtArray<double> d_x;
-	QwtArray<double> d_y;
-};
+public:
 
+  XicPlot(QWidget * parent = NULL, XicProfile * xic_profile);
+  virtual ~XicPlot();
+  
+private slots :
 
-class XicPlots: public QwtPlot {
-Q_OBJECT
+  void plotXic();
 
-public:
-  XicPlots(QWidget * parent = NULL);
-  virtual ~XicPlots();
-  
-  void setXic(Msrun & ms_run,
-	      const XicExtractionMethodBase * p_mz_extraction,
-	      //const msRunHashGroup & group,
-	      unsigned int median_window_length,
-	      unsigned int min_max_window_length);
-  
-  void appendData(double x, double y);
-  void appendData(double * x, double * y, int size);
-  
-  void removeData();
-  
  private:
   
-  void plotXic(const xicBase& the_data, QColor color, QString title);
-  
-  CurveData * d_data;
-  QwtPlotCurve * d_curve;
+  void setStyle(const PlotStyle * style);
 
+  XicProfile * _xic_profile;
+  PlotStyle * _plot_style;
+  
 };
 
-#endif // _XICPLOTS_H_
+#endif // _XICPLOT_H_

masschroq/src/gui/xicPlots.cpp

-#include "xicplot.h"
-
-CurveData::CurveData() {
-}
-
-void CurveData::append(double * x, double * y, int count) {
-  int newSize = ((d_count + count) / 1000 + 1) * 1000;
-  if (newSize > size()) {
-    d_x.resize(newSize);
-    d_y.resize(newSize);
-  }
-  
-  for (register int i = 0; i < count; i++) {
-    d_x[d_count + i] = x[i];
-    d_y[d_count + i] = y[i];
-  }
-  d_count += count;
-}
-
-int CurveData::size() const {
-  return d_x.size();
-}
-
-const double * CurveData::x() const {
-  return d_x.data();
-}
-
-const double * CurveData::y() const {
-  return d_y.data();
-}
-
-XicPlot::XicPlot(QWidget * parent) :
-  QwtPlot(parent), d_data(NULL), d_curve(NULL) {
-  setAutoReplot(false);
-  // enable zooming
-  _zoomer = new Zoomer(canvas());
-  _zoomer->setRubberBandPen(QPen(Qt::red, 2, Qt::DotLine));
-  _zoomer->setTrackerPen(QPen(Qt::red));
-}
-
-XicPlot::~XicPlot() {
-  delete d_data;
-  
-}
-
-void xicPlot::appendData(double x, double y) {
-  appendData(&x, &y, 1);
-}
-
-void xicPlot::appendData(double * x, double * y, int size) {
-  if (d_data == NULL)
-    d_data = new CurveData;
-  
-  if (d_curve == NULL) {
-    d_curve = new QwtPlotCurve("Test Curve");
-    d_curve->setStyle(QwtPlotCurve::NoCurve);
-    d_curve->setPaintAttribute(QwtPlotCurve::PaintFiltered);
-    
-    const QColor &c = Qt::white;
-    d_curve->setSymbol(QwtSymbol(QwtSymbol::XCross, QBrush(c), QPen(c),
-				 QSize(5, 5)));
-    
-    d_curve->attach(this);
-  }
-  
-  d_data->append(x, y, size);
-  d_curve->setRawData(d_data->x(), d_data->y(), d_data->size());
-#ifdef __GNUC__
-#endif
-  
-  const bool cacheMode = canvas()->testPaintAttribute(
-						      QwtPlotCanvas::PaintCached);
-  
-  canvas()->setPaintAttribute(QwtPlotCanvas::PaintCached, false);
-  d_curve->draw(d_curve->dataSize() - size, d_curve->dataSize() - 1);
-  canvas()->setPaintAttribute(QwtPlotCanvas::PaintCached, cacheMode);
-}
-
-void xicPlot::removeData() {
-  clear();
-  delete d_curve;
-  d_curve = NULL;
-  
-  delete d_data;
-  d_data = NULL;
-  
-  replot();
-}
-
-void xicPlot::setXic(Msrun & ms_run,
-		     const XicExtractionMethodBase * p_mz_extraction,
-		     //const msRunHashGroup & group,
-		     unsigned int median_window_length, 
-		     unsigned int min_max_window_length) {
-
-  ms_run.prepareSpectraForQuantification(p_mz_extraction);
-  QuantiItemBase mz_select(*p_mz_extraction);
-  
-  xicBase * the_xic = 
-    ms_run.extractXic(MAX_XIC_TYPE, &mz_select);
-  
-  //  xicMax the_xic(&ms_run, &mz_select);
-  
-  QColor couleur;
-  couleur.setRgb(255, 0, 0);
-  plotXic(*the_xic, couleur, "xic");
-  
-  couleur.setRgb(0, 255, 0, 100);
-  the_xic->applyFilterBackground(median_window_length, min_max_window_length);
-  plotXic(*the_xic, couleur, "filtered");
-  ms_run.doneWithSpectra();
-
-  //delete the_xic;
-}
-
-void 
-xicPlot::plotXic(const xicBase& the_data, QColor color, QString title) {
-  cout << "begin xicPlot::plotXic(const xic& the_data, QColor color, Qstring title)"
-       << endl;
-  //_zoomer->rescale();
-  //dye1
-  unsigned int channel_number;
-  //QString dye_name;
-  
-  //clear();
-  // DYE 1
-  //dye_name = the_data.get_dye_name(channel_number).c_str();
-  channel_number = 1;
-  cout << "Yo 1" << endl;
-  unsigned int plotsize1(the_data.size());
-  QwtPlotCurve * curve1 = new QwtPlotCurve("c1");
-  cout << "Yo 2" << endl;
-  /*
-    QwtPlotCurve *curve1 = new QwtPlotCurve(dye_name);
-  */
-  
-  QPen pinceau;
-  //QColor couleur;
-  //cout << endl << "wavelength" << the_data.get_wavelength(channel_number) << endl;
-  //couleur.setRgb (255,0, 0 );
-  pinceau.setColor(color);
-	curve1->setPen(pinceau);
-	double x1[plotsize1], y1[plotsize1];
-	cout << "Yo 3" << endl;
-	the_data.fill_data_array(x1, y1, plotsize1);
-	cout << "Yo 4" << endl;
-	curve1->setData(x1, y1, plotsize1);
-	curve1->attach(this);
-	// finally, refresh the plot
-	//this->replot();
-
-	/**
-	 QwtPlotCurve * curve2 = new QwtPlotCurve("filter");
-	 the_data.filterBackground(1, 30, 60);
-	 couleur.setRgb (0,255, 0 );
-	 pinceau.setColor(couleur);
-	 curve2->setPen(pinceau);
-	 //double x1[plotsize1], y1[plotsize1];
-	 the_data.fill_data_array(x1, y1, plotsize1);
-	 curve2->setData(x1, y1, plotsize1);
-	 curve2->attach(this);
-	 */
-	// finally, refresh the plot
-
-	setAxisAutoScale ( yLeft);
-	setAxisAutoScale ( yRight);
-	setAxisAutoScale ( xBottom);
-	setAxisAutoScale ( xTop);
-	cout << "Yo 5" << endl;
-	this->replot();
-
-	cout << "Yo 6" << endl;
-	delete _zoomer;
-	_zoomer = new Zoomer(canvas());
-	_zoomer->setRubberBandPen(QPen(Qt::red, 2, Qt::DotLine));
-	_zoomer->setTrackerPen(QPen(Qt::red));
-	
-	_zoomer->rescale();
-	
-}

masschroq/src/gui/xicProfile.cpp

@@ -43,4 +43,5 @@ XicProfile::setIntensityVector(const std::vector<mcq_double> & intensity_v) {
     _intensity_vector->push_back(*it_int);
     std::cout << "int : " << *it_int << std::endl; 
   }
+  Q_EMIT created(this);
 }

masschroq/src/gui/xicProfile.h

@@ -42,8 +42,10 @@
  */
 
 class XicProfile {
-
- public :
+  
+  Q_OBJECT
+    
+    public :
   
   XicProfile();
 
@@ -53,6 +55,10 @@ class XicProfile {
   
   void setIntensityVector(const std::vector<mcq_double> & intensity_v);
   
+ Q_SIGNALS :
+  
+  void changed();
+  
  private :
   
   /// XicProfile's retention times (x-axis)
@@ -62,7 +68,7 @@ class XicProfile {
   std::vector<mcq_double> * _intensity_vector;
     
   /// The XIC this profile corresponds to
-  //xicBase * _xic;
+  /// xicBase * _xic;
   
 };
 

masschroq/src/lib/share/utilities.cpp

 /**
  * \file utilities.cpp
- * \date 29 November, 2010
+ * \date November 29, 2010
  * \author Edlira Nano
  */
 

masschroq/src/lib/share/utilities.h

@@ -49,7 +49,7 @@ mcq_double get_median(constvdoubleit beginit, constvdoubleit endit);
 mcq_double get_spike_to_zero(constvdoubleit beginit, constvdoubleit endit);
 
 /**
-   \class AlgoPlus
+   \class Utilities
    \brief This class implements some calculation algorithms needed by 
    MassChroQ
 */