plots available

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2247 e4b6dbb4-9209-464b-83f7-6257456c460c

masschroq/src/CMakeLists.txt

@@ -131,14 +131,22 @@ SET(GUI_SRCS
   ./gui/mainwindow.cpp
   ./gui/masschroq_gui.cpp
   ./gui/xicSelectionWidget.cpp
+  ./gui/plotStyle.cpp
   ./gui/xicProfile.cpp
+  ./gui/xicPlot.cpp
+  ./gui/plot.cpp
+  
   )
 
 # another list, this time it includes all header files that should be treated with moc
 SET(GUI_MOC_HDRS
+  ./gui/plotStyle.h
+  ./gui/gui_types.h
   ./gui/mainwindow.h
   ./gui/xicSelectionWidget.h
   ./gui/xicProfile.h
+  ./gui/xicPlot.h
+  ./gui/plot.h
   )  
 
 set(CMAKE_MODULE_PATH ${masschroq_SOURCE_DIR}/modules)

masschroq/src/gui/gui_utilities.h → masschroq/src/gui/gui_types.h

@@ -17,35 +17,22 @@
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 */
-
 /**
- * \file gui_utilities.h
- * \date November 22, 2011
+ * \file gui_types.h
+ * \date November 23, 2011
  * \author Edlira Nano
+ * \brief This header contains all the type re-definitions and all 
+ * the global variables definitions used in MassChroQ GUI. 
  */
 
-#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;
+#ifndef _GUI_TYPES_H_
+#define _GUI_TYPES_H_ 1
+
+#include "plotStyle.h"
+
 
+/*********** Global variables definitions*********************************/
 
 const PlotStyle OriginalXicStyle(QPen(Qt::black));
 
@@ -53,22 +40,4 @@ 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_ */
+#endif /* _GUI_TYPES_H_ */

masschroq/src/gui/mainwindow.cpp

@@ -5,6 +5,9 @@
 
 #include "mainwindow.h"
 #include "xicSelectionWidget.h"
+#include "xicProfile.h"
+#include "xicPlot.h"
+
 
 
 MainWindow::MainWindow(QWidget *parent)
@@ -16,8 +19,8 @@ MainWindow::MainWindow(QWidget *parent)
   
   // Central Widget
   
-  QWidget * widget = new QWidget(); 
-  setCentralWidget(widget);
+  _plot_area = new Plot(this);
+  setCentralWidget(_plot_area);
 
   //_plot = new XicPlot(this);
   //const int margin = 4;
@@ -104,9 +107,18 @@ MainWindow::extractXicWidget() {
 }
 
 void
-MainWindow::extractXic(XicSelectionWidget * xic) {
-  XicProfile * original_xic = _masschroq_gui->extractXicProfile(_current_msrun_file, xic);
-  _xic_profiles->push_back[original_xic];
+MainWindow::extractXic(XicSelectionWidget * xic_widget) {
+  XicProfile * xic_profile = new XicProfile();
+  connect(xic_profile, SIGNAL(created(XicProfile *)), this, SLOT(plotXic(XicProfile *)));
+  _xic_profiles.push_back(xic_profile);
+  _masschroq_gui->extractXicProfile(xic_profile, _current_msrun_file, xic_widget);
+}
+
+
+void
+MainWindow::plotXic(XicProfile * xic_profile) {
+  XicPlot * plot = new XicPlot("Original Xic", xic_profile);
+  _plot_area->addPlot(plot);
 }
 
 void

masschroq/src/gui/mainwindow.h

@@ -4,6 +4,7 @@
 #include <QAction>
 
 #include "masschroq_gui.h"
+#include "plot.h"
 
 class MainWindow : public QMainWindow 
 { 
@@ -18,6 +19,7 @@ private slots:
   void loadMsrun();
   void extractXicWidget();
   void extractXic(XicSelectionWidget * xic);
+  void plotXic(XicProfile * xic_profile);
   void filterXic();
   void about();
   
@@ -28,20 +30,21 @@ protected:
   
 
 private:
-
+  
   void createActions();
   void createMenus();
   //createToolbars();
   //createStatusBar();
   //createDockWindows();
 
-  //Plot * _plot;
 
   //QListWidget * filtersList;
   //QListWidget * quantiItemsList;
   
   MasschroqGui * _masschroq_gui;
 
+  Plot * _plot_area;
+
   QMenu * _fileMenu;
   QMenu * _toolsMenu;
   QMenu * _helpMenu;

masschroq/src/gui/masschroq_gui.cpp

@@ -91,46 +91,39 @@ MasschroqGui::getMsRun(const QString & filename) const {
   }
 }
 
-XicProfile *
-MasschroqGui::extractXicProfile(const QString & msrun_filename, XicSelectionWidget * xic) {
-  qDebug() << "Yo 1" << endl; 
+void
+MasschroqGui::extractXicProfile(XicProfile * xic_profile, 
+				const QString & msrun_filename, 
+				XicSelectionWidget * xic) {
+
   Msrun * msrun = getMsRun(msrun_filename); 
+
   if (msrun == NULL) {
     throw mcqError(QObject::tr("The msrun with filename %1, does not exist").arg(msrun_filename));
   }
-  qDebug() << "Yo 2" << endl; 
-  if (xic == NULL) 
-    qDebug() << "Null" << endl; 
+  
   XicExtractionMethodBase * extraction_method = xic->getXicExtractionMethod();
-  qDebug() << "Yo 3" << endl; 
   mcq_xic_type xic_type = xic->getXicType();
   mcq_double mz_value = xic->getMzToExtract();
   mcq_double rt_value = xic->getRtToExtract();
-  qDebug() << "Yo 3" << endl; 
   extraction_method->setMz(mz_value);
-  qDebug() << "Yo 4" << endl; 
   QuantiItemBase * quanti_item;
   if (rt_value != 0) {
     quanti_item = new QuantiItemMzRt(*extraction_method, rt_value);
   } else { 
     quanti_item = new QuantiItemBase(*extraction_method);
   }
+
   // extract XIC
-  qDebug() << "Yo 3" << endl; 
   msrun->prepareSpectraForQuantification(extraction_method);
   xicBase * current_xic = msrun->extractXic(xic_type, quanti_item);
-    qDebug() << "Yo 4" << endl; 
   if (current_xic == 0) {
     qDebug() << "MsrunSelectionXic null xic ";
   }
-  qDebug() << "Yo 5" << endl; 
-  XicProfile * xic_profile = new XicProfile();
-  xic_profile->setRtVector(*(current_xic->getRetentionTimes()));
-  xic_profile->setIntensityVector(*(current_xic->getIntensities()));
-  qDebug() << "Yo 6" << endl; 
-  delete (current_xic);
-  msrun->doneWithSpectra();
   
-  return xic_profile;
-
+  xic_profile->setOriginalXic( *(current_xic->getRetentionTimes()), 
+			       *(current_xic->getIntensities()) );
+  
+  delete (current_xic);
+  msrun->doneWithSpectra();  
 }

masschroq/src/gui/masschroq_gui.h

@@ -56,7 +56,9 @@ class MasschroqGui {
   /// creates and sets an msrun
   void setMsRun(const QString & filename);
   
-  XicProfile * extractXicProfile(const QString & msrun_filename, XicSelectionWidget * xic);
+  void extractXicProfile(XicProfile * xic_profile, 
+			 const QString & msrun_filename, 
+			 XicSelectionWidget * xic);
   
  private :
   

masschroq/src/gui/plot.cpp

+/**
+ * \file plot.cpp
+ * \date November 23, 2011
+ * \author Edlira Nano
+ */
+
+#include "plot.h"
+#include "xicPlot.h"
+#include <qwt_legend.h>
+
+
+Plot::Plot(QWidget *parent) :
+  QwtPlot(parent) {
+  
+  setAutoReplot(false);
+  
+  setTitle("Xic Plots");
+
+  // legend
+  QwtLegend * legend = new QwtLegend;
+  insertLegend(legend, QwtPlot::BottomLegend);
+
+  setAxisTitle(QwtPlot::xBottom, "Retention time (s)");
+  setAxisTitle(QwtPlot::yLeft, "Intensity");
+
+}
+
+void
+Plot::addPlot(XicPlot * plot) {
+  plot->attach(this);
+  this->replot();
+}

masschroq/src/gui/plot.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 plot.h
+ * \date November 23, 2011
+ * \author Edlira Nano
+ */
+
+#ifndef _PLOT_H_
+#define _PLOT_H_ 1
+
+#include <qwt_plot.h>
+
+class XicPlot;
+
+class Plot : public QwtPlot {
+  Q_OBJECT
+
+    public:
+  
+  Plot(QWidget * parent);
+
+  void addPlot(XicPlot * plot);
+
+  //  public Q_SLOTS:
+  
+
+  // private:
+
+};
+
+
+#endif // _PLOT_H_

masschroq/src/gui/plotStyle.cpp

+/**
+ * \file plotStyle.cpp
+ * \date November 22, 2011
+ * \author Edlira Nano
+ */
+
+#include "plotStyle.h"
+
+PlotStyle::PlotStyle(QPen pen, bool lines, bool render) 
+:
+  _pen(pen), 
+  _lines(lines),
+  _render_antialiased(render)
+{ 
+}
+
+PlotStyle::~PlotStyle() {
+}

masschroq/src/gui/plotStyle.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 plotStyle.h
+ * \date November 22, 2011
+ * \author Edlira Nano
+ */
+
+#ifndef _PLOT_STYLE_H_
+#define _PLOT_STYLE_H_ 1
+
+#include <QPen>
+
+/**
+   \class PlotStyle
+   \brief 
+*/
+
+class PlotStyle {
+
+ public :
+ 
+  PlotStyle(QPen pen, bool lines = true, bool render = true);
+  virtual ~PlotStyle();
+ 
+  QPen _pen; 
+  
+  bool _lines; // setStyle(QwtPlotCurve::Lines)
+  
+  bool _render_antialiased;  // setRenderHint(QwtPlotItem::RenderAntialiased)
+
+};
+
+#endif /* _PLOT_STYLE_H_ */

masschroq/src/gui/xicPlot.cpp

+/**
+ * \file xicPlot.cpp
+ * \date November 22, 2011
+ * \author Edlira Nano
+ */
+
+
 #include "xicPlot.h"
 
-XicPlot::XicPlot(QWidget * parent, XicProfile * xic_profile) :
-  QwtPlot(parent), 
+XicPlot::XicPlot(const QString & title, XicProfile * xic_profile) :
+  QwtPlotCurve(title), 
   _xic_profile(xic_profile) 
 {
-  setAutoReplot(false);
-  connect(_xic_profile, SIGNAL(changed()), this, SLOT(plotXic()));
+  setPlotStyle(_xic_profile->getStyle());
+  setPlotData();
 }
 
 XicPlot::~XicPlot() {
 }
 
 void
-XicPlot::setStyle(const PlotStyle * style) {
+XicPlot::setPlotStyle(PlotStyle * style) {
   _plot_style = style;
+  this->setPen(_plot_style->_pen);
+  if (_plot_style->_lines) {
+    this->setStyle(QwtPlotCurve::Lines);
+  }
+  if (_plot_style->_render_antialiased) {
+    this->setRenderHint(QwtPlotItem::RenderAntialiased);
+  }
 }
 
 
 void
-XicPlot::plotXic() {
-  this->setStyle(_xic_profile->getStyle());
-  _curve = new QwtPlotCurve(_plot_style->legend);
-  // setSamples()
-  // attach/add à main_window
+XicPlot::setPlotData() {
+  unsigned int plotsize(_xic_profile->size());
+  mcq_double x1[plotsize], y1[plotsize];
+  _xic_profile->fill_data_array(x1, y1, plotsize);
+  this->setData(x1, y1, plotsize);
 }

masschroq/src/gui/xicPlot.h

@@ -20,32 +20,30 @@
 
 /**
  * \file xicPlot.h
- * \date November 08, 2011
+ * \date November 22, 2011
  * \author Edlira Nano
  */
 
 #ifndef _XICPLOT_H_
 #define _XICPLOT_H_ 1
 
-#include <QwtPlot>
+#include <qwt_plot_curve.h>
+#include "xicProfile.h"
+//#include "plotStyle.h"
 
-class QwtPlotCurve;
 
-class XicPlot : public QwtPlot {
-  Q_OBJECT
-
-public:
-
-  XicPlot(QWidget * parent = NULL, XicProfile * xic_profile);
-  virtual ~XicPlot();
+class XicPlot : public QwtPlotCurve {
+    
+    public:
   
-private slots :
-
-  void plotXic();
-
+  XicPlot(const QString & title, XicProfile * xic_profile);
+  virtual ~XicPlot();
+    
  private:
   
-  void setStyle(const PlotStyle * style);
+  void setPlotData(); 
+
+  void setPlotStyle(PlotStyle * style);
 
   XicProfile * _xic_profile;
   PlotStyle * _plot_style;

masschroq/src/gui/xicProfile.cpp

@@ -5,14 +5,21 @@
  */
 
 #include "xicProfile.h"
+#include "gui_types.h"
 #include <iostream>
 
-XicProfile::XicProfile() {
+
+XicProfile::XicProfile(QObject * parent) 
+  : QObject(parent)
+{
   _rt_vector = new std::vector<mcq_double>;
   _intensity_vector = new std::vector<mcq_double>;
+  _plot_style = new PlotStyle(QPen(Qt::black));
 }
 
 XicProfile::~XicProfile() {
+  delete _plot_style;
+  
   if (_rt_vector != 0) {
     delete _rt_vector;
     _rt_vector = 0;
@@ -23,8 +30,20 @@ XicProfile::~XicProfile() {
   }
 }
 
+void 
+XicProfile::setOriginalXic(const std::vector<mcq_double> & rt_v, 
+			   const std::vector<mcq_double> & intensity_v) {
+  setRtVector(rt_v);
+  setIntensityVector(intensity_v);
+  setStyle(OriginalXicStyle);
+  Q_EMIT created(this);
+}
+
+
 void
 XicProfile::setRtVector(const std::vector<mcq_double> & rt_v) {
+  _rt_vector->clear();
+
   std::vector<mcq_double>::const_iterator it_rt;  
   for (it_rt = rt_v.begin();
        it_rt != rt_v.end(); 
@@ -36,6 +55,8 @@ XicProfile::setRtVector(const std::vector<mcq_double> & rt_v) {
 
 void
 XicProfile::setIntensityVector(const std::vector<mcq_double> & intensity_v) {
+  _intensity_vector->clear();
+
   std::vector<mcq_double>::const_iterator it_int;  
   for (it_int = intensity_v.begin();
        it_int != intensity_v.end(); 
@@ -43,5 +64,48 @@ 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);
+}
+
+const std::vector<mcq_double> * 
+XicProfile::getRtVector() const {
+  return _rt_vector;
+}
+
+const std::vector<mcq_double> * 
+XicProfile::getIntensityVector() const {
+  return _intensity_vector;
+} 
+
+void
+XicProfile::setStyle(const PlotStyle & plot_style) {
+  *_plot_style = plot_style;
+}
+
+PlotStyle *
+XicProfile::getStyle() const {
+  return _plot_style;
+}
+
+
+void 
+XicProfile::fill_data_array(mcq_double * xdata, 
+			    mcq_double * ydata,
+			    unsigned int plotsize) const {
+  
+  std::vector<mcq_double>::const_iterator itrt;
+  std::vector<mcq_double>::const_iterator itint;
+  unsigned int i;
+  /// _p_v_rt and _p_v_intensity have the same size
+  for (itrt = _rt_vector->begin(), itint = _intensity_vector->begin(), i = 0;
+       itrt != _rt_vector->end() || itint != _intensity_vector->end(); 
+       ++itrt, ++itint, ++i) 
+    {
+      xdata[i] = *itrt;
+      ydata[i] = *itint;
+    }
+}
+
+unsigned int 
+XicProfile::size() const {
+  return _rt_vector->size();
 }

masschroq/src/gui/xicProfile.h

@@ -28,7 +28,9 @@
 #define XIC_PROFILE_H_ 1
 
 #include <vector>
+
 #include "../mcq_types.h"
+#include "plotStyle.h"
 
 //class xicBase;
 
@@ -41,32 +43,50 @@
  * an original unaltered XIC or a filtered XIC. 
  */
 
-class XicProfile {