xicSelectionWidget working :)

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2244 e4b6dbb4-9209-464b-83f7-6257456c460c

masschroq/CMakeLists.txt

@@ -58,8 +58,8 @@ if (NOT CMAKE_INSTALL_PREFIX)
   SET (CMAKE_INSTALL_PREFIX /usr/local)
 endif (NOT CMAKE_INSTALL_PREFIX)
 
-SET(CMAKE_BUILD_TYPE "Release")
-#SET(CMAKE_BUILD_TYPE "RelWithDebInfo")
+#SET(CMAKE_BUILD_TYPE "Release")
+SET(CMAKE_BUILD_TYPE "RelWithDebInfo")
 #SET( CMAKE_BUILD_TYPE "Debug")
 
 IF(CMAKE_BUILD_TYPE MATCHES "Release")

masschroq/src/CMakeLists.txt

@@ -131,12 +131,14 @@ SET(GUI_SRCS
   ./gui/mainwindow.cpp
   ./gui/masschroq_gui.cpp
   ./gui/xicSelectionWidget.cpp
+  ./gui/xicProfile.cpp
   )
 
 # another list, this time it includes all header files that should be treated with moc
 SET(GUI_MOC_HDRS
   ./gui/mainwindow.h
   ./gui/xicSelectionWidget.h
+  ./gui/xicProfile.h
   )  
 
 set(CMAKE_MODULE_PATH ${masschroq_SOURCE_DIR}/modules)

masschroq/src/gui/mainwindow.cpp

@@ -76,7 +76,7 @@ MainWindow::createActions() {
 
   _aboutAct = new QAction(tr("&About"), this);
   _aboutAct->setStatusTip(tr("About MassChroQ GUI"));
-  connect(_quitAct, SIGNAL(triggered()), this, SLOT(about()));
+  connect(_aboutAct, SIGNAL(triggered()), this, SLOT(about()));
   
   
 }
@@ -100,13 +100,12 @@ MainWindow::extractXicWidget() {
   XicSelectionWidget * xic = new XicSelectionWidget(dock);
   dock->setWidget(xic);
   addDockWidget(Qt::LeftDockWidgetArea, dock);
-
-  connect(xic, SIGNAL(extract()), this, SLOT(extractXic(xic)));
+  connect(xic, SIGNAL(extract(XicSelectionWidget *)), this, SLOT(extractXic(XicSelectionWidget *)));
 }
 
 void
 MainWindow::extractXic(XicSelectionWidget * xic) {
-  _masschroq_gui->extractXic(xic);
+  _masschroq_gui->extractXicProfile(_current_msrun_file, xic);
 }
 
 void
@@ -115,9 +114,6 @@ MainWindow::filterXic() {
 }
 
 
-
-
-
 void MainWindow::about() {
   QMessageBox::about(this, tr("About MassChroQ"),
 		     tr("This is <b>MassChroQ GUI</b> version beta."));

masschroq/src/gui/mainwindow.h

@@ -17,7 +17,7 @@ private slots:
   
   void loadMsrun();
   void extractXicWidget();
-  void extractXic(XicSelectionWidget *);
+  void extractXic(XicSelectionWidget * xic);
   void filterXic();
   void about();
   

masschroq/src/gui/masschroq_gui.cpp

@@ -6,10 +6,15 @@
 
 
 #include "masschroq_gui.h"
-#include "../mcq_types.h"
+#include "xicProfile.h"
+#include "xicSelectionWidget.h"
 #include "../lib/mcq_error.h"
 #include "../lib/msrun/msrun_classic.h"
 #include "../lib/msrun/msrun_sliced.h"
+#include "../lib/xicExtractionMethods/xicExtractionMethodBase.h"
+#include "../lib/quanti_items/quantiItemMzRt.h"
+#include "../lib/xic/xic_base.h"
+
 #include <math.h>
 
 MasschroqGui::MasschroqGui() {
@@ -71,15 +76,15 @@ MasschroqGui::setMsRun(const QString & filename) {
 }
 
 void
-MasschroqGui::addMsRun(const QString & filename, const Msrun * msrun) {
+MasschroqGui::addMsRun(const QString & filename, Msrun * msrun) {
   _msrun_map[filename] = msrun; 
 }
 
 Msrun * 
-MassChroq::getMsRun(const QString & filename) const {
+MasschroqGui::getMsRun(const QString & filename) const {
   std::map<QString, Msrun *>::const_iterator it;
   it = _msrun_map.find(filename);
-  if (it == end()) {
+  if (it == _msrun_map.end()) {
     return (NULL);
   } else {
     return (it->second);
@@ -87,27 +92,44 @@ MassChroq::getMsRun(const QString & filename) const {
 }
 
 XicProfile *
-MassChroq::extractXicProfile(XicSelectionWidget * xic) {
-  
+MasschroqGui::extractXicProfile(const QString & msrun_filename, XicSelectionWidget * xic) {
+  qDebug() << "Yo 1" << endl; 
+  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
-  _msrun->prepareSpectraForQuantification(extraction_method);
-  xicBase * current_xic = _msrun->extractXic(xic_type, quanti_item);
-  
+  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();
+  msrun->doneWithSpectra();
   
   return xic_profile;
 

masschroq/src/gui/masschroq_gui.h

@@ -38,6 +38,9 @@
 /* #include "peptides/protein.h" */
 /* #include "peptides/isotope_label.h" */
 
+class XicProfile;
+class XicSelectionWidget;
+
 /**
  * \class MasschroqGui
  * \brief The super API class in MassChroq GUI: it coordinates the main actions in the GUI
@@ -53,11 +56,11 @@ class MasschroqGui {
   /// creates and sets an msrun
   void setMsRun(const QString & filename);
   
-  XicProfile * extractXicProfile(XicSelectionWidget xic);
+  XicProfile * extractXicProfile(const QString & msrun_filename, XicSelectionWidget * xic);
   
  private :
   
-  void addMsRun(const QString & filename, const Msrun * msrun);
+  void addMsRun(const QString & filename, Msrun * msrun);
   Msrun * getMsRun(const QString & filename) const;
 
   std::map<QString, Msrun *> _msrun_map;

masschroq/src/gui/xicPlots.h

@@ -18,8 +18,14 @@
 *
 */
 
-#ifndef _XICPLOT_H_
-#define _XICPLOT_H_ 1
+/**
+ * \file xicPlots.h
+ * \date November 08, 2011
+ * \author Edlira Nano
+ */
+
+#ifndef _XICPLOTS_H_
+#define _XICPLOTS_H_ 1
 
 
 class QwtPlotCurve;
@@ -43,29 +49,32 @@ private:
 	QwtArray<double> d_y;
 };
 
-class XicPlot: public QwtPlot {
-Q_OBJECT
-public:
-	XicPlot(QWidget * parent = NULL);
-	virtual ~XicPlot();
-	
-	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 plotXicMinusBackground(const xic& the_data);
-	void appendData(double x, double y);
-	void appendData(double * x, double * y, int size);
 
-	void removeData();
+class XicPlots: public QwtPlot {
+Q_OBJECT
 
-private:
-	void plotXic(const xicBase& the_data, QColor color, QString title);
+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;
 
-	CurveData * d_data;
-	QwtPlotCurve * d_curve;
-	Zoomer * _zoomer;
 };
 
-#endif // _XICPLOT_H_
+#endif // _XICPLOTS_H_

masschroq/src/gui/xicProfile.cpp

@@ -5,6 +5,7 @@
  */
 
 #include "xicProfile.h"
+#include <iostream>
 
 XicProfile::XicProfile() {
   _rt_vector = new std::vector<mcq_double>;
@@ -29,6 +30,7 @@ XicProfile::setRtVector(const std::vector<mcq_double> & rt_v) {
        it_rt != rt_v.end(); 
        ++it_rt) {
     _rt_vector->push_back(*it_rt);
+    std::cout << "rt : " << *it_rt << std::endl; 
   }
 }
 
@@ -39,5 +41,6 @@ XicProfile::setIntensityVector(const std::vector<mcq_double> & intensity_v) {
        it_int != intensity_v.end(); 
        ++it_int) {
     _intensity_vector->push_back(*it_int);
+    std::cout << "int : " << *it_int << std::endl; 
   }
 }

masschroq/src/gui/xicProfile.h

@@ -24,10 +24,13 @@
  * \author Edlira Nano
  */
 
-#ifndef XICPROFILE_H_
-#define XICPROFILE_H_ 1
+#ifndef XIC_PROFILE_H_
+#define XIC_PROFILE_H_ 1
 
 #include <vector>
+#include "../mcq_types.h"
+
+//class xicBase;
 
 /**
  * \class XicProfile
@@ -46,24 +49,22 @@ class XicProfile {
 
   virtual ~XicProfile();
 
- protected :
-
   void setRtVector(const std::vector<mcq_double> & rt_v);
   
   void setIntensityVector(const std::vector<mcq_double> & intensity_v);
   
+ private :
+  
   /// XicProfile's retention times (x-axis)
   std::vector<mcq_double> * _rt_vector;
   
   /// XicProfile's intensities (y-axis)
   std::vector<mcq_double> * _intensity_vector;
-  
- private :
-  
+    
   /// The XIC this profile corresponds to
-  xicBase * _xic;
+  //xicBase * _xic;
   
 };
 
 
-#endif /* XICPROFILE_H_*/
+#endif /* XIC_PROFILE_H_*/

masschroq/src/gui/xicSelectionWidget.cpp

@@ -5,10 +5,14 @@
  */
 
 #include <QtGui>
+#include "../lib/mcq_error.h"
 #include "xicSelectionWidget.h"
+#include "../lib/xicExtractionMethods/xicExtractionMethodMzRange.h"
+#include "../lib/xicExtractionMethods/xicExtractionMethodPpmRange.h"
 
 XicSelectionWidget::XicSelectionWidget(QWidget * parent) : QWidget(parent) {
   
+  _xic_extraction_method = 0;
   create_xic_type_group();
   create_xic_range_group();
   create_mz_group();
@@ -19,6 +23,7 @@ XicSelectionWidget::XicSelectionWidget(QWidget * parent) : QWidget(parent) {
   _button_box->addButton(extractButton, QDialogButtonBox::AcceptRole);
   _button_box->addButton(QDialogButtonBox::Cancel);
   
+
   connect(_button_box, SIGNAL(accepted()), this, SLOT(extractXic()));
   connect(_button_box, SIGNAL(rejected()), this, SLOT(cancel()));
 
@@ -29,7 +34,6 @@ XicSelectionWidget::XicSelectionWidget(QWidget * parent) : QWidget(parent) {
   mainLayout->addWidget(_button_box);
   setLayout(mainLayout);
   setWindowTitle(tr("XIC extraction"));
-
 }
 
 XicSelectionWidget::~XicSelectionWidget() {
@@ -67,7 +71,7 @@ XicSelectionWidget::create_xic_range_group() {
   
   QCheckBox * ppm_range = new QCheckBox(tr("ppm range"));
   ppm_range->setChecked(true);
-  XicExtractionMethodPpmRange extraction_method = new XicExtractionMethodPpmRange();
+  XicExtractionMethodPpmRange * extraction_method = new XicExtractionMethodPpmRange();
   setXicExtractionMethod(extraction_method);
   QCheckBox * mz_range = new QCheckBox(tr("mz range"));
 
@@ -99,6 +103,8 @@ XicSelectionWidget::create_xic_range_group() {
 
   _xic_range_group->setLayout(layout);
 
+  
+
   connect(xic_range_buttons, SIGNAL(buttonClicked(QAbstractButton * )), 
 	  this, SLOT(setXicExtractionMethod(QAbstractButton *)));
 
@@ -114,11 +120,13 @@ XicSelectionWidget::create_mz_group() {
   _mz_group = new QGroupBox(tr("m/z value selection"));
   QFormLayout * layout = new QFormLayout;
   QDoubleSpinBox * mz_value = new QDoubleSpinBox;
+  mz_value->setDecimals(4);
   mz_value->setMaximum(5000.0000);
   mz_value->setSingleStep(10.0000);
   setMzToExtract(0);
 
   QDoubleSpinBox * rt_value = new QDoubleSpinBox;
+  rt_value->setDecimals(4);
   rt_value->setMaximum(5000.0000);
   rt_value->setSingleStep(10.0000);
   setRtToExtract(0);
@@ -135,8 +143,8 @@ XicSelectionWidget::create_mz_group() {
 
 
 void
-XicSelectionWidget::setXicType(mcq_xic_type & type) {
-  if ( (type != MAX_XIC_TYPE) || (type != SUM_XIC_TYPE) ) {
+XicSelectionWidget::setXicType(const mcq_xic_type & type) {
+  if ( (type != MAX_XIC_TYPE) && (type != SUM_XIC_TYPE) ) {
     throw mcqError(QObject::tr("XicSelectionWidget::setXicType(mcq_xic_type) : invalid xic type"));
   }
   
@@ -186,30 +194,30 @@ XicSelectionWidget::setXicExtractionMethod(QAbstractButton * button) {
 }
 
 void
-XicSelectionWidget::setMinRange(mcq_double min) {
+XicSelectionWidget::setMinRange(double min) {
   _min_range = min;
-  _xic_extraction_method->set_low_mz_range(_min_range);
+  _xic_extraction_method->set_min_range(_min_range);
 }
 
 void
-XicSelectionWidget::setMaxRange(mcq_double max) {
+XicSelectionWidget::setMaxRange(double max) {
   _max_range = max;
-  _xic_extraction_method->set_high_mz_range(_max_range);
+  _xic_extraction_method->set_max_range(_max_range);
 } 
 
 void
-XicSelectionWidget::setMzToExtract(mcq_double mz) {
+XicSelectionWidget::setMzToExtract(double mz) {
   _mz_to_extract = mz;
 }
 
 void
-XicSelectionWidget::setRtToExtract(mcq_double rt) {
+XicSelectionWidget::setRtToExtract(double rt) {
   _rt_to_extract = rt;
 }
 
 void
 XicSelectionWidget::extractXic() {
-  emit extract();
+  emit extract(this);
 }
 
 void
@@ -218,7 +226,7 @@ XicSelectionWidget::cancel() {
   this->deleteLater();
 }
 
-const XicExtractionMethodBase * 
+XicExtractionMethodBase * 
 XicSelectionWidget::getXicExtractionMethod() const {
   return _xic_extraction_method;
 }

masschroq/src/gui/xicSelectionWidget.h

@@ -28,10 +28,13 @@
 #define XIC_SELECTION_WIDGET_H_ 1
 
 #include <QDialog>
+#include "../mcq_types.h"
 
 class QButtonGroup;
 class QGroupBox;
 class QDialogButtonBox;
+class QAbstractButton;
+class XicExtractionMethodBase;
 
 
 /**
@@ -51,7 +54,7 @@ class XicSelectionWidget : public QWidget {
   
   virtual ~XicSelectionWidget();
   
-  const XicExtractionMethodBase * getXicExtractionMethod() const;
+  XicExtractionMethodBase * getXicExtractionMethod() const;
   
   const mcq_xic_type getXicType() const;
 
@@ -63,17 +66,16 @@ class XicSelectionWidget : public QWidget {
   
   void setXicType(QAbstractButton *);
   void setXicExtractionMethod(QAbstractButton *);
-  void setMinRange(mcq_double min);
-  void setMaxRange(mcq_double max);
-  void setMzToExtract(mcq_double mz);
-  void setRtToExtract(mcq_double rt);
-  
+  void setMinRange(double min);
+  void setMaxRange(double max);
+  void setMzToExtract(double mz);
+  void setRtToExtract(double rt); 
   void extractXic();
   void cancel();
 
  signals :
   
-  void extract();
+  void extract(XicSelectionWidget *);
   
  protected :
 
@@ -84,7 +86,7 @@ class XicSelectionWidget : public QWidget {
   mcq_double _mz_to_extract;
   mcq_double _rt_to_extract;
   
-  void setXicType(mcq_xic_type & type);
+  void setXicType(const mcq_xic_type & type);
   void setXicExtractionMethod(XicExtractionMethodBase * extraction_method);
 
  private :

masschroq/src/lib/msrun/slicer.cpp

@@ -146,8 +146,8 @@ Slicer::closeCacheInSlices() {
 
 const mcq_slice_index_id
 Slicer::getSliceIdForMz(const QuantiItemBase * quanti_item) const {
-  const mcq_double high_mz = quanti_item->get_high_mz();
-  const mcq_double low_mz = quanti_item->get_low_mz();
+  const mcq_double high_mz = quanti_item->get_max_mz();
+  const mcq_double low_mz = quanti_item->get_min_mz();
  
   std::vector<Slice * >::const_iterator it_slice;
   for (it_slice = _slices.begin();

masschroq/src/lib/peak/xic_peak.cpp

@@ -56,8 +56,8 @@ xicPeak::print(std::ostream & out) const {
   mcq_double aligned_rtime_max = this->get_aligned_max_rt();
   out << "rtime max\tmax intensity\tarea\tmz_start\tmz_stop" << std::endl;
   out << aligned_rtime_max << "\t" << _max_intensity << "\t" << _area << "\t"
-      << _xic_quanti_item.get_low_mz() << "\t"
-      << _xic_quanti_item.get_high_mz() << std::endl;
+      << _xic_quanti_item.get_min_mz() << "\t"
+      << _xic_quanti_item.get_max_mz() << std::endl;
 }
 
 void 

masschroq/src/lib/quanti_items/quantiItemBase.cpp

@@ -10,8 +10,8 @@
 
 QuantiItemBase::QuantiItemBase(const XicExtractionMethodBase & extraction_method) {
   _mz = extraction_method.get_mz();
-  _low_mz = extraction_method.get_low_mz();
-  _high_mz = extraction_method.get_high_mz();
+  _low_mz = extraction_method.get_min_mz();
+  _high_mz = extraction_method.get_max_mz();
   this->setType();
 }
 
@@ -24,12 +24,12 @@ QuantiItemBase::get_mz() const {
 }
   
 mcq_double 
-QuantiItemBase::get_low_mz() const {
+QuantiItemBase::get_min_mz() const {
   return (_low_mz);
 }
 
 mcq_double 
-QuantiItemBase::get_high_mz() const {
+QuantiItemBase::get_max_mz() const {
   return (_high_mz);
 }
 
@@ -64,9 +64,9 @@ QuantiItemBase::getSimpleName(const Msrun * msrun) const {
   QString name("mz_"), tmp;
   tmp.setNum(get_mz());
   name.append(tmp).append("_l_");
-  tmp.setNum(get_low_mz()).append("_");
+  tmp.setNum(get_min_mz()).append("_");
   name.append(tmp).append("_h_");
-  tmp.setNum(get_high_mz());
+  tmp.setNum(get_max_mz());
   name.append(tmp);
   name = name.replace(".", "-");
   //name.append(suffixName());

masschroq/src/lib/quanti_items/quantiItemBase.h

@@ -55,9 +55,9 @@ class QuantiItemBase {
    
   mcq_double get_mz() const;
   
-  mcq_double get_low_mz() const;
+  mcq_double get_min_mz() const;
   
-  mcq_double get_high_mz() const;
+  mcq_double get_max_mz() const;
   
   virtual const unsigned int * getZ() const {
     return (NULL);

masschroq/src/lib/quanti_items/quantiItemMzRt.cpp

@@ -47,9 +47,9 @@ QuantiItemMzRt::getSimpleName(const Msrun * msrun) const {
   name.append(tmp).append("_rt_");
   tmp.setNum(_rt);
   name.append(tmp).append("_l_");
-  tmp.setNum(get_low_mz());
+  tmp.setNum(get_min_mz());
   name.append(tmp).append("_h_");
-  tmp.setNum(get_high_mz());
+  tmp.setNum(get_max_mz());
   name.append(tmp);
   name = name.replace(".", "-");
   //  name.append(suffixName());

masschroq/src/lib/quanti_items/quantiItemPeptide.cpp

@@ -73,9 +73,9 @@ QuantiItemPeptide::getSimpleName(const Msrun * msrun) const {
   name.append(tmp).append("_rt_");
   tmp.setNum(getMatchingRt(msrun));
   name.append(tmp).append("_l_");
-  tmp.setNum(get_low_mz());
+  tmp.setNum(get_min_mz());
   name.append(tmp).append("_h_");
-  tmp.setNum(get_high_mz());
+  tmp.setNum(get_max_mz());
   name.append(tmp).append("_z_");
   tmp.setNum(_z);
   name.append(tmp);

masschroq/src/lib/xic/xic_base.cpp

@@ -16,8 +16,8 @@ xicBase::xicBase(const Msrun * p_ms_run,
   _p_quanti_item(quanti_item),
   _p_ms_run(p_ms_run)
 {
-  _mz_start = _p_quanti_item->get_low_mz();
-  _mz_stop = _p_quanti_item->get_high_mz();
+  _mz_start = _p_quanti_item->get_min_mz();
+  _mz_stop = _p_quanti_item->get_max_mz();
   
   _p_v_rt = new std::vector<mcq_double>;
   _p_v_intensity = new std::vector<mcq_double>;

masschroq/src/lib/xicExtractionMethods/xicExtractionMethodBase.h

@@ -51,19 +51,22 @@ class XicExtractionMethodBase {