docs/html/c_parameters_widget_8h_source.html

#ifndef _CPARAMETERSWIDGET_H

#define _CPARAMETERSWIDGET_H


#include <iostream>

#include <string>


#include <QWidget>

#include <QDesktopServices>

#include <QUrl>

#include <QFileInfo>

#include <QLineEdit>

#include <QPushButton>


#include "core/utilities.h"

#include "core/cGlobalPreferences.h"

#include "core/cSummaryFormula.h"

#include "core/cParameters.h"

#include "gui/cFragmentIonsListWidget.h"

#include "gui/cNeutralLossesListWidget.h"


using namespace std;


// forward declarations

class QFormLayout;

class QGridLayout;

class QTextEdit;

class QVBoxLayout;

class QHBoxLayout;

class QComboBox;

class QSpinBox;

class QDoubleSpinBox;

class QDialogButtonBox;

class QGroupBox;

class QCheckBox;

class QTableWidget;

class QListWidget;

class QMessageBox;

class QScrollArea;

class QLabel;


class cParametersWidget : public QWidget

{

    Q_OBJECT


public:


    cParametersWidget(cGlobalPreferences* globalpreferences, QWidget* parent = (QWidget *)0);


    ~cParametersWidget();


    cParameters& getParameters();


    void setAndRestoreParameters(cParameters& parameters);


    void closeEvent(QCloseEvent *event);


    void setSequence(int peptidetypeindex, QString sequence);


    void setTag(int peptidetypeindex, QString tag);


    void applyGlobalPreferences(cGlobalPreferences* globalpreferences);


private:


    bool hideunusedparameters;


    QWidget* parent;


    cGlobalPreferences* globalpreferences;

    cParameters parameters;


    QVBoxLayout* vlayout1;

    QVBoxLayout* vlayout2;

    QVBoxLayout* vlayout;

    QHBoxLayout* hlayout;

    QWidget* hlayoutwidget;

    QScrollArea* hlayoutscroll;


    QString settingsfile;

    QString oldsettingsfile;


    QDialogButtonBox* stdbuttons;

    QHBoxLayout* buttons;

    QPushButton* load;

    QPushButton* save;

    QPushButton* saveas;


    QGroupBox* searchgroupbox;

    QGridLayout* searchgridlayout;

    QLabel* modelabel;

    QComboBox* mode;

    eModeType oldmodetype;

    QSpinBox* maximumnumberofthreads;

    QLabel* maximumnumberofthreadslabel;


    QGroupBox* experimentalspectragroupbox;

    QGridLayout* experimentalspectragridlayout;

    QLabel* peptidetypelabel;

    QComboBox* peptidetype;

    QLabel* peaklistlabel;

    QLineEdit* peaklistline;

    QCheckBox* useprofiledata;

    QPushButton* peaklistbutton;

    QHBoxLayout* peaklistlayout;

    QWidget* peaklistwidget;

    QLabel* scannumberlabel;

    QSpinBox* scannumber;

    QLabel* precursormasslabel;

    QDoubleSpinBox* precursormass;

    QLabel* precursoradductlabel;

    QLineEdit* precursoradduct;

    QLabel* precursorchargelabel;

    QSpinBox* precursorcharge;

    QLabel* precursormasserrortolerancelabel;

    QDoubleSpinBox* precursormasserrortolerance;

    QLabel* fragmentmasserrortolerancelabel;

    QDoubleSpinBox* fragmentmasserrortolerance;

    QLabel* minimumrelativeintensitythresholdlabel;

    QDoubleSpinBox* minimumrelativeintensitythreshold;

    QLabel* minimumabsoluteintensitythresholdlabel;

    QSpinBox* minimumabsoluteintensitythreshold;

    QLabel* mzratiolabel;

    QDoubleSpinBox* minimummz;

    QDoubleSpinBox* maximummz;

    QHBoxLayout* mzratiolayout;

    QWidget* mzratiowidget;

    QLabel* rtlabel;

    QDoubleSpinBox* minimumrt;

    QDoubleSpinBox* maximumrt;

    QHBoxLayout* rtlayout;

    QWidget* rtwidget;

    QLabel* fwhmlabel;

    QDoubleSpinBox* fwhm;


    QGroupBox* isotoperatiosgroupbox;

    QGridLayout* isotoperatiosgridlayout;


    QLabel* ratio54Fe56FeLabel;

    QCheckBox* ratio54Fe56FeEnabled;

    QDoubleSpinBox* minratio54Fe56Fe;

    QDoubleSpinBox* maxratio54Fe56Fe;

    QHBoxLayout* ratio54Fe56FeLayout;

    QWidget* ratio54Fe56FeWidget;


    QLabel* ratio60Ni58NiLabel;

    QCheckBox* ratio60Ni58NiEnabled;

    QDoubleSpinBox* minratio60Ni58Ni;

    QDoubleSpinBox* maxratio60Ni58Ni;

    QHBoxLayout* ratio60Ni58NiLayout;

    QWidget* ratio60Ni58NiWidget;


    QLabel* ratio62Ni58NiLabel;

    QCheckBox* ratio62Ni58NiEnabled;

    QDoubleSpinBox* minratio62Ni58Ni;

    QDoubleSpinBox* maxratio62Ni58Ni;

    QHBoxLayout* ratio62Ni58NiLayout;

    QWidget* ratio62Ni58NiWidget;


    QLabel* ratio65Cu63CuLabel;

    QCheckBox* ratio65Cu63CuEnabled;

    QDoubleSpinBox* minratio65Cu63Cu;

    QDoubleSpinBox* maxratio65Cu63Cu;

    QHBoxLayout* ratio65Cu63CuLayout;

    QWidget* ratio65Cu63CuWidget;


    QLabel* ratio66Zn64ZnLabel;

    QCheckBox* ratio66Zn64ZnEnabled;

    QDoubleSpinBox* minratio66Zn64Zn;

    QDoubleSpinBox* maxratio66Zn64Zn;

    QHBoxLayout* ratio66Zn64ZnLayout;

    QWidget* ratio66Zn64ZnWidget;


    QLabel* ratio67Zn64ZnLabel;

    QCheckBox* ratio67Zn64ZnEnabled;

    QDoubleSpinBox* minratio67Zn64Zn;

    QDoubleSpinBox* maxratio67Zn64Zn;

    QHBoxLayout* ratio67Zn64ZnLayout;

    QWidget* ratio67Zn64ZnWidget;


    QLabel* ratio68Zn64ZnLabel;

    QCheckBox* ratio68Zn64ZnEnabled;

    QDoubleSpinBox* minratio68Zn64Zn;

    QDoubleSpinBox* maxratio68Zn64Zn;

    QHBoxLayout* ratio68Zn64ZnLayout;

    QWidget* ratio68Zn64ZnWidget;


    QGroupBox* brickdatabasegroupbox;

    QGridLayout* brickdatabasegridlayout;

    QLabel* brickdatabaselabel;

    QLineEdit* brickdatabaseline;

    QPushButton* brickdatabasebutton;

    QHBoxLayout* brickdatabaselayout;

    QWidget* brickdatabasewidget;

    QLabel* maximumbricksincombinatiolabel;

    QSpinBox* maximumbricksincombinationbegin;

    QSpinBox* maximumbricksincombinationmiddle;

    QSpinBox* maximumbricksincombinationend;

    QHBoxLayout* maximumbricksincombinationlayout;

    QWidget* maximumbricksincombinationwidget;

    QLabel* maximumcumulativemasslabel;

    QDoubleSpinBox* maximumcumulativemass;

    QLabel* modificationslabel;

    QLineEdit* modificationsline;

    QPushButton* modificationsbutton;

    QHBoxLayout* modificationslayout;

    QWidget* modificationswidget;


    QGroupBox* miscgroupbox;

    QGridLayout* miscgridlayout;

    QLabel* blindedgeslabel;

    QComboBox* blindedges;

    QLabel* cyclicnterminuslabel;

    QCheckBox* cyclicnterminus;

    QLabel* cycliccterminuslabel;

    QCheckBox* cycliccterminus;

    QLabel* internalfragmentslabel;

    QCheckBox* internalfragments;

    QLabel* enablescramblinglabel;

    QCheckBox* enablescrambling;

    QLabel* similaritysearchlabel;

    QCheckBox* similaritysearch;

    QLabel* regularblocksorderlabel;

    QCheckBox* regularblocksorder;


    QGroupBox* theoreticalspectragroupbox;

    QGridLayout* theoreticalspectragridlayout;

    QLabel* sequencedatabaselabel;

    QLineEdit* sequencedatabaseline;

    QPushButton* sequencedatabasebutton;

    QHBoxLayout* sequencedatabaselayout;

    QWidget* sequencedatabasewidget;

    QLabel* scoretypelabel;

    QComboBox* scoretype;

    QLabel* hitsreportedlabel;

    QSpinBox* hitsreported;

    QLabel* sequencetaglabel;

    QLineEdit* sequencetag;

    QLabel* iontypeslabel;

    cFragmentIonsListWidget* iontypes;

    QLabel* neutrallosstypeslabel;

    cNeutralLossesListWidget* neutrallosstypes;

    QLabel* maximumcombinedlosseslabel;

    QSpinBox* maximumcombinedlosses;

    QLabel* elementstypeslabel;

    cNeutralLossesListWidget* elementstypes;

    QLabel* maximumcombinedelementslabel;

    QSpinBox* maximumcombinedelements;

    //QCheckBox* clearhitswithoutparent;

    QLabel* reportunmatchedtheoreticalpeakslabel;

    QCheckBox* reportunmatchedtheoreticalpeaks;

    QLabel* generateisotopepatternlabel;

    QCheckBox* generateisotopepattern;

    QLabel* minimumpatternsizelabel;

    QSpinBox* minimumpatternsize;

    QLabel* minimumfeaturesizelabel;

    QSpinBox* minimumfeaturesize;

    QLabel* minimumiontypeslabel;

    QSpinBox* minimumiontypes;

    QLabel* basicformulachecklabel;

    QCheckBox* basicformulacheck;

    QLabel* advancedformulachecklabel;

    QCheckBox* advancedformulacheck;

    QLabel* noratiochecklabel;

    QCheckBox* noratiocheck;

    QLabel* calculatefdrslabel;

    QCheckBox* calculatefdrs;


    QLabel* minimumannotationintensitylabel;

    QDoubleSpinBox* minimumannotationintensityrelative;

    QSpinBox* minimumannotationintensityabsolute;

    QHBoxLayout* minimumannotationintensitylayout;

    QWidget* minimumannotationintensitywidget;


    QLabel* mzdifftolerancelabel;

    QDoubleSpinBox* mzdifftolerance;

    QLabel* intensitytolerancelabel;

    QDoubleSpinBox* intensitytolerance;


    QGroupBox* searchedsequencegroupbox;

    QGridLayout* searchedsequencegridlayout;

    QLabel* searchedsequencelabel;

    QLineEdit* searchedsequenceline;

    QPushButton* searchedsequencebutton;

    QHBoxLayout* searchedsequencelayout;

    QWidget* searchedsequencewidget;

    QLabel* searchedsequencemodiflabel;

    QLineEdit* searchedsequenceNtermmodif;

    QLineEdit* searchedsequenceCtermmodif;

    QLineEdit* searchedsequenceTmodif;

    QHBoxLayout* searchedsequencemodiflayout;

    QWidget* searchedsequencemodifwidget;

    QLabel* searchedsequenceformulalabel;

    QLineEdit* searchedsequenceformula;


    QString lastdirloadsettings;

    QString lastdirsavesettings;


    QString defaultdirselectpeaklist;

    QString defaultdirselectbricksdatabase;

    QString defaultdirselectmodifications;

    QString defaultdirselectsequencedatabase;


protected:


    void keyPressEvent(QKeyEvent *event);


private slots:


    void loadSettings();


    void saveSettings();


    void saveSettingsAs();


    void peaklistButtonReleased();


    void brickDatabaseButtonReleased();


    void modificationsButtonReleased();


    void sequenceDatabaseButtonReleased();


    bool updateParameters();


    void updateParametersAndHide();


    void restoreParameters();


    void updateSettingsWhenPeptideTypeChanged(int index);


    void updateSettingsWhenModeChanged(int index);


    void resetFragmentIonTypes();


    void drawPeptideButtonReleased();


signals:


    void sendSequenceLine(int peptidetypeindex, QString sequence);


    void setHCON();


    void clearIonSelection();


};


#endif

cFragmentIonsListWidget.h
The implementation of a widget where types of fragment ions generated in theoretical spectra are sele...

cGlobalPreferences.h
The representation of a set of peptide sequence candidates.

cNeutralLossesListWidget.h
The implementation of a widget where types of neutral losses generated in theoretical spectra are sel...

cParameters.h
Definitions of program parameters.

cSummaryFormula.h
The representation of a summary formula.

cFragmentIonsListWidget
The widget for selection of fragment ion types.
Definition: cFragmentIonsListWidget.h:26

cGlobalPreferences
The class storing global preferences.
Definition: cGlobalPreferences.h:104

cNeutralLossesListWidget
The widget for selection of types of neutral losses.
Definition: cNeutralLossesListWidget.h:26

cParameters
The class storing parameters of the application.
Definition: cParameters.h:82

cParametersWidget
The class representing a widget for editing parameters of the application.
Definition: cParametersWidget.h:54

cParametersWidget::sendSequenceLine
void sendSequenceLine(int peptidetypeindex, QString sequence)
Send index of peptide type and searched sequence.

cParametersWidget::getParameters
cParameters & getParameters()
Get parameters.
Definition: cParametersWidget.cpp:1219

cParametersWidget::setAndRestoreParameters
void setAndRestoreParameters(cParameters &parameters)
Set and restore parameters.
Definition: cParametersWidget.cpp:1224

cParametersWidget::applyGlobalPreferences
void applyGlobalPreferences(cGlobalPreferences *globalpreferences)
Apply new global preferences.
Definition: cParametersWidget.cpp:1263

cParametersWidget::setHCON
void setHCON()
Set list of neutral losses to HCON.

cParametersWidget::~cParametersWidget
~cParametersWidget()
The destructor.
Definition: cParametersWidget.cpp:998

cParametersWidget::cParametersWidget
cParametersWidget(cGlobalPreferences *globalpreferences, QWidget *parent=(QWidget *) 0)
The constructor.
Definition: cParametersWidget.cpp:34

cParametersWidget::clearIonSelection
void clearIonSelection()
Clear the selection of ions.

cParametersWidget::closeEvent
void closeEvent(QCloseEvent *event)
Handle the window close event.
Definition: cParametersWidget.cpp:1239

cParametersWidget::setSequence
void setSequence(int peptidetypeindex, QString sequence)
Set peptide type and searched sequence.
Definition: cParametersWidget.cpp:1245

cParametersWidget::keyPressEvent
void keyPressEvent(QKeyEvent *event)
Handle a key press event.
Definition: cParametersWidget.cpp:1284

cParametersWidget::setTag
void setTag(int peptidetypeindex, QString tag)
Set peptide type and sequence tag.
Definition: cParametersWidget.cpp:1254

utilities.h
Auxiliary funtions and structures.

eModeType
eModeType
Running modes of the application.
Definition: utilities.h:92