WIP: building tandem param form

src/gui/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui

@@ -116,7 +116,7 @@
                <item>
                 <layout class="QGridLayout" name="gridLayout_2">
                  <item row="0" column="1">
-                  <widget class="QComboBox" name="comboBox">
+                  <widget class="QComboBox" name="parent_ion_window_unit_combo_box">
                    <item>
                     <property name="text">
                      <string>dalton</string>
@@ -130,13 +130,16 @@
                   </widget>
                  </item>
                  <item row="0" column="2">
-                  <widget class="QPushButton" name="pushButton">
+                  <widget class="QPushButton" name="parent_ion_window_unit_combo_push_button">
                    <property name="sizePolicy">
                     <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
                      <horstretch>0</horstretch>
                      <verstretch>0</verstretch>
                     </sizepolicy>
                    </property>
+                   <property name="accessibleName">
+                    <string notr="true">parent_ion_window_unit</string>
+                   </property>
                    <property name="text">
                     <string>?</string>
                    </property>
@@ -150,7 +153,7 @@
                   </widget>
                  </item>
                  <item row="2" column="2">
-                  <widget class="QPushButton" name="pushButton_3">
+                  <widget class="QPushButton" name="parent_ion_upper_window_push_button">
                    <property name="sizePolicy">
                     <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
                      <horstretch>0</horstretch>
@@ -163,7 +166,7 @@
                   </widget>
                  </item>
                  <item row="1" column="2">
-                  <widget class="QPushButton" name="pushButton_2">
+                  <widget class="QPushButton" name="parent_ion_lower_window_push_button">
                    <property name="sizePolicy">
                     <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
                      <horstretch>0</horstretch>
@@ -183,7 +186,7 @@
                   </widget>
                  </item>
                  <item row="3" column="2">
-                  <widget class="QPushButton" name="pushButton_4">
+                  <widget class="QPushButton" name="anticipate_carbon_push_button">
                    <property name="sizePolicy">
                     <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
                      <horstretch>0</horstretch>
@@ -196,7 +199,7 @@
                   </widget>
                  </item>
                  <item row="3" column="1">
-                  <widget class="QComboBox" name="comboBox_2">
+                  <widget class="QComboBox" name="anticipate_carbon_combo_box">
                    <item>
                     <property name="text">
                      <string>yes</string>
@@ -224,10 +227,10 @@
                   </widget>
                  </item>
                  <item row="1" column="1">
-                  <widget class="QLineEdit" name="lineEdit"/>
+                  <widget class="QLineEdit" name="parent_ion_lower_window_edit"/>
                  </item>
                  <item row="2" column="1">
-                  <widget class="QLineEdit" name="lineEdit_2"/>
+                  <widget class="QLineEdit" name="parent_ion_upper_window_edit"/>
                  </item>
                 </layout>
                </item>
@@ -386,8 +389,8 @@
    <slot>reject()</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>675</x>
-     <y>527</y>
+     <x>777</x>
+     <y>498</y>
     </hint>
     <hint type="destinationlabel">
      <x>881</x>
@@ -402,8 +405,8 @@
    <slot>accept()</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>764</x>
-     <y>518</y>
+     <x>863</x>
+     <y>498</y>
     </hint>
     <hint type="destinationlabel">
      <x>879</x>
@@ -411,12 +414,76 @@
     </hint>
    </hints>
   </connection>
+  <connection>
+   <sender>parent_ion_window_unit_combo_push_button</sender>
+   <signal>clicked()</signal>
+   <receiver>EditTandemPresetView</receiver>
+   <slot>doHelp()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>556</x>
+     <y>227</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>949</x>
+     <y>153</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>parent_ion_lower_window_push_button</sender>
+   <signal>clicked()</signal>
+   <receiver>EditTandemPresetView</receiver>
+   <slot>doHelp()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>573</x>
+     <y>262</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>936</x>
+     <y>272</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>parent_ion_upper_window_push_button</sender>
+   <signal>clicked()</signal>
+   <receiver>EditTandemPresetView</receiver>
+   <slot>doHelp()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>564</x>
+     <y>296</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>952</x>
+     <y>297</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>anticipate_carbon_push_button</sender>
+   <signal>clicked()</signal>
+   <receiver>EditTandemPresetView</receiver>
+   <slot>doHelp()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>566</x>
+     <y>331</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>994</x>
+     <y>332</y>
+    </hint>
+   </hints>
+  </connection>
  </connections>
  <slots>
   <slot>doNotValidHide(bool)</slot>
   <slot>doNotCheckedHide(bool)</slot>
   <slot>doNotGroupedHide(bool)</slot>
-  <slot>doActionBrowse()</slot>
+  <slot>doHelp()</slot>
   <slot>doActionReplace()</slot>
   <slot>reject()</slot>
   <slot>accept()</slot>

src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp

@@ -54,4 +54,55 @@ EditTandemPresetDialog::EditTandemPresetDialog(QWidget * parent):
 EditTandemPresetDialog::~EditTandemPresetDialog()
 {
     delete ui;
+    if (_p_tandem_preset_file != nullptr) {
+        delete _p_tandem_preset_file;
+    }
+}
+
+void EditTandemPresetDialog::setTandemParametersFiles(const TandemParametersFile & tandem_preset_file) {
+    _p_tandem_preset_file = new TandemParametersFile( tandem_preset_file);
+
+    _tandem_params = _p_tandem_preset_file->getTandemParameters();
+
+    populate();
+}
+
+void EditTandemPresetDialog::doHelp() {
+    QObject *senderObj = sender();
+    QString senderObjName = senderObj->objectName();
+    qDebug() << "EditTandemPresetDialog::doHelp begin " << senderObjName;
+    if(senderObjName == "parent_ion_window_unit_push_button")
+    {
+        //Implement Button A Specific
+    }
+    qDebug() << "EditTandemPresetDialog::doHelp end " << senderObjName;
+}
+
+void EditTandemPresetDialog::readUi() {
+    _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error units", ui->parent_ion_window_unit_combo_box->itemData(ui->parent_ion_window_unit_combo_box->currentIndex()).toString());
+
+    _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error minus", ui->parent_ion_lower_window_edit->text());
+
+    _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error plus", ui->parent_ion_upper_window_edit->text());
+
+    _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass isotope error", ui->anticipate_carbon_combo_box->itemData(ui->anticipate_carbon_combo_box->currentIndex()).toString());
+}
+
+void EditTandemPresetDialog::populate() {
+    /*
+     * <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
+     * */
+    int index = ui->parent_ion_window_unit_combo_box->findText(_tandem_params.getValue("spectrum, parent monoisotopic mass error units"));
+    if ( index != -1 ) { // -1 for not found
+        ui->parent_ion_window_unit_combo_box->setCurrentIndex(index);
+    }
+    //<note type="input" label="spectrum, parent monoisotopic mass error minus">10</note>
+    ui->parent_ion_lower_window_edit->setText(_tandem_params.getValue("spectrum, parent monoisotopic mass error minus"));
+    //<note type="input" label="spectrum, parent monoisotopic mass error plus">10</note>
+    ui->parent_ion_upper_window_edit->setText(_tandem_params.getValue("spectrum, parent monoisotopic mass error plus"));
+    //<note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
+    index = ui->anticipate_carbon_combo_box->findText(_tandem_params.getValue("spectrum, parent monoisotopic mass isotope error"));
+    if ( index != -1 ) { // -1 for not found
+        ui->anticipate_carbon_combo_box->setCurrentIndex(index);
+    }
 }

src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h

@@ -30,6 +30,7 @@
 #ifndef EDITTANDEMPRESETDIALOG_H
 #define EDITTANDEMPRESETDIALOG_H
 
+#include "../../files/tandemparametersfile.h"
 #include<QDialog>
 
 namespace Ui {
@@ -43,10 +44,19 @@ class EditTandemPresetDialog: public QDialog
 public:
     explicit EditTandemPresetDialog(QWidget * parent);
     ~EditTandemPresetDialog();
+    
+    void setTandemParametersFiles(const TandemParametersFile & tandem_preset_file);
 
+public slots:
+    void doHelp ();
+private:
+    void populate();
+    void readUi();
 
 private:
     Ui::EditTandemPresetView *ui;
+    TandemParametersFile * _p_tandem_preset_file = nullptr;
+    TandemParameters _tandem_params;
 };
 
 #endif // EDITTANDEMPRESETDIALOG_H

src/gui/tandem_run_dialog/tandemrundialog.cpp

@@ -148,6 +148,7 @@ void TandemRunDialog::editPresets() {
     if (_p_preset_dialog == nullptr) {
         _p_preset_dialog = new EditTandemPresetDialog(this);
     }
+    _p_preset_dialog->setTandemParametersFiles(TandemParametersFile(ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QString>()));
     _p_preset_dialog->show();
 
 }

src/resources/model/QExactive_analysis_FDR_nosemi.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<bioml label="example api document">
+  <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
+  <note type="input" label="spectrum, parent monoisotopic mass error minus">10</note>
+  <note type="input" label="spectrum, parent monoisotopic mass error plus">10</note>
+  <note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
+  <note type="input" label="spectrum, maximum parent charge">4</note>
+  <note type="input" label="spectrum, fragment mass type">monoisotopic</note>
+  <note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
+  <note type="input" label="spectrum, fragment monoisotopic mass error">0.02</note>
+  <note type="input" label="spectrum, use neutral loss window">yes</note>
+  <note type="input" label="spectrum, neutral loss mass">18.01057</note>
+  <note type="input" label="spectrum, neutral loss window">0.02</note>
+  <note type="input" label="spectrum, use noise suppression">yes</note>
+  <note type="input" label="spectrum, dynamic range">100.0</note>
+  <note type="input" label="spectrum, total peaks">100</note>
+  <note type="input" label="spectrum, minimum peaks">15</note>
+  <note type="input" label="spectrum, minimum fragment mz">150.0</note>
+  <note type="input" label="spectrum, minimum parent m+h">500.0</note>
+  <note type="input" label="spectrum, sequence batch size">1000</note>
+  <note type="input" label="spectrum, use contrast angle">no</note>
+  <note type="input" label="spectrum, threads">1</note>
+  <note type="input" label="protein, cleavage site">[RK]|{P}</note>
+  <note type="input" label="protein, cleavage semi">no</note>
+  <note type="input" label="protein, cleavage C-terminal mass change">+17.00305</note>
+  <note type="input" label="protein, cleavage N-terminal mass change">+1.00794</note>
+  <note type="input" label="protein, C-terminal residue modification mass">0.0</note>
+  <note type="input" label="protein, N-terminal residue modification mass">0.0</note>
+  <note type="input" label="protein, quick acetyl">yes</note>
+  <note type="input" label="protein, quick pyrolidone">yes</note>
+  <note type="input" label="protein, stP bias">yes</note>
+  <note type="input" label="protein, modified residue mass file"></note>
+  <note type="input" label="residue, modification mass">57.02146@C</note>
+  <note type="input" label="residue, modification mass 1"></note>
+  <note type="input" label="residue, modification mass 2"></note>
+  <note type="input" label="residue, potential modification mass">15.99491@M</note>
+  <note type="input" label="residue, potential modification mass 1"></note>
+  <note type="input" label="residue, potential modification mass 2"></note>
+  <note type="input" label="residue, potential modification motif"></note>
+  <note type="input" label="residue, potential modification motif 1"></note>
+  <note type="input" label="residue, potential modification motif 2"></note>
+  <note type="input" label="scoring, minimum ion count">4</note>
+  <note type="input" label="scoring, maximum missed cleavage sites">1</note>
+  <note type="input" label="scoring, cyclic permutation">yes</note>
+  <note type="input" label="scoring, include reverse">yes</note>
+  <note type="input" label="scoring, y ions">yes</note>
+  <note type="input" label="scoring, b ions">yes</note>
+  <note type="input" label="scoring, c ions">no</note>
+  <note type="input" label="scoring, z ions">no</note>
+  <note type="input" label="scoring, a ions">no</note>
+  <note type="input" label="scoring, x ions">no</note>
+  <note type="input" label="refine">yes</note>
+  <note type="input" label="refine, maximum valid expectation value">0.01</note>
+  <note type="input" label="refine, potential N-terminus modifications">+42.01056@[</note>
+  <note type="input" label="refine, potential C-terminus modifications"></note>
+  <note type="input" label="refine, modification mass">57.02146@C</note>
+  <note type="input" label="refine, modification mass 1"></note>
+  <note type="input" label="refine, modification mass 2"></note>
+  <note type="input" label="refine, potential modification mass">15.99491@M</note>
+  <note type="input" label="refine, potential modification mass 1"></note>
+  <note type="input" label="refine, potential modification mass 2"></note>
+  <note type="input" label="refine, potential modification motif"></note>
+  <note type="input" label="refine, potential modification motif 1"></note>
+  <note type="input" label="refine, potential modification motif 2"></note>
+  <note type="input" label="refine, use potential modifications for full refinement">yes</note>
+  <note type="input" label="refine, cleavage semi">no</note>
+  <note type="input" label="refine, unanticipated cleavage">no</note>
+  <note type="input" label="refine, spectrum synthesis">yes</note>
+  <note type="input" label="refine, point mutations">no</note>
+  <note type="input" label="output, maximum valid expectation value">0.05</note>
+  <note type="input" label="output, maximum valid protein expectation value">0.05</note>
+  <note type="input" label="output, results">valid</note>
+  <note type="input" label="output, sort results by">spectrum</note>
+  <note type="input" label="output, proteins">yes</note>
+  <note type="input" label="output, sequences">yes</note>
+  <note type="input" label="output, one sequence copy">yes</note>
+  <note type="input" label="output, spectra">yes</note>
+  <note type="input" label="output, parameters">yes</note>
+  <note type="input" label="output, performance">yes</note>
+  <note type="input" label="output, histograms">yes</note>
+  <note type="input" label="output, histogram column width">30</note>
+  <note type="input" label="output, path hashing">no</note>
+  <note type="input" label="output, xsl path">tandem-style.xsl</note>
+  <note type="input" label="output, mzid">no</note>
+</bioml>
\ No newline at end of file

src/xtpcpp.qrc

@@ -89,6 +89,7 @@
         <file>resources/html_doc/syi.html</file>
         <file>resources/html_doc/szi.html</file>
         <file>resources/html_doc/uml_index.html</file>
+        <file>resources/model/QExactive_analysis_FDR_nosemi.xml</file>
     </qresource>
     <qresource prefix="/xtpcpp_xpip">
         <file>resources/xtandempipeline_xpip.svg</file>