<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
 <class>IsotopicClusterShaperDlg</class>
 <widget class="QDialog" name="IsotopicClusterShaperDlg">
  <property name="geometry">
   <rect>
    <x>0</x>
    <y>0</y>
    <width>939</width>
    <height>1127</height>
   </rect>
  </property>
  <property name="windowTitle">
   <string/>
  </property>
  <layout class="QVBoxLayout" name="verticalLayout_4">
   <item>
    <widget class="QTabWidget" name="tabWidget">
     <property name="whatsThis">
      <string>This windows allows one to compute, for each (m/z,i) pair in the corresponding edit wiget, to compute all the points needed to create a peak shape in the form of either a Gaussian curve or of a Lorentzian curve. Once all the peaks have been computed they are combined to create a full mass spectrum with as many peaks as there are values in the Data points (m/z,i) text edit widget.</string>
     </property>
     <property name="currentIndex">
      <number>0</number>
     </property>
     <widget class="QWidget" name="inputDataTab">
      <attribute name="title">
       <string>Input data</string>
      </attribute>
      <layout class="QVBoxLayout" name="verticalLayout_2">
       <item>
        <widget class="QSplitter" name="splitter">
         <property name="orientation">
          <enum>Qt::Orientation::Horizontal</enum>
         </property>
         <widget class="QGroupBox" name="dataPointsGroupBox">
          <property name="sizePolicy">
           <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <property name="title">
           <string>Data centroid points (format: m/z&lt;space&gt;i)</string>
          </property>
          <layout class="QGridLayout" name="gridLayout">
           <item row="1" column="0">
            <widget class="QPlainTextEdit" name="inputDataPointsPlainTextEdit">
             <property name="placeholderText">
              <string>Once the list of isotopic peaks has been edited in place or pasted, click the button above to validate the new text.</string>
             </property>
            </widget>
           </item>
           <item row="0" column="0">
            <widget class="QPushButton" name="importPushButton">
             <property name="toolTip">
              <string>To modify manually the peak centroid list
edit the text below and click onto &quot;Import from text&quot;</string>
             </property>
             <property name="text">
              <string>Import from text</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
         <widget class="QWidget" name="layoutWidget">
          <layout class="QVBoxLayout" name="verticalLayout">
           <item>
            <widget class="QScrollArea" name="scrollArea">
             <property name="widgetResizable">
              <bool>true</bool>
             </property>
             <widget class="QWidget" name="scrollAreaWidgetContents">
              <property name="geometry">
               <rect>
                <x>0</x>
                <y>0</y>
                <width>468</width>
                <height>948</height>
               </rect>
              </property>
              <layout class="QVBoxLayout" name="verticalLayout_8">
               <item>
                <widget class="QFrame" name="peakShaperConfigFrame">
                 <property name="frameShape">
                  <enum>QFrame::Shape::StyledPanel</enum>
                 </property>
                 <property name="frameShadow">
                  <enum>QFrame::Shadow::Raised</enum>
                 </property>
                </widget>
               </item>
               <item>
                <widget class="QGroupBox" name="chargeGroupBox">
                 <property name="sizePolicy">
                  <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
                   <horstretch>0</horstretch>
                   <verstretch>0</verstretch>
                  </sizepolicy>
                 </property>
                 <property name="title">
                  <string>Charge</string>
                 </property>
                 <layout class="QVBoxLayout" name="verticalLayout_6">
                  <item>
                   <widget class="QLabel" name="ionChargeLabel">
                    <property name="toolTip">
                     <string>The charge reaction must have been accounted for </string>
                    </property>
                    <property name="text">
                     <string>Shape the peak centroids as charged ions:
Note that the ionizing protons must have
been accounted for in the m/z value.</string>
                    </property>
                    <property name="buddy">
                     <cstring>ionChargeSpinBox</cstring>
                    </property>
                   </widget>
                  </item>
                  <item>
                   <widget class="QSpinBox" name="ionChargeSpinBox">
                    <property name="toolTip">
                     <string>Charge level for which the isotopic cluster
centroid peaks were calculated</string>
                    </property>
                    <property name="minimum">
                     <number>1</number>
                    </property>
                    <property name="maximum">
                     <number>10000</number>
                    </property>
                   </widget>
                  </item>
                 </layout>
                </widget>
               </item>
               <item>
                <widget class="QGroupBox" name="normalizationGroupBox">
                 <property name="sizePolicy">
                  <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
                   <horstretch>0</horstretch>
                   <verstretch>0</verstretch>
                  </sizepolicy>
                 </property>
                 <property name="title">
                  <string>Normalize spectrum intensities</string>
                 </property>
                 <property name="checkable">
                  <bool>true</bool>
                 </property>
                 <layout class="QVBoxLayout" name="verticalLayout_3">
                  <item>
                   <layout class="QHBoxLayout" name="horizontalLayout_3">
                    <item>
                     <widget class="QLabel" name="label_3">
                      <property name="text">
                       <string>The most intense peak will
have this intensity:</string>
                      </property>
                     </widget>
                    </item>
                    <item>
                     <widget class="QSpinBox" name="normalizingIntensitySpinBox">
                      <property name="minimum">
                       <number>1</number>
                      </property>
                      <property name="maximum">
                       <number>1000000000</number>
                      </property>
                     </widget>
                    </item>
                   </layout>
                  </item>
                 </layout>
                </widget>
               </item>
               <item>
                <widget class="QGroupBox" name="massSpectrumSynthesisGroupBox">
                 <property name="sizePolicy">
                  <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
                   <horstretch>0</horstretch>
                   <verstretch>0</verstretch>
                  </sizepolicy>
                 </property>
                 <property name="title">
                  <string>Mass spectrum synthesis</string>
                 </property>
                 <layout class="QVBoxLayout" name="verticalLayout_7">
                  <item>
                   <widget class="QLineEdit" name="massSpectrumTitleLineEdit">
                    <property name="placeholderText">
                     <string>Set the title of the mass spectrum</string>
                    </property>
                   </widget>
                  </item>
                  <item>
                   <widget class="QPushButton" name="colorSelectorPushButton">
                    <property name="toolTip">
                     <string>Select the color to be used for the trace plotting</string>
                    </property>
                    <property name="text">
                     <string>Trace color</string>
                    </property>
                    <property name="autoDefault">
                     <bool>false</bool>
                    </property>
                   </widget>
                  </item>
                 </layout>
                </widget>
               </item>
              </layout>
             </widget>
            </widget>
           </item>
          </layout>
         </widget>
        </widget>
       </item>
       <item>
        <widget class="QGroupBox" name="actionsGroupBox">
         <property name="sizePolicy">
          <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
           <horstretch>0</horstretch>
           <verstretch>0</verstretch>
          </sizepolicy>
         </property>
         <property name="title">
          <string>Actions</string>
         </property>
         <layout class="QGridLayout" name="gridLayout_4">
          <item row="0" column="2">
           <widget class="QPushButton" name="runPushButton">
            <property name="text">
             <string>&amp;Run</string>
            </property>
            <property name="autoDefault">
             <bool>false</bool>
            </property>
            <property name="default">
             <bool>false</bool>
            </property>
           </widget>
          </item>
          <item row="0" column="0">
           <widget class="QPushButton" name="outputFilePushButton">
            <property name="toolTip">
             <string>Choose a file in which to store the data for the plotting of the isotopic peak. </string>
            </property>
            <property name="text">
             <string>&amp;Output file...</string>
            </property>
            <property name="autoDefault">
             <bool>false</bool>
            </property>
           </widget>
          </item>
          <item row="0" column="1">
           <widget class="QPushButton" name="checkParametersPushButton">
            <property name="text">
             <string>&amp;Check parameters</string>
            </property>
           </widget>
          </item>
         </layout>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="messageLineEdit"/>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="logTab">
      <attribute name="title">
       <string>Log</string>
      </attribute>
      <layout class="QGridLayout" name="gridLayout_8">
       <item row="0" column="0">
        <widget class="QPlainTextEdit" name="logPlainTextEdit"/>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="resultsTab">
      <attribute name="title">
       <string>Results</string>
      </attribute>
      <layout class="QVBoxLayout" name="verticalLayout_5">
       <item>
        <widget class="QGroupBox" name="massSpectrumNameGroupBox2">
         <property name="sizePolicy">
          <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
           <horstretch>0</horstretch>
           <verstretch>0</verstretch>
          </sizepolicy>
         </property>
         <property name="title">
          <string>Mass spectrum name</string>
         </property>
         <layout class="QHBoxLayout" name="horizontalLayout_2">
          <item>
           <widget class="QLineEdit" name="massSpectrumNameResultsLineEdit"/>
          </item>
         </layout>
        </widget>
       </item>
       <item>
        <widget class="QPlainTextEdit" name="resultPlainTextEdit">
         <property name="acceptDrops">
          <bool>false</bool>
         </property>
         <property name="readOnly">
          <bool>true</bool>
         </property>
         <property name="textInteractionFlags">
          <set>Qt::TextInteractionFlag::TextSelectableByKeyboard|Qt::TextInteractionFlag::TextSelectableByMouse</set>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QGroupBox" name="groupBox">
         <property name="title">
          <string>Actions</string>
         </property>
         <layout class="QHBoxLayout" name="horizontalLayout">
          <item>
           <widget class="QPushButton" name="copyMassSpectrumToClipboardPushButton">
            <property name="text">
             <string>&amp;Copy mass spectrum to clipboard</string>
            </property>
            <property name="icon">
             <iconset resource="../../xpertmassgui_resources.qrc">
              <normaloff>:/gui/images/svg/profiled_peaks.svg</normaloff>:/gui/images/svg/profiled_peaks.svg</iconset>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QPushButton" name="displayMassSpectrumPushButton">
            <property name="text">
             <string>&amp;Display mass spectrum</string>
            </property>
            <property name="icon">
             <iconset resource="../../xpertmassgui_resources.qrc">
              <normaloff>:/gui/images/svg/profiled_peaks.svg</normaloff>:/gui/images/svg/profiled_peaks.svg</iconset>
            </property>
           </widget>
          </item>
         </layout>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="tab">
      <attribute name="title">
       <string>Help</string>
      </attribute>
      <layout class="QGridLayout" name="gridLayout_3">
       <item row="0" column="0">
        <widget class="QTextEdit" name="textEdit">
         <property name="html">
          <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;meta charset=&quot;utf-8&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
hr { height: 1px; border-width: 0; }
li.unchecked::marker { content: &quot;\2610&quot;; }
li.checked::marker { content: &quot;\2612&quot;; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Noto Sans'; font-size:9pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;This mass peak shaper feature helps create the Gaussian peak shape around a peak centroid.&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The Input data tab contains two different sides:&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The left hand side contains the list of peak centroids for which the Gaussian/Lorentzian shape must be created;&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The right hand side contains all the parameters that are needed to configure the way the shape has to be created.&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;A Gaussian shape is characterized by three main parameters:&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The peak position (the m/z value, in our case);&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The peak height (intensity, in our case);&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The peak width (full width at half maximum [FWHM], in our case).&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The peak position (x axis) is the m/z value of the peak centroid;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The peak height is the intensity of the peak centroid;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The peak width (FWHM). The smallest this value, the thinnest the peak. The FWHM of a peak relates to the resolving power (R) of a mass spectrometer: the greater R is, the smaller FWHM will be (a highly resolutive instrument gives very thin peaks).&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;In this window, the configuration logic is as follows:&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;If the user elicits to enter a resolving power value, then the program will compute automatically the FWHM on the basis of the m/z value of the most intense peak centroid. That value is updated in the corresponding spin box widget.&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;If the user elicits to enter a FWHM value, that value is going to be used irrespective of the resolving power value possibly displayed in the corresponding spin box widget.&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The program then needs to determine the proper m/z bin size to properly combine all the peak shapes that have been computed into a single mass spectrum. The m/z bin size is determined according to the following logic:&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;If the user does not activate the corresponding group box, the program will update the bin size automatically based on the following parameters:&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The m/z value of the most intense peak centroid;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The FWHM (either set manually or deduced using the set resolving power);&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;- The number of points requested for actually creating the peak shape (Points in the Peak shape group box).&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Instead, if the user activates the &amp;quot;Bin size&amp;quot; group box, either two possibilities are presented:&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;If the user checks the &amp;quot;Do not create bins&amp;quot; check box, then the integration of all the peak shapes into a single mass spectrum will be performed without binning.&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;If the user sets a bin size manually, then, that bin size will be used no matter how they have configured the resolving power or the FWHM settings.&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
         </property>
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       </item>
      </layout>
     </widget>
    </widget>
   </item>
  </layout>
 </widget>
 <tabstops>
  <tabstop>outputFilePushButton</tabstop>
  <tabstop>runPushButton</tabstop>
 </tabstops>
 <resources>
  <include location="../../xpertmassgui_resources.qrc"/>
 </resources>
 <connections/>
</ui>
