<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
 <class>toppicWindow</class>
 <widget class="QMainWindow" name="toppicWindow">
  <property name="geometry">
   <rect>
    <x>0</x>
    <y>0</y>
    <width>920</width>
    <height>700</height>
   </rect>
  </property>
  <property name="sizePolicy">
   <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
    <horstretch>100</horstretch>
    <verstretch>100</verstretch>
   </sizepolicy>
  </property>
  <property name="minimumSize">
   <size>
    <width>920</width>
    <height>700</height>
   </size>
  </property>
  <property name="maximumSize">
   <size>
    <width>920</width>
    <height>700</height>
   </size>
  </property>
  <property name="windowTitle">
   <string>TopPIC</string>
  </property>
  <property name="windowIcon">
   <iconset resource="icon.qrc">
    <normaloff>:/icon/toppic.ico</normaloff>:/icon/toppic.ico</iconset>
  </property>
  <widget class="QWidget" name="centralWidget">
   <widget class="QTextBrowser" name="outputTextBrowser">
    <property name="geometry">
     <rect>
      <x>20</x>
      <y>350</y>
      <width>881</width>
      <height>301</height>
     </rect>
    </property>
    <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;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Ubuntu'; font-size:11pt; 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;&lt;span style=&quot; font-family:'Cantarell';&quot;&gt;Click the Start button to process the spectrum file.&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
    </property>
   </widget>
   <widget class="QWidget" name="horizontalLayoutWidget_7">
    <property name="geometry">
     <rect>
      <x>20</x>
      <y>650</y>
      <width>881</width>
      <height>55</height>
     </rect>
    </property>
    <layout class="QHBoxLayout" name="horizontalLayout_7">
     <property name="spacing">
      <number>30</number>
     </property>
     <item>
      <widget class="QPushButton" name="exitButton">
       <property name="text">
        <string>Exit</string>
       </property>
      </widget>
     </item>
     <item>
      <widget class="QPushButton" name="clearButton">
       <property name="text">
        <string>Clear Input Files</string>
       </property>
      </widget>
     </item>
     <item>
      <widget class="QPushButton" name="defaultButton">
       <property name="text">
        <string>Default Parameters</string>
       </property>
      </widget>
     </item>
     <item>
      <widget class="QPushButton" name="outputButton">
       <property name="enabled">
        <bool>false</bool>
       </property>
       <property name="text">
        <string>Output Folder</string>
       </property>
       <property name="default">
        <bool>true</bool>
       </property>
      </widget>
     </item>
     <item>
      <widget class="QPushButton" name="startButton">
       <property name="enabled">
        <bool>true</bool>
       </property>
       <property name="acceptDrops">
        <bool>false</bool>
       </property>
       <property name="text">
        <string>Start</string>
       </property>
       <property name="checkable">
        <bool>false</bool>
       </property>
       <property name="autoDefault">
        <bool>true</bool>
       </property>
       <property name="default">
        <bool>true</bool>
       </property>
       <property name="flat">
        <bool>false</bool>
       </property>
      </widget>
     </item>
    </layout>
   </widget>
   <widget class="QTabWidget" name="tabWidget">
    <property name="geometry">
     <rect>
      <x>20</x>
      <y>10</y>
      <width>881</width>
      <height>321</height>
     </rect>
    </property>
    <property name="currentIndex">
     <number>2</number>
    </property>
    <widget class="QWidget" name="tab_4">
     <attribute name="title">
      <string>Files</string>
     </attribute>
     <widget class="QListWidget" name="listWidget">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>90</y>
        <width>851</width>
        <height>151</height>
       </rect>
      </property>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>10</y>
        <width>851</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout">
       <item>
        <widget class="QLabel" name="label">
         <property name="text">
          <string>Database file: </string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="databaseFileEdit">
         <property name="enabled">
          <bool>true</bool>
         </property>
         <property name="maximumSize">
          <size>
           <width>650</width>
           <height>16777215</height>
          </size>
         </property>
         <property name="readOnly">
          <bool>true</bool>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QPushButton" name="databaseFileButton">
         <property name="maximumSize">
          <size>
           <width>85</width>
           <height>16777215</height>
          </size>
         </property>
         <property name="text">
          <string>Select</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_2">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>50</y>
        <width>351</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_2">
       <item>
        <widget class="QLabel" name="label_2">
         <property name="text">
          <string>Spectrum files: </string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QPushButton" name="addButton">
         <property name="text">
          <string>Add</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QPushButton" name="delButton">
         <property name="text">
          <string>Remove</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_6">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>250</y>
        <width>851</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_6">
       <property name="spacing">
        <number>30</number>
       </property>
       <item>
        <widget class="QLabel" name="label_7">
         <property name="text">
          <string>Combined output filename: </string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="combinedOutputEdit">
         <property name="enabled">
          <bool>true</bool>
         </property>
         <property name="maximumSize">
          <size>
           <width>400000</width>
           <height>300</height>
          </size>
         </property>
         <property name="text">
          <string/>
         </property>
         <property name="readOnly">
          <bool>false</bool>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
    </widget>
    <widget class="QWidget" name="tab">
     <attribute name="title">
      <string>Basic Parameters</string>
     </attribute>
     <widget class="QWidget" name="horizontalLayoutWidget_4">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>10</y>
        <width>861</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_4">
       <item>
        <widget class="QLabel" name="label_4">
         <property name="text">
          <string>Fixed modifications:</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QComboBox" name="fixedModComboBox">
         <item>
          <property name="text">
           <string>NONE</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>C57</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>C58</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>A fixed modification file</string>
          </property>
         </item>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="fixedModFileEdit">
         <property name="enabled">
          <bool>false</bool>
         </property>
         <property name="readOnly">
          <bool>true</bool>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QPushButton" name="fixedModFileButton">
         <property name="enabled">
          <bool>false</bool>
         </property>
         <property name="maximumSize">
          <size>
           <width>85</width>
           <height>16777215</height>
          </size>
         </property>
         <property name="text">
          <string>File</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_21">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>60</y>
        <width>581</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_21">
       <item>
        <widget class="QCheckBox" name="decoyCheckBox">
         <property name="text">
          <string>Decoy database</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QCheckBox" name="topfdFeatureCheckBox">
         <property name="text">
          <string>Missing MS1 feature file</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_11">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>230</y>
        <width>301</width>
        <height>31</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_11">
       <item>
        <widget class="QLabel" name="label_9">
         <property name="text">
          <string>Mass error tolerance (PPM):</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="errorToleranceEdit">
         <property name="text">
          <string>15</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_16">
      <property name="geometry">
       <rect>
        <x>590</x>
        <y>60</y>
        <width>284</width>
        <height>31</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_16">
       <item>
        <widget class="QCheckBox" name="lookupTableCheckBox">
         <property name="text">
          <string>Lookup table for E-value computation</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QGroupBox" name="groupBox_3">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>110</y>
        <width>861</width>
        <height>111</height>
       </rect>
      </property>
      <property name="title">
       <string>Cutoff settings</string>
      </property>
      <widget class="QLabel" name="label_11">
       <property name="geometry">
        <rect>
         <x>20</x>
         <y>20</y>
         <width>151</width>
         <height>41</height>
        </rect>
       </property>
       <property name="text">
        <string>Spectrum level:</string>
       </property>
      </widget>
      <widget class="QGroupBox" name="groupBox">
       <property name="geometry">
        <rect>
         <x>170</x>
         <y>10</y>
         <width>191</width>
         <height>91</height>
        </rect>
       </property>
       <property name="title">
        <string/>
       </property>
       <widget class="QWidget" name="verticalLayoutWidget">
        <property name="geometry">
         <rect>
          <x>10</x>
          <y>10</y>
          <width>171</width>
          <height>80</height>
         </rect>
        </property>
        <layout class="QVBoxLayout" name="verticalLayout">
         <item>
          <widget class="QComboBox" name="cutoffSpectralTypeComboBox">
           <property name="editable">
            <bool>false</bool>
           </property>
           <item>
            <property name="text">
             <string>EVALUE</string>
            </property>
           </item>
           <item>
            <property name="text">
             <string>FDR</string>
            </property>
           </item>
          </widget>
         </item>
         <item>
          <widget class="QLineEdit" name="cutoffSpectralValueEdit">
           <property name="text">
            <string>0.01</string>
           </property>
           <property name="readOnly">
            <bool>false</bool>
           </property>
          </widget>
         </item>
        </layout>
       </widget>
      </widget>
      <widget class="QLabel" name="label_13">
       <property name="geometry">
        <rect>
         <x>480</x>
         <y>20</y>
         <width>171</width>
         <height>31</height>
        </rect>
       </property>
       <property name="text">
        <string>Proteoform level:</string>
       </property>
      </widget>
      <widget class="QGroupBox" name="groupBox_5">
       <property name="geometry">
        <rect>
         <x>650</x>
         <y>10</y>
         <width>191</width>
         <height>91</height>
        </rect>
       </property>
       <property name="title">
        <string/>
       </property>
       <widget class="QWidget" name="layoutWidget">
        <property name="geometry">
         <rect>
          <x>10</x>
          <y>10</y>
          <width>171</width>
          <height>81</height>
         </rect>
        </property>
        <layout class="QVBoxLayout" name="verticalLayout_2">
         <item>
          <widget class="QComboBox" name="cutoffProteoformTypeComboBox">
           <property name="editable">
            <bool>false</bool>
           </property>
           <item>
            <property name="text">
             <string>EVALUE</string>
            </property>
           </item>
           <item>
            <property name="text">
             <string>FDR</string>
            </property>
           </item>
          </widget>
         </item>
         <item>
          <widget class="QLineEdit" name="cutoffProteoformValueEdit">
           <property name="text">
            <string>0.01</string>
           </property>
           <property name="readOnly">
            <bool>false</bool>
           </property>
          </widget>
         </item>
        </layout>
       </widget>
      </widget>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_13">
      <property name="geometry">
       <rect>
        <x>540</x>
        <y>230</y>
        <width>331</width>
        <height>31</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_13">
       <item>
        <widget class="QLabel" name="label_14">
         <property name="text">
          <string>PrSM cluster error tolerance (Da):</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="formErrorToleranceEdit">
         <property name="text">
          <string>1.2</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
    </widget>
    <widget class="QWidget" name="tab_2">
     <attribute name="title">
      <string>Advanced Parameters</string>
     </attribute>
     <widget class="QWidget" name="horizontalLayoutWidget_3">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>50</y>
        <width>341</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_3">
       <property name="sizeConstraint">
        <enum>QLayout::SetDefaultConstraint</enum>
       </property>
       <item>
        <widget class="QLabel" name="label_3">
         <property name="text">
          <string>Activation:</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QComboBox" name="activationComboBox">
         <property name="maximumSize">
          <size>
           <width>110</width>
           <height>16777215</height>
          </size>
         </property>
         <item>
          <property name="text">
           <string>FILE</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>CID</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>HCD</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>ETD</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>UVPD</string>
          </property>
         </item>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_22">
      <property name="geometry">
       <rect>
        <x>500</x>
        <y>140</y>
        <width>341</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_22">
       <item>
        <widget class="QLabel" name="label_23">
         <property name="text">
          <string>Thread number:</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="threadNumberEdit">
         <property name="maximumSize">
          <size>
           <width>110</width>
           <height>16777215</height>
          </size>
         </property>
         <property name="text">
          <string>1</string>
         </property>
         <property name="readOnly">
          <bool>false</bool>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_15">
      <property name="geometry">
       <rect>
        <x>500</x>
        <y>100</y>
        <width>341</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_15">
       <item>
        <widget class="QLabel" name="label_16">
         <property name="text">
          <string>Nummber of combined spectra:</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="numCombinedEdit">
         <property name="maximumSize">
          <size>
           <width>110</width>
           <height>16777215</height>
          </size>
         </property>
         <property name="text">
          <string>1</string>
         </property>
         <property name="readOnly">
          <bool>false</bool>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_10">
      <property name="geometry">
       <rect>
        <x>500</x>
        <y>10</y>
        <width>341</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_10">
       <item>
        <widget class="QLabel" name="label_8">
         <property name="text">
          <string>Maximum mass shift (Da):</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="maxModEdit">
         <property name="maximumSize">
          <size>
           <width>110</width>
           <height>16777215</height>
          </size>
         </property>
         <property name="text">
          <string>500</string>
         </property>
         <property name="readOnly">
          <bool>false</bool>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_9">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>10</y>
        <width>341</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_9">
       <item>
        <widget class="QLabel" name="label_12">
         <property name="text">
          <string>Maximum number of mass shifts:</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QComboBox" name="numModComboBox">
         <property name="editable">
          <bool>false</bool>
         </property>
         <property name="currentIndex">
          <number>1</number>
         </property>
         <item>
          <property name="text">
           <string>0</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>1</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>2</string>
          </property>
         </item>
        </widget>
       </item>
      </layout>
     </widget>
     <widget class="QGroupBox" name="groupBox_2">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>90</y>
        <width>341</width>
        <height>91</height>
       </rect>
      </property>
      <property name="title">
       <string>N-terminal forms</string>
      </property>
      <widget class="QWidget" name="gridLayoutWidget">
       <property name="geometry">
        <rect>
         <x>9</x>
         <y>17</y>
         <width>321</width>
         <height>70</height>
        </rect>
       </property>
       <layout class="QGridLayout" name="gridLayout">
        <item row="0" column="0">
         <widget class="QCheckBox" name="NONECheckBox">
          <property name="enabled">
           <bool>true</bool>
          </property>
          <property name="text">
           <string>NONE</string>
          </property>
          <property name="checked">
           <bool>true</bool>
          </property>
          <property name="autoRepeat">
           <bool>false</bool>
          </property>
         </widget>
        </item>
        <item row="1" column="0">
         <widget class="QCheckBox" name="NMECheckBox">
          <property name="text">
           <string>NME</string>
          </property>
          <property name="checked">
           <bool>true</bool>
          </property>
         </widget>
        </item>
        <item row="0" column="1">
         <widget class="QCheckBox" name="NMEACCheckBox">
          <property name="text">
           <string>NME_ACETYLATION</string>
          </property>
          <property name="checked">
           <bool>true</bool>
          </property>
         </widget>
        </item>
        <item row="1" column="1">
         <widget class="QCheckBox" name="MACCheckBox">
          <property name="text">
           <string>M_ACETYLATION</string>
          </property>
          <property name="checked">
           <bool>true</bool>
          </property>
         </widget>
        </item>
       </layout>
      </widget>
     </widget>
     <widget class="QGroupBox" name="groupBox_4">
      <property name="geometry">
       <rect>
        <x>10</x>
        <y>190</y>
        <width>851</width>
        <height>91</height>
       </rect>
      </property>
      <property name="title">
       <string>Modification localization    </string>
      </property>
      <widget class="QWidget" name="horizontalLayoutWidget_17">
       <property name="geometry">
        <rect>
         <x>10</x>
         <y>20</y>
         <width>831</width>
         <height>33</height>
        </rect>
       </property>
       <layout class="QHBoxLayout" name="horizontalLayout_17">
        <item>
         <widget class="QLabel" name="label_18">
          <property name="text">
           <string>Modification file for localization:</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QLineEdit" name="modFileEdit">
          <property name="enabled">
           <bool>true</bool>
          </property>
          <property name="readOnly">
           <bool>true</bool>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QPushButton" name="modFileButton">
          <property name="enabled">
           <bool>true</bool>
          </property>
          <property name="text">
           <string>File</string>
          </property>
         </widget>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="horizontalLayoutWidget_18">
       <property name="geometry">
        <rect>
         <x>10</x>
         <y>60</y>
         <width>341</width>
         <height>33</height>
        </rect>
       </property>
       <layout class="QHBoxLayout" name="horizontalLayout_18">
        <item>
         <widget class="QLabel" name="label_19">
          <property name="text">
           <string>MIScore threshold:</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QLineEdit" name="miscoreThresholdEdit">
          <property name="text">
           <string>0.45</string>
          </property>
          <property name="readOnly">
           <bool>false</bool>
          </property>
         </widget>
        </item>
       </layout>
      </widget>
     </widget>
     <widget class="QWidget" name="horizontalLayoutWidget_12">
      <property name="geometry">
       <rect>
        <x>500</x>
        <y>50</y>
        <width>341</width>
        <height>33</height>
       </rect>
      </property>
      <layout class="QHBoxLayout" name="horizontalLayout_12">
       <item>
        <widget class="QLabel" name="label_10">
         <property name="text">
          <string>Minimum mass shift (Da):</string>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QLineEdit" name="minModEdit">
         <property name="maximumSize">
          <size>
           <width>110</width>
           <height>16777215</height>
          </size>
         </property>
         <property name="text">
          <string>-500</string>
         </property>
         <property name="readOnly">
          <bool>false</bool>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
    </widget>
   </widget>
   <zorder>tabWidget</zorder>
   <zorder>outputTextBrowser</zorder>
   <zorder>horizontalLayoutWidget_7</zorder>
  </widget>
 </widget>
 <layoutdefault spacing="6" margin="11"/>
 <resources>
  <include location="icon.qrc"/>
 </resources>
 <connections/>
</ui>
