mainwindow.ui

<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
 <class>MainWindow</class>
 <widget class="QMainWindow" name="MainWindow">
  <property name="geometry">
   <rect>
    <x>0</x>
    <y>0</y>
    <width>1024</width>
    <height>700</height>
   </rect>
  </property>
  <property name="minimumSize">
   <size>
    <width>1024</width>
    <height>700</height>
   </size>
  </property>
  <property name="maximumSize">
   <size>
    <width>16777215</width>
    <height>900</height>
   </size>
  </property>
  <property name="windowTitle">
   <string>MAPster</string>
  </property>
  <widget class="QWidget" name="centralWidget">
   <layout class="QHBoxLayout" name="horizontalLayout">
    <item>
     <widget class="QTabWidget" name="tabs">
      <property name="enabled">
       <bool>true</bool>
      </property>
      <property name="font">
       <font>
        <weight>50</weight>
        <bold>false</bold>
       </font>
      </property>
      <property name="autoFillBackground">
       <bool>false</bool>
      </property>
      <property name="tabPosition">
       <enum>QTabWidget::North</enum>
      </property>
      <property name="tabShape">
       <enum>QTabWidget::Rounded</enum>
      </property>
      <property name="currentIndex">
       <number>0</number>
      </property>
      <property name="iconSize">
       <size>
        <width>20</width>
        <height>20</height>
       </size>
      </property>
      <property name="elideMode">
       <enum>Qt::ElideMiddle</enum>
      </property>
      <property name="usesScrollButtons">
       <bool>false</bool>
      </property>
      <property name="documentMode">
       <bool>false</bool>
      </property>
      <property name="tabsClosable">
       <bool>false</bool>
      </property>
      <property name="movable">
       <bool>false</bool>
      </property>
      <property name="tabBarAutoHide">
       <bool>false</bool>
      </property>
      <widget class="QWidget" name="main_tab">
       <attribute name="title">
        <string>Main</string>
       </attribute>
       <layout class="QVBoxLayout" name="verticalLayout">
        <item>
         <layout class="QVBoxLayout" name="verticalLayout_3">
          <property name="spacing">
           <number>1</number>
          </property>
          <item>
           <widget class="QLabel" name="selected_files1_label">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>13</height>
             </size>
            </property>
            <property name="text">
             <string>Paired Reads [-1]</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="VListWidget" name="selected_files_list1">
            <property name="alternatingRowColors">
             <bool>true</bool>
            </property>
            <property name="selectionMode">
             <enum>QAbstractItemView::MultiSelection</enum>
            </property>
            <property name="isWrapping" stdset="0">
             <bool>true</bool>
            </property>
            <property name="spacing">
             <number>2</number>
            </property>
            <property name="uniformItemSizes">
             <bool>true</bool>
            </property>
            <property name="wordWrap">
             <bool>true</bool>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="selected_files2_label">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>13</height>
             </size>
            </property>
            <property name="text">
             <string>Paired Reads [-2]</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="VListWidget" name="selected_files_list2">
            <property name="alternatingRowColors">
             <bool>true</bool>
            </property>
            <property name="selectionMode">
             <enum>QAbstractItemView::MultiSelection</enum>
            </property>
            <property name="isWrapping" stdset="0">
             <bool>true</bool>
            </property>
            <property name="spacing">
             <number>2</number>
            </property>
            <property name="uniformItemSizes">
             <bool>true</bool>
            </property>
            <property name="wordWrap">
             <bool>true</bool>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_14">
          <item>
           <widget class="QGroupBox" name="main_parameters_group">
            <property name="minimumSize">
             <size>
              <width>0</width>
              <height>200</height>
             </size>
            </property>
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>200</height>
             </size>
            </property>
            <property name="title">
             <string>Required Parameters</string>
            </property>
            <layout class="QGridLayout" name="gridLayout">
             <property name="leftMargin">
              <number>8</number>
             </property>
             <property name="topMargin">
              <number>2</number>
             </property>
             <property name="rightMargin">
              <number>8</number>
             </property>
             <property name="bottomMargin">
              <number>0</number>
             </property>
             <property name="horizontalSpacing">
              <number>-1</number>
             </property>
             <property name="verticalSpacing">
              <number>0</number>
             </property>
             <item row="0" column="2">
              <layout class="QHBoxLayout" name="pairwise_layout">
               <property name="sizeConstraint">
                <enum>QLayout::SetFixedSize</enum>
               </property>
               <item>
                <widget class="QGroupBox" name="pairwise_group">
                 <property name="enabled">
                  <bool>true</bool>
                 </property>
                 <property name="title">
                  <string/>
                 </property>
                 <property name="flat">
                  <bool>true</bool>
                 </property>
                 <property name="checkable">
                  <bool>false</bool>
                 </property>
                 <layout class="QHBoxLayout" name="horizontalLayout_3">
                  <property name="sizeConstraint">
                   <enum>QLayout::SetFixedSize</enum>
                  </property>
                  <property name="leftMargin">
                   <number>0</number>
                  </property>
                  <property name="topMargin">
                   <number>0</number>
                  </property>
                  <property name="rightMargin">
                   <number>0</number>
                  </property>
                  <property name="bottomMargin">
                   <number>0</number>
                  </property>
                  <item>
                   <widget class="QRadioButton" name="pairwise_on">
                    <property name="minimumSize">
                     <size>
                      <width>100</width>
                      <height>0</height>
                     </size>
                    </property>
                    <property name="text">
                     <string>On</string>
                    </property>
                    <property name="checked">
                     <bool>true</bool>
                    </property>
                   </widget>
                  </item>
                  <item>
                   <spacer name="horizontalSpacer_2">
                    <property name="orientation">
                     <enum>Qt::Horizontal</enum>
                    </property>
                    <property name="sizeHint" stdset="0">
                     <size>
                      <width>40</width>
                      <height>20</height>
                     </size>
                    </property>
                   </spacer>
                  </item>
                  <item>
                   <widget class="QRadioButton" name="pairwise_off">
                    <property name="minimumSize">
                     <size>
                      <width>100</width>
                      <height>0</height>
                     </size>
                    </property>
                    <property name="text">
                     <string>Off</string>
                    </property>
                    <property name="checked">
                     <bool>false</bool>
                    </property>
                   </widget>
                  </item>
                 </layout>
                </widget>
               </item>
              </layout>
             </item>
             <item row="1" column="0">
              <widget class="QLabel" name="genome_label">
               <property name="minimumSize">
                <size>
                 <width>100</width>
                 <height>20</height>
                </size>
               </property>
               <property name="maximumSize">
                <size>
                 <width>150</width>
                 <height>20</height>
                </size>
               </property>
               <property name="text">
                <string>Genome [-x]</string>
               </property>
               <property name="alignment">
                <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
               </property>
              </widget>
             </item>
             <item row="1" column="2">
              <widget class="QComboBox" name="genome_box">
               <property name="toolTip">
                <string/>
               </property>
              </widget>
             </item>
             <item row="2" column="0">
              <widget class="QLabel" name="threads_label">
               <property name="maximumSize">
                <size>
                 <width>150</width>
                 <height>20</height>
                </size>
               </property>
               <property name="text">
                <string>Threads [-p]</string>
               </property>
               <property name="alignment">
                <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
               </property>
              </widget>
             </item>
             <item row="0" column="0">
              <widget class="QLabel" name="pairwise_label">
               <property name="minimumSize">
                <size>
                 <width>100</width>
                 <height>20</height>
                </size>
               </property>
               <property name="maximumSize">
                <size>
                 <width>150</width>
                 <height>20</height>
                </size>
               </property>
               <property name="text">
                <string>Pairwise</string>
               </property>
               <property name="alignment">
                <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
               </property>
              </widget>
             </item>
             <item row="3" column="0">
              <widget class="QLabel" name="output_label">
               <property name="maximumSize">
                <size>
                 <width>150</width>
                 <height>20</height>
                </size>
               </property>
               <property name="text">
                <string>Output Filename [-S]</string>
               </property>
               <property name="alignment">
                <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
               </property>
              </widget>
             </item>
             <item row="2" column="2">
              <widget class="QSpinBox" name="threads_sbox">
               <property name="alignment">
                <set>Qt::AlignCenter</set>
               </property>
               <property name="minimum">
                <number>1</number>
               </property>
               <property name="maximum">
                <number>64</number>
               </property>
               <property name="value">
                <number>2</number>
               </property>
              </widget>
             </item>
             <item row="3" column="2">
              <widget class="QLineEdit" name="output_filename">
               <property name="placeholderText">
                <string>Enter filename</string>
               </property>
              </widget>
             </item>
            </layout>
           </widget>
          </item>
          <item>
           <widget class="QGroupBox" name="groupBox_4">
            <property name="minimumSize">
             <size>
              <width>150</width>
              <height>0</height>
             </size>
            </property>
            <property name="title">
             <string>Parameter Presets</string>
            </property>
            <layout class="QVBoxLayout" name="verticalLayout_12">
             <item>
              <widget class="QRadioButton" name="genome">
               <property name="text">
                <string>Genome</string>
               </property>
               <property name="checked">
                <bool>true</bool>
               </property>
              </widget>
             </item>
             <item>
              <widget class="QRadioButton" name="rnaseq">
               <property name="text">
                <string>RNASeq</string>
               </property>
              </widget>
             </item>
             <item>
              <widget class="QRadioButton" name="shrna">
               <property name="text">
                <string>CRISPR</string>
               </property>
              </widget>
             </item>
            </layout>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_16">
          <property name="spacing">
           <number>-1</number>
          </property>
          <property name="sizeConstraint">
           <enum>QLayout::SetMinimumSize</enum>
          </property>
          <item>
           <widget class="QPushButton" name="open_output">
            <property name="text">
             <string>Open Output Directory</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QPushButton" name="reference_dir">
            <property name="text">
             <string>Open Reference Directory</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QPushButton" name="preferences">
            <property name="text">
             <string>Set Default Directories</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="QLabel" name="download_label">
          <property name="text">
           <string>Downloading...</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QProgressBar" name="progress_bar">
          <property name="value">
           <number>0</number>
          </property>
          <property name="invertedAppearance">
           <bool>false</bool>
          </property>
         </widget>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="second_tab">
       <property name="enabled">
        <bool>true</bool>
       </property>
       <attribute name="title">
        <string>Input</string>
       </attribute>
       <layout class="QVBoxLayout" name="verticalLayout_8">
        <item>
         <widget class="QGroupBox" name="reads_format">
          <property name="title">
           <string>Sequence Read Format</string>
          </property>
          <layout class="QVBoxLayout" name="verticalLayout_4">
           <property name="spacing">
            <number>12</number>
           </property>
           <item>
            <widget class="QRadioButton" name="fastq_reads">
             <property name="enabled">
              <bool>true</bool>
             </property>
             <property name="text">
              <string>FASTQ. Files usually have extension .fq or .fastq. [-q]</string>
             </property>
             <property name="checked">
              <bool>true</bool>
             </property>
            </widget>
           </item>
           <item>
            <widget class="QRadioButton" name="fasta_reads">
             <property name="enabled">
              <bool>true</bool>
             </property>
             <property name="text">
              <string>FASTA. Files usually have extension .fa, .fasta, .mfa, .fna or similar. [-f]</string>
             </property>
            </widget>
           </item>
           <item>
            <widget class="QRadioButton" name="custom_reads">
             <property name="text">
              <string>Custom. Reads are files with one input sequence per line [-r]</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_2">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QGroupBox" name="groupBox">
          <property name="title">
           <string>Encoding</string>
          </property>
          <layout class="QVBoxLayout" name="verticalLayout_5">
           <item>
            <widget class="QRadioButton" name="phread33">
             <property name="text">
              <string>Input qualities are ASCII chars equal to the Phred quality plus 33 [--phred33]</string>
             </property>
             <property name="checked">
              <bool>true</bool>
             </property>
            </widget>
           </item>
           <item>
            <spacer name="verticalSpacer">
             <property name="orientation">
              <enum>Qt::Vertical</enum>
             </property>
             <property name="sizeType">
              <enum>QSizePolicy::Fixed</enum>
             </property>
             <property name="sizeHint" stdset="0">
              <size>
               <width>20</width>
               <height>0</height>
              </size>
             </property>
            </spacer>
           </item>
           <item>
            <widget class="QRadioButton" name="phread64">
             <property name="text">
              <string>Input qualities are ASCII chars equal to the Phred quality plus 64 [--phred64]</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_7">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_2">
          <property name="leftMargin">
           <number>0</number>
          </property>
          <item>
           <widget class="QLabel" name="label">
            <property name="maximumSize">
             <size>
              <width>91</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="text">
             <string>Skip the first </string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="skip_first">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="maximum">
             <number>999999999</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_2">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="text">
             <string>reads or pairs in the input. [-s/--skip]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_6">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_4">
          <item>
           <widget class="QLabel" name="label_3">
            <property name="maximumSize">
             <size>
              <width>91</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="text">
             <string>Align the first </string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="align_first">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="maximum">
             <number>999999999</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_4">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="text">
             <string>reads or pairs in the input, then stop. [-u/--qupto]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_5">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_7">
          <item>
           <widget class="QLabel" name="label_5">
            <property name="maximumSize">
             <size>
              <width>91</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="font">
             <font>
              <pointsize>13</pointsize>
             </font>
            </property>
            <property name="text">
             <string>Trim</string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="trim5">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="maximum">
             <number>999999999</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_6">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="font">
             <font>
              <pointsize>13</pointsize>
             </font>
            </property>
            <property name="text">
             <string>bases from 5' (left) end of each read before alignment. [-5]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_4">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_8">
          <item>
           <widget class="QLabel" name="label_7">
            <property name="maximumSize">
             <size>
              <width>91</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="font">
             <font>
              <pointsize>13</pointsize>
             </font>
            </property>
            <property name="text">
             <string>Trim</string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="trim3">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="maximum">
             <number>999999999</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_8">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="font">
             <font>
              <pointsize>13</pointsize>
             </font>
            </property>
            <property name="text">
             <string>bases from 3' (right) end of each read before alignment. [-3]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="third_tab">
       <property name="enabled">
        <bool>true</bool>
       </property>
       <attribute name="title">
        <string>Alignment</string>
       </attribute>
       <layout class="QVBoxLayout" name="verticalLayout_6">
        <item>
         <widget class="QCheckBox" name="ignore_quals">
          <property name="font">
           <font>
            <pointsize>12</pointsize>
           </font>
          </property>
          <property name="text">
           <string>Ignore quality value for penalizing mismatches. [--ignore-quals]</string>
          </property>
          <property name="checked">
           <bool>false</bool>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_20">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="nofw">
          <property name="font">
           <font>
            <pointsize>12</pointsize>
           </font>
          </property>
          <property name="text">
           <string>Do not align unpaired reads to the forward (Watson) reference strand. [--nofw]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_21">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="norc">
          <property name="font">
           <font>
            <pointsize>13</pointsize>
           </font>
          </property>
          <property name="text">
           <string> Do not align unpaired reads with the reverse-complement (Crick) reference. [--norc]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_22">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="dta">
          <property name="text">
           <string>Report alignments tailored for transcript assemblers. [--dta]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_15">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="mm">
          <property name="text">
           <string>Memory Mapped I/O to load the index file.  [--mm]</string>
          </property>
         </widget>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="fourth_tab">
       <property name="enabled">
        <bool>true</bool>
       </property>
       <attribute name="title">
        <string>Scoring</string>
       </attribute>
       <layout class="QVBoxLayout" name="verticalLayout_7">
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_5">
          <item>
           <widget class="QLabel" name="label_10">
            <property name="text">
             <string>Maximum</string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="mp_mx">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>6</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_11">
            <property name="text">
             <string>and Minimum</string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="mp_mn">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>2</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_9">
            <property name="text">
             <string>mismatch penalties. [--mp]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="softclipping">
          <property name="text">
           <string>Allow soft-clipping [!--no-softclip]</string>
          </property>
          <property name="checked">
           <bool>true</bool>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_9">
          <item>
           <widget class="QLabel" name="sp_max_lbl">
            <property name="text">
             <string>Maximum</string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="sp_mx">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>2</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="sp_min_lbl">
            <property name="text">
             <string>and Minimum</string>
            </property>
            <property name="alignment">
             <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="sp_mn">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>1</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="sp_tail_lbl">
            <property name="text">
             <string>penalties for soft-clipping per base. [--sp]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_8">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_10">
          <item>
           <widget class="QLabel" name="label_16">
            <property name="text">
             <string>Read gap open </string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="rdg1">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>5</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_17">
            <property name="text">
             <string>and extend</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="rdg2">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>3</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_18">
            <property name="text">
             <string>penalties. [--rdg]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_19">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_11">
          <item>
           <widget class="QLabel" name="label_19">
            <property name="text">
             <string>Reference gap open </string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="rfg1">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>5</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_20">
            <property name="text">
             <string>and extend</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="rfg2">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>3</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_21">
            <property name="text">
             <string>penalties. [--rfg]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_9">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_15">
          <item>
           <widget class="QLabel" name="label_15">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>16777215</height>
             </size>
            </property>
            <property name="font">
             <font>
              <pointsize>13</pointsize>
             </font>
            </property>
            <property name="text">
             <string>Penalty for read, reference or both containing an ambiguous character</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="np">
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="minimum">
             <number>1</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_26">
            <property name="text">
             <string>[--np]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="sixth_tab">
       <property name="enabled">
        <bool>true</bool>
       </property>
       <attribute name="title">
        <string>Output</string>
       </attribute>
       <layout class="QVBoxLayout" name="verticalLayout_11">
        <item>
         <widget class="QGroupBox" name="groupBox_2">
          <property name="title">
           <string/>
          </property>
          <layout class="QVBoxLayout" name="verticalLayout_9">
           <item>
            <widget class="QCheckBox" name="un">
             <property name="text">
              <string>Write unparied reads that fail to align. [--un]</string>
             </property>
            </widget>
           </item>
           <item>
            <widget class="QCheckBox" name="ungz">
             <property name="enabled">
              <bool>false</bool>
             </property>
             <property name="text">
              <string>gzip. [--un-gz]</string>
             </property>
            </widget>
           </item>
           <item>
            <widget class="QCheckBox" name="unbz2">
             <property name="enabled">
              <bool>false</bool>
             </property>
             <property name="text">
              <string>bzip2. [--un-bz2]</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item>
         <widget class="QGroupBox" name="groupBox_3">
          <property name="title">
           <string/>
          </property>
          <layout class="QVBoxLayout" name="verticalLayout_10">
           <item>
            <widget class="QCheckBox" name="al">
             <property name="text">
              <string>Write unparied reads that align at least once. [--al]</string>
             </property>
            </widget>
           </item>
           <item>
            <widget class="QCheckBox" name="algz">
             <property name="enabled">
              <bool>false</bool>
             </property>
             <property name="text">
              <string>gzip. [--al-gz]</string>
             </property>
            </widget>
           </item>
           <item>
            <widget class="QCheckBox" name="albz2">
             <property name="enabled">
              <bool>false</bool>
             </property>
             <property name="text">
              <string>bzip2. [--al-bz2]</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_12">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_13">
          <item>
           <widget class="QLabel" name="label_22">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>30</height>
             </size>
            </property>
            <property name="text">
             <string>Search for at most </string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="k">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>30</height>
             </size>
            </property>
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>5</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_23">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>30</height>
             </size>
            </property>
            <property name="text">
             <string>distinct primary alignments for each read. [-k]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_11">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_12">
          <item>
           <widget class="QLabel" name="label_24">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>30</height>
             </size>
            </property>
            <property name="text">
             <string>Maximum number of seeds that will be extended</string>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QSpinBox" name="max_seeds">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>30</height>
             </size>
            </property>
            <property name="alignment">
             <set>Qt::AlignCenter</set>
            </property>
            <property name="value">
             <number>5</number>
            </property>
           </widget>
          </item>
          <item>
           <widget class="QLabel" name="label_25">
            <property name="maximumSize">
             <size>
              <width>16777215</width>
              <height>30</height>
             </size>
            </property>
            <property name="text">
             <string>[--max-seeds]</string>
            </property>
           </widget>
          </item>
         </layout>
        </item>
        <item>
         <widget class="Line" name="line_10">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="secondary">
          <property name="text">
           <string>Report secondary alignments. [--secondary]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_18">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="time">
          <property name="text">
           <string>Print the wall-clock time required to load the index filkes and align the reads. [-t]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_16">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="quiet">
          <property name="text">
           <string>Print nothing besides alignments and serious errors. [--quiet]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_14">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="metrics">
          <property name="text">
           <string>Write metrics every 5 seconds. [--met-file]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_13">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="reorder">
          <property name="text">
           <string>Output SAM records in the order of the reads in the original input file. [--reorder]</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_3">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="bzip_sam">
          <property name="text">
           <string>Bzip SAM files (checking this box will delete the .sam file)</string>
          </property>
         </widget>
        </item>
        <item>
         <widget class="Line" name="line_17">
          <property name="orientation">
           <enum>Qt::Horizontal</enum>
          </property>
         </widget>
        </item>
        <item>
         <widget class="QCheckBox" name="chr">
          <property name="text">
           <string>Add &quot;chr&quot; to the reference names in alignment. [--add-chrname/--remove-chrname]</string>
          </property>
          <property name="checked">
           <bool>true</bool>
          </property>
         </widget>
        </item>
       </layout>
       <zorder>groupBox_2</zorder>
       <zorder>groupBox_3</zorder>
       <zorder>line_18</zorder>
       <zorder>time</zorder>
       <zorder>line_16</zorder>
       <zorder>quiet</zorder>
       <zorder>line_14</zorder>
       <zorder>metrics</zorder>
       <zorder>line_13</zorder>
       <zorder>reorder</zorder>
       <zorder>line_17</zorder>
       <zorder>chr</zorder>
       <zorder>secondary</zorder>
       <zorder>line_10</zorder>
       <zorder>line_11</zorder>
       <zorder>line_12</zorder>
       <zorder>bzip_sam</zorder>
       <zorder>line_3</zorder>
      </widget>
     </widget>
    </item>
   </layout>
  </widget>
  <widget class="QMenuBar" name="menuBar">
   <property name="geometry">
    <rect>
     <x>0</x>
     <y>0</y>
     <width>1024</width>
     <height>22</height>
    </rect>
   </property>
   <widget class="QMenu" name="menuHelp">
    <property name="title">
     <string>About</string>
    </property>
    <addaction name="actionContents"/>
   </widget>
   <widget class="QMenu" name="menuLoad">
    <property name="title">
     <string>Load</string>
    </property>
    <addaction name="actionDefault_Parameters"/>
    <addaction name="actionParameters"/>
   </widget>
   <widget class="QMenu" name="menuPreferences">
    <property name="title">
     <string>Dummy</string>
    </property>
    <addaction name="actionSet_Default_Paths"/>
   </widget>
   <addaction name="menuPreferences"/>
   <addaction name="menuLoad"/>
   <addaction name="menuHelp"/>
  </widget>
  <widget class="QStatusBar" name="statusBar"/>
  <widget class="QDockWidget" name="dockWidget">
   <property name="minimumSize">
    <size>
     <width>400</width>
     <height>377</height>
    </size>
   </property>
   <property name="maximumSize">
    <size>
     <width>400</width>
     <height>524287</height>
    </size>
   </property>
   <property name="features">
    <set>QDockWidget::DockWidgetFloatable|QDockWidget::DockWidgetVerticalTitleBar</set>
   </property>
   <property name="allowedAreas">
    <set>Qt::RightDockWidgetArea</set>
   </property>
   <property name="windowTitle">
    <string>Mapping Queue</string>
   </property>
   <attribute name="dockWidgetArea">
    <number>2</number>
   </attribute>
   <widget class="QWidget" name="dockWidgetContents">
    <layout class="QVBoxLayout" name="verticalLayout_2">
     <item>
      <layout class="QHBoxLayout" name="horizontalLayout_17">
       <item>
        <widget class="QLabel" name="label_12">
         <property name="font">
          <font>
           <pointsize>11</pointsize>
          </font>
         </property>
         <property name="text">
          <string>Jobs</string>
         </property>
        </widget>
       </item>
       <item>
        <spacer name="horizontalSpacer">
         <property name="orientation">
          <enum>Qt::Horizontal</enum>
         </property>
         <property name="sizeHint" stdset="0">
          <size>
           <width>40</width>
           <height>20</height>
          </size>
         </property>
        </spacer>
       </item>
       <item>
        <widget class="QPushButton" name="clear_queue_button">
         <property name="minimumSize">
          <size>
           <width>130</width>
           <height>0</height>
          </size>
         </property>
         <property name="font">
          <font>
           <pointsize>11</pointsize>
           <weight>50</weight>
           <bold>false</bold>
          </font>
         </property>
         <property name="text">
          <string>Clear Selected</string>
         </property>
         <property name="flat">
          <bool>false</bool>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QPushButton" name="quit_current_job_button">
         <property name="minimumSize">
          <size>
           <width>130</width>
           <height>0</height>
          </size>
         </property>
         <property name="font">
          <font>
           <pointsize>11</pointsize>
          </font>
         </property>
         <property name="text">
          <string>Quit Current Job</string>
         </property>
         <property name="iconSize">
          <size>
           <width>20</width>
           <height>20</height>
          </size>
         </property>
        </widget>
       </item>
      </layout>
     </item>
     <item>
      <widget class="QTableWidget" name="jobs_table">
       <property name="frameShape">
        <enum>QFrame::Box</enum>
       </property>
       <property name="editTriggers">
        <set>QAbstractItemView::NoEditTriggers</set>
       </property>
       <property name="alternatingRowColors">
        <bool>true</bool>
       </property>
       <property name="selectionMode">
        <enum>QAbstractItemView::SingleSelection</enum>
       </property>
       <property name="selectionBehavior">
        <enum>QAbstractItemView::SelectRows</enum>
       </property>
       <property name="iconSize">
        <size>
         <width>48</width>
         <height>48</height>
        </size>
       </property>
       <property name="rowCount">
        <number>0</number>
       </property>
       <property name="columnCount">
        <number>2</number>
       </property>
       <attribute name="horizontalHeaderVisible">
        <bool>true</bool>
       </attribute>
       <attribute name="horizontalHeaderShowSortIndicator" stdset="0">
        <bool>false</bool>
       </attribute>
       <attribute name="horizontalHeaderStretchLastSection">
        <bool>true</bool>
       </attribute>
       <attribute name="verticalHeaderVisible">
        <bool>false</bool>
       </attribute>
       <attribute name="verticalHeaderStretchLastSection">
        <bool>false</bool>
       </attribute>
       <column>
        <property name="text">
         <string>Status</string>
        </property>
       </column>
       <column>
        <property name="text">
         <string>Name</string>
        </property>
       </column>
      </widget>
     </item>
     <item>
      <widget class="QLabel" name="label_13">
       <property name="font">
        <font>
         <pointsize>11</pointsize>
        </font>
       </property>
       <property name="text">
        <string>Job Parameters</string>
       </property>
      </widget>
     </item>
     <item>
      <widget class="QTableWidget" name="parameter_table">
       <property name="font">
        <font>
         <pointsize>11</pointsize>
        </font>
       </property>
       <property name="frameShape">
        <enum>QFrame::Box</enum>
       </property>
       <property name="sizeAdjustPolicy">
        <enum>QAbstractScrollArea::AdjustIgnored</enum>
       </property>
       <property name="alternatingRowColors">
        <bool>true</bool>
       </property>
       <property name="selectionMode">
        <enum>QAbstractItemView::NoSelection</enum>
       </property>
       <property name="selectionBehavior">
        <enum>QAbstractItemView::SelectRows</enum>
       </property>
       <property name="cornerButtonEnabled">
        <bool>true</bool>
       </property>
       <property name="columnCount">
        <number>2</number>
       </property>
       <attribute name="horizontalHeaderVisible">
        <bool>true</bool>
       </attribute>
       <attribute name="horizontalHeaderStretchLastSection">
        <bool>true</bool>
       </attribute>
       <attribute name="verticalHeaderVisible">
        <bool>false</bool>
       </attribute>
       <column>
        <property name="text">
         <string>Parameter</string>
        </property>
       </column>
       <column>
        <property name="text">
         <string>Value</string>
        </property>
       </column>
      </widget>
     </item>
     <item>
      <widget class="QLabel" name="label_14">
       <property name="font">
        <font>
         <pointsize>11</pointsize>
        </font>
       </property>
       <property name="text">
        <string>Job Command</string>
       </property>
      </widget>
     </item>
     <item>
      <widget class="QLineEdit" name="command_line">
       <property name="font">
        <font>
         <pointsize>11</pointsize>
        </font>
       </property>
       <property name="readOnly">
        <bool>true</bool>
       </property>
      </widget>
     </item>
     <item>
      <layout class="QHBoxLayout" name="horizontalLayout_6">
       <item>
        <widget class="QPushButton" name="add_to_queue_button">
         <property name="minimumSize">
          <size>
           <width>0</width>
           <height>40</height>
          </size>
         </property>
         <property name="maximumSize">
          <size>
           <width>150</width>
           <height>40</height>
          </size>
         </property>
         <property name="font">
          <font>
           <pointsize>12</pointsize>
           <weight>75</weight>
           <bold>true</bold>
          </font>
         </property>
         <property name="text">
          <string>Add to Queue</string>
         </property>
         <property name="flat">
          <bool>false</bool>
         </property>
        </widget>
       </item>
       <item>
        <widget class="QPushButton" name="run_button">
         <property name="minimumSize">
          <size>
           <width>100</width>
           <height>40</height>
          </size>
         </property>
         <property name="maximumSize">
          <size>
           <width>150</width>
           <height>40</height>
          </size>
         </property>
         <property name="font">
          <font>
           <pointsize>12</pointsize>
           <weight>75</weight>
           <bold>true</bold>
          </font>
         </property>
         <property name="text">
          <string>Run Queue</string>
         </property>
        </widget>
       </item>
      </layout>
     </item>
    </layout>
   </widget>
  </widget>
  <action name="actionSave">
   <property name="text">
    <string>Save...</string>
   </property>
  </action>
  <action name="actionAbout_MAPster">
   <property name="text">
    <string>About</string>
   </property>
  </action>
  <action name="actionContents">
   <property name="text">
    <string>Mapster</string>
   </property>
  </action>
  <action name="actionLoad">
   <property name="text">
    <string>Load...</string>
   </property>
  </action>
  <action name="actionParameters">
   <property name="text">
    <string>Parameters From File...</string>
   </property>
  </action>
  <action name="actionDefault_Parameters">
   <property name="text">
    <string>Default Parameters</string>
   </property>
  </action>
  <action name="actionSet_Default_Paths">
   <property name="text">
    <string>Preferences...</string>
   </property>
  </action>
 </widget>
 <layoutdefault spacing="6" margin="11"/>
 <customwidgets>
  <customwidget>
   <class>VListWidget</class>
   <extends>QListWidget</extends>
   <header>customui/vlistwidget.h</header>
  </customwidget>
 </customwidgets>
 <resources/>
 <connections/>
</ui>