<?xml version="1.0" encoding="UTF-8" ?>

<Form version="1.5" maxVersion="1.5" type="org.netbeans.modules.form.forminfo.JDialogFormInfo">
  <NonVisualComponents>
    <Component class="javax.swing.ButtonGroup" name="featureStyleButtonGroup">
    </Component>
    <Component class="javax.swing.ButtonGroup" name="probeMappingButtonGroup">
    </Component>
    <Component class="javax.swing.ButtonGroup" name="rnaiMapapingButtonGroup">
    </Component>
  </NonVisualComponents>
  <Properties>
    <Property name="defaultCloseOperation" type="int" value="2"/>
    <Property name="resizable" type="boolean" value="false"/>
  </Properties>
  <SyntheticProperties>
    <SyntheticProperty name="formSizePolicy" type="int" value="1"/>
  </SyntheticProperties>
  <AuxValues>
    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="2"/>
    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
    <AuxValue name="designerSize" type="java.awt.Dimension" value="-84,-19,0,5,115,114,0,18,106,97,118,97,46,97,119,116,46,68,105,109,101,110,115,105,111,110,65,-114,-39,-41,-84,95,68,20,2,0,2,73,0,6,104,101,105,103,104,116,73,0,5,119,105,100,116,104,120,112,0,0,2,58,0,0,3,22"/>
  </AuxValues>

  <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
  <SubComponents>
    <Container class="javax.swing.JTabbedPane" name="tabbedPane">
      <AccessibilityProperties>
        <Property name="AccessibleContext.accessibleName" type="java.lang.String" value="Advanced"/>
      </AccessibilityProperties>
      <Constraints>
        <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
          <BorderConstraints direction="After"/>
        </Constraint>
      </Constraints>

      <Layout class="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout"/>
      <SubComponents>
        <Container class="javax.swing.JPanel" name="generalPanel">
          <Constraints>
            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
              <JTabbedPaneConstraints tabName="General">
                <Property name="tabTitle" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
                  <PlainString value="General"/>
                </Property>
              </JTabbedPaneConstraints>
            </Constraint>
          </Constraints>

          <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
            <Property name="useNullLayout" type="boolean" value="true"/>
          </Layout>
          <SubComponents>
            <Container class="javax.swing.JPanel" name="jPanel10">
              <Constraints>
                <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                  <AbsoluteConstraints x="0" y="0" width="610" height="290"/>
                </Constraint>
              </Constraints>

              <Layout>
                <DimensionLayout dim="0">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="42" max="-2" attributes="0"/>
                                  <Component id="showAttributesDisplayDescription" min="-2" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <Component id="showAttributesDisplayLabel" min="-2" max="-2" attributes="0"/>
                                  <EmptySpace min="-2" pref="26" max="-2" attributes="0"/>
                                  <Component id="showAttributesDisplayCheckBox" min="-2" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="44" max="-2" attributes="0"/>
                                  <Component id="missingDataExplanation1" min="-2" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <Component id="jLabel9" min="-2" max="-2" attributes="0"/>
                                  <EmptySpace max="-2" attributes="0"/>
                                  <Component id="joinSegmentsCB" min="-2" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <Component id="missingDataLabel" min="-2" max="-2" attributes="0"/>
                                  <EmptySpace min="-2" pref="81" max="-2" attributes="0"/>
                                  <Component id="showMissingDataCB" min="-2" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="35" max="-2" attributes="0"/>
                                  <Component id="missingDataExplanation" min="-2" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <Component id="comginePanelLabel" min="-2" max="-2" attributes="0"/>
                                  <EmptySpace max="-2" attributes="0"/>
                                  <Component id="combinePanelsCB" min="-2" max="-2" attributes="0"/>
                              </Group>
                          </Group>
                          <EmptySpace pref="36" max="32767" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
                <DimensionLayout dim="1">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Component id="missingDataLabel" min="-2" max="-2" attributes="0"/>
                              <Component id="showMissingDataCB" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="missingDataExplanation" min="-2" max="-2" attributes="0"/>
                          <EmptySpace min="-2" pref="26" max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="3" attributes="0">
                              <Component id="comginePanelLabel" alignment="3" min="-2" max="-2" attributes="0"/>
                              <Component id="combinePanelsCB" alignment="3" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace min="-2" pref="13" max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="3" attributes="0">
                              <Component id="jLabel9" alignment="3" min="-2" max="-2" attributes="0"/>
                              <Component id="joinSegmentsCB" alignment="3" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace min="-2" pref="11" max="-2" attributes="0"/>
                          <Component id="missingDataExplanation1" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Component id="showAttributesDisplayLabel" min="-2" max="-2" attributes="0"/>
                              <Component id="showAttributesDisplayCheckBox" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="showAttributesDisplayDescription" min="-2" max="-2" attributes="0"/>
                          <EmptySpace pref="35" max="32767" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
              </Layout>
              <SubComponents>
                <Component class="javax.swing.JLabel" name="missingDataLabel">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Distinguish Missing Data:" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JLabel" name="missingDataExplanation">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;Distinguish  regions with zero values from regions with no data on plots &lt;br&gt;(e.g. bar charts).  Regions with no data are indicated with a gray background." noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="showMissingDataCB">
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="showMissingDataCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="comginePanelLabel">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Combine Data and Feature Panels:" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="combinePanelsCB">
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="combinePanelsCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel9">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Join Adjacent CopyNumber Segments:" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="joinSegmentsCB">
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="joinSegmentsCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="missingDataExplanation1">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;This option applies to segmented copy number data only.  When selected, gaps between&lt;br&gt;adjacent segments are filled by extending segment endpoints." noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JLabel" name="showAttributesDisplayLabel">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Show Attribute Display:" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="showAttributesDisplayCheckBox">
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="showAttributesDisplayCheckBoxActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="showAttributesDisplayDescription">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;Determine whether the attribute header display is shown" noResource="true"/>
                  </Properties>
                </Component>
              </SubComponents>
            </Container>
          </SubComponents>
        </Container>
        <Container class="javax.swing.JPanel" name="tracksPanel">
          <Constraints>
            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
              <JTabbedPaneConstraints tabName="Tracks">
                <Property name="tabTitle" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
                  <PlainString value="Tracks"/>
                </Property>
              </JTabbedPaneConstraints>
            </Constraint>
          </Constraints>

          <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
            <Property name="useNullLayout" type="boolean" value="true"/>
          </Layout>
          <SubComponents>
            <Container class="javax.swing.JPanel" name="jPanel6">
              <Constraints>
                <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                  <AbsoluteConstraints x="40" y="20" width="540" height="320"/>
                </Constraint>
              </Constraints>

              <Layout>
                <DimensionLayout dim="0">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="24" max="-2" attributes="0"/>
                                  <Component id="missingDataExplanation4" min="-2" pref="354" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="24" max="-2" attributes="0"/>
                                  <Component id="missingDataExplanation2" min="-2" pref="354" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <Component id="trackNameAttributeLabel" min="-2" max="-2" attributes="0"/>
                                  <EmptySpace max="-2" attributes="0"/>
                                  <Component id="trackNameAttributeField" min="-2" pref="216" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <Component id="jLabel8" min="-2" max="-2" attributes="0"/>
                                  <EmptySpace min="-2" pref="39" max="-2" attributes="0"/>
                                  <Component id="defaultTrackHeightField" min="-2" pref="57" max="-2" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="24" max="-2" attributes="0"/>
                                  <Component id="missingDataExplanation5" pref="484" max="32767" attributes="0"/>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <Component id="jLabel5" min="-2" max="-2" attributes="0"/>
                                  <EmptySpace min="-2" pref="36" max="-2" attributes="0"/>
                                  <Component id="defaultChartTrackHeightField" min="-2" pref="57" max="-2" attributes="0"/>
                              </Group>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
                <DimensionLayout dim="1">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="3" attributes="0">
                              <Component id="jLabel5" alignment="3" min="-2" max="-2" attributes="0"/>
                              <Component id="defaultChartTrackHeightField" alignment="3" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="missingDataExplanation4" min="-2" pref="25" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="3" attributes="0">
                              <Component id="jLabel8" alignment="3" min="-2" max="-2" attributes="0"/>
                              <Component id="defaultTrackHeightField" alignment="3" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="missingDataExplanation5" min="-2" pref="25" max="-2" attributes="0"/>
                          <EmptySpace min="-2" pref="26" max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="3" attributes="0">
                              <Component id="trackNameAttributeLabel" alignment="3" min="-2" max="-2" attributes="0"/>
                              <Component id="trackNameAttributeField" alignment="3" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="missingDataExplanation2" min="-2" pref="65" max="-2" attributes="0"/>
                          <EmptySpace pref="43" max="32767" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
              </Layout>
              <SubComponents>
                <Component class="javax.swing.JLabel" name="jLabel5">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Default Track Height, Charts (Pixels)" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JTextField" name="defaultChartTrackHeightField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="40" noResource="true"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="defaultChartTrackHeightFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="defaultChartTrackHeightFieldFocusLost"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="trackNameAttributeLabel">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Track Name Attribute" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JTextField" name="trackNameAttributeField">
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="trackNameAttributeFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="trackNameAttributeFieldFocusLost"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="missingDataExplanation2">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;Name of an attribute to be used to label  tracks.  If provided tracks will be labeled with the corresponding attribute values from the sample information file" noResource="true"/>
                  </Properties>
                  <AccessibilityProperties>
                    <Property name="AccessibleContext.accessibleName" type="java.lang.String" value="&lt;html&gt;Name of an attribute to be used to label  tracks.  If provided   &lt;br&gt;tracks will be labeled with the corresponding attribute values from the sample information file. "/>
                  </AccessibilityProperties>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel8">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Default Track Height, Other (Pixels)" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JTextField" name="defaultTrackHeightField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="15" noResource="true"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="defaultTrackHeightFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="defaultTrackHeightFieldFocusLost"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="missingDataExplanation4">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;Default height of chart tracks (barcharts, scatterplots, etc)" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JLabel" name="missingDataExplanation5">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;Default height of all other tracks" noResource="true"/>
                  </Properties>
                </Component>
              </SubComponents>
            </Container>
          </SubComponents>
        </Container>
        <Container class="javax.swing.JPanel" name="overlaysPanel">
          <Constraints>
            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
              <JTabbedPaneConstraints tabName="Overlays">
                <Property name="tabTitle" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
                  <PlainString value="Overlays"/>
                </Property>
              </JTabbedPaneConstraints>
            </Constraint>
          </Constraints>

          <Layout>
            <DimensionLayout dim="0">
              <Group type="103" groupAlignment="0" attributes="0">
                  <Group type="102" alignment="0" attributes="0">
                      <EmptySpace min="-2" pref="28" max="-2" attributes="0"/>
                      <Component id="jPanel5" min="-2" max="-2" attributes="0"/>
                      <EmptySpace pref="196" max="32767" attributes="0"/>
                  </Group>
              </Group>
            </DimensionLayout>
            <DimensionLayout dim="1">
              <Group type="103" groupAlignment="0" attributes="0">
                  <Group type="102" alignment="0" attributes="0">
                      <EmptySpace min="-2" pref="55" max="-2" attributes="0"/>
                      <Component id="jPanel5" min="-2" max="-2" attributes="0"/>
                      <EmptySpace pref="194" max="32767" attributes="0"/>
                  </Group>
              </Group>
            </DimensionLayout>
          </Layout>
          <SubComponents>
            <Container class="javax.swing.JPanel" name="jPanel5">

              <Layout>
                <DimensionLayout dim="0">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Component id="displayTracksCB" alignment="0" min="-2" max="-2" attributes="0"/>
                              <Component id="jLabel4" alignment="0" min="-2" max="-2" attributes="0"/>
                              <Component id="overlayTrackCB" alignment="0" min="-2" max="-2" attributes="0"/>
                              <Component id="jLabel2" alignment="0" min="-2" max="-2" attributes="0"/>
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="59" max="-2" attributes="0"/>
                                  <Group type="103" groupAlignment="0" attributes="0">
                                      <Group type="102" alignment="0" attributes="0">
                                          <EmptySpace max="-2" attributes="0"/>
                                          <Component id="colorOverlyCB" min="-2" max="-2" attributes="0"/>
                                          <EmptySpace max="-2" attributes="0"/>
                                          <Component id="chooseOverlayColorsButton" min="-2" max="-2" attributes="0"/>
                                      </Group>
                                      <Group type="102" alignment="0" attributes="0">
                                          <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
                                          <EmptySpace max="-2" attributes="0"/>
                                          <Component id="overlayAttributeTextField" min="-2" pref="228" max="-2" attributes="0"/>
                                      </Group>
                                  </Group>
                              </Group>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
                <DimensionLayout dim="1">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="jLabel2" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="jLabel4" min="-2" max="-2" attributes="0"/>
                          <EmptySpace min="-2" pref="39" max="-2" attributes="0"/>
                          <Component id="overlayTrackCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="3" attributes="0">
                              <Component id="jLabel3" alignment="3" min="-2" max="-2" attributes="0"/>
                              <Component id="overlayAttributeTextField" alignment="3" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace min="-2" pref="6" max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="1" attributes="0">
                              <Component id="colorOverlyCB" min="-2" max="-2" attributes="0"/>
                              <Component id="chooseOverlayColorsButton" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace min="-2" pref="36" max="-2" attributes="0"/>
                          <Component id="displayTracksCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace pref="30" max="32767" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
              </Layout>
              <SubComponents>
                <Component class="javax.swing.JLabel" name="jLabel3">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Overlay tracks based on attribute:" noResource="true"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JTextField" name="overlayAttributeTextField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="LINKING_ID" noResource="true"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="overlayAttributeTextFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="overlayAttributeTextFieldFocusLost"/>
                    <EventHandler event="keyTyped" listener="java.awt.event.KeyListener" parameters="java.awt.event.KeyEvent" handler="overlayAttributeTextFieldKeyTyped"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JCheckBox" name="overlayTrackCB">
                  <Properties>
                    <Property name="selected" type="boolean" value="true"/>
                    <Property name="text" type="java.lang.String" value="Overlay mutation tracks" noResource="true"/>
                    <Property name="actionCommand" type="java.lang.String" value="overlayTracksCB" noResource="true"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="overlayTrackCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel2">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="text" type="java.lang.String" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
                      <Connection code="getOverlayText()" type="code"/>
                    </Property>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="displayTracksCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Display mutation data as distinct tracks" noResource="true"/>
                    <Property name="actionCommand" type="java.lang.String" value="displayTracksCB" noResource="true"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="displayTracksCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel4">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="colorOverlyCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Color code overlay" noResource="true"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="colorOverlyCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="com.jidesoft.swing.JideButton" name="chooseOverlayColorsButton">
                  <Properties>
                    <Property name="foreground" type="java.awt.Color" editor="org.netbeans.beaninfo.editors.ColorEditor">
                      <Color blue="f7" green="0" red="0" type="rgb"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="Choose colors" noResource="true"/>
                    <Property name="buttonStyle" type="int" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
                      <Connection code="&#xa;com.jidesoft.swing.ButtonStyle.HYPERLINK_STYLE &#xa;" type="code"/>
                    </Property>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
                      <Font name="Lucida Grande" size="12" style="2"/>
                    </Property>
                    <Property name="verticalAlignment" type="int" value="3"/>
                    <Property name="verticalTextPosition" type="int" value="3"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="chooseOverlayColorsButtonActionPerformed"/>
                  </Events>
                </Component>
              </SubComponents>
            </Container>
          </SubComponents>
        </Container>
        <Container class="javax.swing.JPanel" name="chartPanel">
          <Constraints>
            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
              <JTabbedPaneConstraints tabName="Charts">
                <Property name="tabTitle" type="java.lang.String" value="Charts"/>
              </JTabbedPaneConstraints>
            </Constraint>
          </Constraints>

          <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
            <Property name="useNullLayout" type="boolean" value="true"/>
          </Layout>
          <SubComponents>
            <Container class="javax.swing.JPanel" name="jPanel4">
              <Constraints>
                <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                  <AbsoluteConstraints x="20" y="30" width="580" height="330"/>
                </Constraint>
              </Constraints>

              <Layout>
                <DimensionLayout dim="0">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Component id="label1" alignment="0" min="-2" max="-2" attributes="0"/>
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="20" max="-2" attributes="0"/>
                                  <Group type="103" groupAlignment="0" attributes="0">
                                      <Group type="102" alignment="0" attributes="0">
                                          <Component id="chartDrawTrackNameCB" min="-2" max="-2" attributes="0"/>
                                          <EmptySpace min="-2" pref="61" max="-2" attributes="0"/>
                                          <Component id="jLabel7" min="-2" max="-2" attributes="0"/>
                                      </Group>
                                      <Component id="topBorderCB" alignment="0" min="-2" max="-2" attributes="0"/>
                                      <Component id="colorBordersCB" alignment="0" min="-2" max="-2" attributes="0"/>
                                      <Component id="bottomBorderCB" alignment="0" min="-2" max="-2" attributes="0"/>
                                      <Component id="labelYAxisCB" alignment="0" min="-2" max="-2" attributes="0"/>
                                  </Group>
                              </Group>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
                <DimensionLayout dim="1">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="label1" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="topBorderCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="bottomBorderCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace min="-2" pref="7" max="-2" attributes="0"/>
                          <Component id="colorBordersCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Component id="jLabel7" min="-2" max="-2" attributes="0"/>
                              <Component id="chartDrawTrackNameCB" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace min="-2" pref="32" max="-2" attributes="0"/>
                          <Component id="labelYAxisCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace min="-2" pref="122" max="-2" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
              </Layout>
              <SubComponents>
                <Component class="javax.swing.JCheckBox" name="topBorderCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Draw Top Border"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="topBorderCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="java.awt.Label" name="label1">
                  <Properties>
                    <Property name="font" type="java.awt.Font" editor="org.netbeans.modules.form.editors2.FontEditor">
                      <FontInfo relative="true">
                        <Font component="label1" property="font" relativeSize="true" size="0"/>
                      </FontInfo>
                    </Property>
                    <Property name="text" type="java.lang.String" value="Settings for barcharts and scatterplots:"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="chartDrawTrackNameCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Draw Track Label"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="chartDrawTrackNameCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JCheckBox" name="bottomBorderCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Draw Bottom Border"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="bottomBorderCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel7">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;&lt;i&gt;Draw a label centered over the track provided&lt;br&gt;the track height is at least 25 pixels. "/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JCheckBox" name="colorBordersCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Color Borders"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="colorBordersCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JCheckBox" name="labelYAxisCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Label Y Axis"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="labelYAxisCBActionPerformed"/>
                  </Events>
                </Component>
              </SubComponents>
            </Container>
          </SubComponents>
        </Container>
        <Container class="javax.swing.JPanel" name="alignmentPanel">
          <Constraints>
            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
              <JTabbedPaneConstraints tabName="Alignments">
                <Property name="tabTitle" type="java.lang.String" value="Alignments"/>
              </JTabbedPaneConstraints>
            </Constraint>
          </Constraints>

          <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
            <Property name="useNullLayout" type="boolean" value="true"/>
          </Layout>
          <SubComponents>
            <Container class="javax.swing.JPanel" name="jPanel1">
              <Constraints>
                <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                  <AbsoluteConstraints x="20" y="0" width="740" height="490"/>
                </Constraint>
              </Constraints>

              <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
                <Property name="useNullLayout" type="boolean" value="true"/>
              </Layout>
              <SubComponents>
                <Component class="javax.swing.JTextField" name="samMaxWindowSizeField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="jTextField1"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="samMaxWindowSizeFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="samMaxWindowSizeFieldFocusLost"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="220" y="30" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel11">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Visibility range threshold (kb)"/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="30" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JCheckBox" name="samShowDuplicatesCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Show duplicate reads"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="samShowDuplicatesCBActionPerformed"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="190" width="290" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel12">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;&lt;i&gt;Nominal window size at which alignments become visible"/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="320" y="30" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JCheckBox" name="samFlagUnmappedPairCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Flag unmapped pairs"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="samFlagUnmappedPairCBActionPerformed"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="220" width="310" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JCheckBox" name="samShadeMismatchedBaseCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Shade mismatched bases by quality. "/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="samShadeMismatchedBaseCBActionPerformed"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="310" width="340" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel13">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Maximum read depth"/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="70" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JTextField" name="samMaxLevelField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="jTextField1"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="samMaxLevelFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="samMaxLevelFieldFocusLost"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="220" y="70" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel14">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;&lt;i&gt;Maximum number of rows of alignments to display."/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="320" y="70" width="390" height="30"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel15">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Mapping quality threshold:"/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="110" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JTextField" name="mappingQualityThresholdField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="0"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="mappingQualityThresholdFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="mappingQualityThresholdFieldFocusLost"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="220" y="110" width="70" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel16">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;&lt;i&gt;Reads with qualities  below the threshold are not shown."/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="320" y="110" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel17">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Insert size flagging threshold:"/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="160" width="200" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JTextField" name="insertSizeThresholdField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="0"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="insertSizeThresholdFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="insertSizeThresholdFieldFocusLost"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="220" y="160" width="70" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel18">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;&lt;i&gt;Paired end alignments with insert sizes &gt; this value are flagged."/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="320" y="160" width="360" height="40"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel10">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;Chromosome color legend &amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;i&gt;Used to flag paired end reads with mates on other chromosomes"/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="370" width="640" height="30"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Container class="javax.swing.JPanel" name="jPanel2">
                  <AuxValues>
                    <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="new ChromosomeColorLegend();"/>
                  </AuxValues>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="30" y="410" width="670" height="50"/>
                    </Constraint>
                  </Constraints>

                  <Layout>
                    <DimensionLayout dim="0">
                      <Group type="103" groupAlignment="0" attributes="0">
                          <EmptySpace min="0" pref="670" max="32767" attributes="0"/>
                      </Group>
                    </DimensionLayout>
                    <DimensionLayout dim="1">
                      <Group type="103" groupAlignment="0" attributes="0">
                          <EmptySpace min="0" pref="50" max="32767" attributes="0"/>
                      </Group>
                    </DimensionLayout>
                  </Layout>
                </Container>
                <Component class="javax.swing.JCheckBox" name="autosortCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Order alignments at center line from left to right"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="autosortCBActionPerformed"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="250" width="450" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JTextField" name="samMinBaseQualityField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="0"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="samMinBaseQualityFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="samMinBaseQualityFieldFocusLost"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="130" y="340" width="50" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel19">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Min: "/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="90" y="340" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel20">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Max:"/>
                  </Properties>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="200" y="340" width="-1" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JTextField" name="samMaxBaseQualityField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="0"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="samMaxBaseQualityFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="samMaxBaseQualityFieldFocusLost"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="240" y="340" width="50" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
                <Component class="javax.swing.JCheckBox" name="shadeCenteredAlignmentsCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Shade alignments intersecting center"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="shadeCenteredAlignmentsCBActionPerformed"/>
                  </Events>
                  <Constraints>
                    <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                      <AbsoluteConstraints x="20" y="280" width="450" height="-1"/>
                    </Constraint>
                  </Constraints>
                </Component>
              </SubComponents>
            </Container>
          </SubComponents>
        </Container>
        <Container class="javax.swing.JPanel" name="expressionPane">
          <Constraints>
            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
              <JTabbedPaneConstraints tabName="Probes">
                <Property name="tabTitle" type="java.lang.String" value="Probes"/>
              </JTabbedPaneConstraints>
            </Constraint>
          </Constraints>

          <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
            <Property name="useNullLayout" type="boolean" value="true"/>
          </Layout>
          <SubComponents>
            <Container class="javax.swing.JPanel" name="jPanel8">
              <Constraints>
                <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                  <AbsoluteConstraints x="10" y="30" width="720" height="310"/>
                </Constraint>
              </Constraints>

              <Layout>
                <DimensionLayout dim="0">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="45" max="-2" attributes="0"/>
                                  <Group type="103" groupAlignment="0" attributes="0">
                                      <Component id="expMapToLociCB" alignment="0" min="-2" max="-2" attributes="0"/>
                                      <Component id="expMapToGeneCB" alignment="0" min="-2" max="-2" attributes="0"/>
                                  </Group>
                              </Group>
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace max="-2" attributes="0"/>
                                  <Group type="103" groupAlignment="0" attributes="0">
                                      <Group type="102" attributes="0">
                                          <EmptySpace min="24" pref="24" max="24" attributes="0"/>
                                          <Component id="jLabel21" min="-2" pref="497" max="-2" attributes="0"/>
                                      </Group>
                                      <Component id="jLabel24" alignment="0" min="-2" max="-2" attributes="0"/>
                                  </Group>
                              </Group>
                          </Group>
                          <EmptySpace pref="179" max="32767" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
                <DimensionLayout dim="1">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" alignment="0" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="jLabel24" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="jLabel21" min="-2" pref="44" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Component id="expMapToLociCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace min="-2" pref="14" max="-2" attributes="0"/>
                          <Component id="expMapToGeneCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace pref="158" max="32767" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
              </Layout>
              <SubComponents>
                <Component class="javax.swing.JRadioButton" name="expMapToGeneCB">
                  <Properties>
                    <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
                      <ComponentRef name="probeMappingButtonGroup"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="Map probes to genes"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="expMapToGeneCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel24">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Expression probe mapping options: "/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JRadioButton" name="expMapToLociCB">
                  <Properties>
                    <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
                      <ComponentRef name="probeMappingButtonGroup"/>
                    </Property>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;Map probes to target loci"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="expMapToLociCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel21">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="&lt;html&gt;&lt;i&gt;Note: Changes will not affect currently loaded datasets."/>
                  </Properties>
                </Component>
              </SubComponents>
            </Container>
          </SubComponents>
        </Container>
        <Container class="javax.swing.JPanel" name="advancedPanel">
          <Properties>
            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
              <Border info="org.netbeans.modules.form.compat2.border.EmptyBorderInfo">
                <EmptyBorder bottom="1" left="10" right="10" top="1"/>
              </Border>
            </Property>
          </Properties>
          <Constraints>
            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
              <JTabbedPaneConstraints tabName="Advanced">
                <Property name="tabTitle" type="java.lang.String" value="Advanced"/>
              </JTabbedPaneConstraints>
            </Constraint>
          </Constraints>

          <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
            <Property name="useNullLayout" type="boolean" value="true"/>
          </Layout>
          <SubComponents>
            <Container class="javax.swing.JPanel" name="jPanel3">
              <Constraints>
                <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
                  <AbsoluteConstraints x="10" y="30" width="710" height="290"/>
                </Constraint>
              </Constraints>

              <Layout>
                <DimensionLayout dim="0">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="0" attributes="0">
                              <Group type="102" alignment="0" attributes="0">
                                  <EmptySpace min="-2" pref="29" max="-2" attributes="0"/>
                                  <Group type="103" groupAlignment="0" attributes="0">
                                      <Component id="jLabel1" alignment="0" min="-2" max="-2" attributes="0"/>
                                      <Group type="102" alignment="0" attributes="0">
                                          <Component id="jLabel6" min="-2" max="-2" attributes="0"/>
                                          <EmptySpace min="-2" pref="44" max="-2" attributes="0"/>
                                          <Group type="103" groupAlignment="0" max="-2" attributes="0">
                                              <Component id="dataServerURLTextField" max="32767" attributes="1"/>
                                              <Component id="genomeServerURLTextField" alignment="0" pref="494" max="32767" attributes="1"/>
                                          </Group>
                                      </Group>
                                  </Group>
                              </Group>
                              <Component id="editServerPropertiesCB" alignment="0" min="-2" max="-2" attributes="0"/>
                              <Component id="clearGenomeCacheButton" alignment="0" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace min="-2" pref="14" max="-2" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
                <DimensionLayout dim="1">
                  <Group type="103" groupAlignment="0" attributes="0">
                      <Group type="102" attributes="0">
                          <EmptySpace min="-2" pref="84" max="-2" attributes="0"/>
                          <Component id="editServerPropertiesCB" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="2" attributes="0">
                              <Component id="jLabel1" alignment="2" min="-2" max="-2" attributes="0"/>
                              <Component id="genomeServerURLTextField" alignment="2" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace max="-2" attributes="0"/>
                          <Group type="103" groupAlignment="3" attributes="0">
                              <Component id="jLabel6" alignment="3" min="-2" max="-2" attributes="0"/>
                              <Component id="dataServerURLTextField" alignment="3" min="-2" max="-2" attributes="0"/>
                          </Group>
                          <EmptySpace pref="68" max="32767" attributes="0"/>
                          <Component id="clearGenomeCacheButton" min="-2" max="-2" attributes="0"/>
                          <EmptySpace max="-2" attributes="0"/>
                      </Group>
                  </Group>
                </DimensionLayout>
              </Layout>
              <SubComponents>
                <Component class="javax.swing.JLabel" name="jLabel1">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Genome Server URL"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JTextField" name="genomeServerURLTextField">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="jTextField1"/>
                    <Property name="enabled" type="boolean" value="false"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="genomeServerURLTextFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="genomeServerURLTextFieldFocusLost"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JLabel" name="jLabel6">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Data Registry URL"/>
                  </Properties>
                </Component>
                <Component class="javax.swing.JTextField" name="dataServerURLTextField">
                  <Properties>
                    <Property name="enabled" type="boolean" value="false"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="dataServerURLTextFieldActionPerformed"/>
                    <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="dataServerURLTextFieldFocusLost"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JCheckBox" name="editServerPropertiesCB">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Edit server properties"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="editServerPropertiesCBActionPerformed"/>
                  </Events>
                </Component>
                <Component class="javax.swing.JButton" name="clearGenomeCacheButton">
                  <Properties>
                    <Property name="text" type="java.lang.String" value="Clear Genome Cache"/>
                  </Properties>
                  <Events>
                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="clearGenomeCacheButtonActionPerformed"/>
                  </Events>
                </Component>
              </SubComponents>
            </Container>
          </SubComponents>
        </Container>
      </SubComponents>
    </Container>
    <Container class="com.jidesoft.dialog.ButtonPanel" name="okCancelButtonPanel">
      <Constraints>
        <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
          <BorderConstraints direction="South"/>
        </Constraint>
      </Constraints>
      <SubComponents>
        <Component class="javax.swing.JButton" name="okButton">
          <Properties>
            <Property name="text" type="java.lang.String" value="OK" noResource="true"/>
          </Properties>
          <Events>
            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="okButtonActionPerformed"/>
          </Events>
        </Component>
        <Component class="javax.swing.JButton" name="cancelButton">
          <Properties>
            <Property name="text" type="java.lang.String" value="Cancel" noResource="true"/>
          </Properties>
          <Events>
            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="cancelButtonActionPerformed"/>
          </Events>
        </Component>
      </SubComponents>
    </Container>
  </SubComponents>
</Form>
