<?xml version="1.0" encoding="UTF-8"?>
<otrunk id="f080c070-7c8a-417c-a3fe-0737a7302806">
  <imports>
    <import class="org.concord.graph.util.state.OTDrawingTool" />
    <import class="org.concord.otrunk.OTSystem" />
    <import class="org.concord.otrunk.OTInclude" />
    <import class="org.concord.otrunk.OTIncludeRootObject" />
    <import class="org.concord.otrunk.view.OTViewBundle" />
    <import class="org.concord.otrunk.view.OTViewMode" />
    <import class="org.concord.otrunk.view.OTViewEntry" />
    <import class="org.concord.otrunk.script.ui.OTXHTMLScriptViewEntry" />
    <import class="org.concord.otrunk.view.OTMultiUserRoot" />
    <import class="org.concord.otrunk.view.document.OTCompoundDoc" />
    <import class="org.concord.otrunk.view.document.OTDocumentViewConfig" />
    <import class="org.concord.otrunk.script.ui.OTXHTMLScript" />
    <import class="org.concord.otrunk.script.js.OTJavascript" />
    <import class="org.concord.otrunk.script.jruby.OTJRuby" />
    <import class="org.concord.otrunk.script.OTScriptEngineBundle" />
    <import class="org.concord.otrunk.script.OTScriptEngineEntry" />
    <import class="org.concord.otrunk.script.ui.OTScriptVariable" />
    <import class="org.concord.framework.otrunk.wrapper.OTBlob" />
    <import class="org.concord.otrunk.view.OTViewChild" />
    <import class="org.concord.otrunk.biologica.OTOrganism" />
    <import class="org.concord.otrunk.biologica.OTWorld" />
    <import class="org.concord.otrunk.biologica.OTStaticOrganism" />
    <import class="org.concord.otrunk.biologica.OTBreedOffspring" />
    <import class="org.concord.otrunk.biologica.OTChromosome" />
    <import class="org.concord.otrunk.biologica.OTSex" />
		<import class="org.concord.otrunk.biologica.OTPedigree" />
		<import class="org.concord.otrunk.biologica.OTMultipleOrganism" />
    <import class="org.concord.otrunk.ui.OTChoiceWithFeedback" />
    <import class="org.concord.otrunk.ui.OTText" />
    <import class="org.concord.otrunk.script.ui.OTScriptButton" />
    <import class="org.concord.framework.otrunk.wrapper.OTBoolean" />
    <import class="org.concord.otrunk.ui.OTButton" />
    <import class="org.concord.otrunk.script.ui.OTScriptVariableRealObject" />
    <import class="org.concord.otrunk.script.ui.OTScriptVariableComponent" />
    <import class="org.concord.otrunk.script.ui.OTScriptVariableView" />
    <import class="org.concord.otrunk.script.ui.OTScriptObject" />
  </imports>
  <objects>
    <OTSystem local_id="system">
      <bundles>
        <OTViewBundle>
          <viewEntries>
						<OTViewEntry objectClass="org.concord.otrunk.biologica.OTPedigree"
viewClass="org.concord.otrunk.biologica.ui.OTPedigreeView" />
            <OTViewEntry objectClass="org.concord.otrunk.script.ui.OTXHTMLScript" viewClass="org.concord.otrunk.script.ui.OTXHTMLScriptView" />
            <OTDocumentViewConfig objectClass="org.concord.otrunk.view.document.OTDocument" viewClass="org.concord.otrunk.view.document.OTDocumentView" css="body {color: purple; background-color: #FFFFFF } .caption {color: black; padding-left: 5px;} .staticOrganism {width: 150px; float:right;} #introOrganisms {width: 400px;} " />
            <OTViewEntry objectClass="org.concord.otrunk.biologica.OTBreedOffspring" viewClass="org.concord.otrunk.biologica.ui.OTBreedOffspringView" />
            <OTViewEntry objectClass="org.concord.otrunk.biologica.OTSex" viewClass="org.concord.otrunk.biologica.ui.OTSexView" />
            <OTViewEntry objectClass="org.concord.otrunk.biologica.OTChromosome" viewClass="org.concord.otrunk.biologica.ui.OTChromosomeView" />
            <OTViewEntry objectClass="org.concord.otrunk.biologica.OTOrganism" viewClass="org.concord.otrunk.biologica.ui.OTOrganismView" />
            <OTViewEntry objectClass="org.concord.otrunk.biologica.OTStaticOrganism" viewClass="org.concord.otrunk.biologica.ui.OTStaticOrganismView" />
            <OTViewEntry objectClass="org.concord.otrunk.biologica.OTMultipleOrganism" viewClass="org.concord.otrunk.biologica.ui.OTMultipleOrganismView" />
            <OTViewEntry local_id="choice_feedback_radio_view" objectClass="org.concord.otrunk.ui.OTChoiceWithFeedback" viewClass="org.concord.otrunk.ui.swing.OTChoiceRadioButtonWithFeedbackView" />
            <OTViewEntry local_id="menu-horizontal-circle" objectClass="org.concord.otrunk.udl3.OTUDLMenu" viewClass="org.concord.otrunk.udl.ui.OTUDLMenuPageView" />
            <OTViewEntry objectClass="org.concord.otrunk.ui.OTCardContainer" viewClass="org.concord.otrunk.ui.swing.OTCardContainerView" />
            <OTViewEntry objectClass="org.concord.otrunk.ui.OTBorderContainer" viewClass="org.concord.otrunk.ui.swing.OTBorderContainerView" />
            <OTViewEntry objectClass="org.concord.otrunk.ui.OTPlacementContainer" viewClass="org.concord.otrunk.ui.swing.OTPlacementContainerView" />
            <OTViewEntry local_id="text-edit" objectClass="org.concord.otrunk.ui.OTText" viewClass="org.concord.otrunk.ui.swing.OTTextEditView" />
            <OTViewEntry objectClass="org.concord.otrunk.ui.OTText" viewClass="org.concord.otrunk.ui.swing.OTTextView" />
            <OTViewEntry local_id="mode-switcher" objectClass="org.concord.otrunk.ui.OTModeSwitcher" viewClass="org.concord.otrunk.ui.swing.OTModeSwitcherBypassView" />
            <OTViewEntry objectClass="org.concord.otrunk.ui.OTModeSwitcher" viewClass="org.concord.otrunk.ui.swing.OTModeSwitcherView" />
            <OTDocumentViewConfig local_id="compound-doc-view" objectClass="org.concord.otrunk.view.document.OTCompoundDoc" viewClass="org.concord.otrunk.view.document.OTDocumentView" />
            <OTViewEntry local_id="script-button-view" objectClass="org.concord.otrunk.script.ui.OTScriptButton" viewClass="org.concord.otrunk.script.ui.OTScriptButtonView" />
            <OTViewEntry local_id="script-object-view" objectClass="org.concord.otrunk.script.ui.OTScriptObject" viewClass="org.concord.otrunk.script.ui.OTScriptObjectView" />
          </viewEntries>
        </OTViewBundle>
        <OTScriptEngineBundle>
          <engines>
            <OTScriptEngineEntry objectClass="org.concord.otrunk.script.jruby.OTJRuby" engineClass="org.concord.otrunk.script.jruby.OTJRubyEngine" />
            <OTScriptEngineEntry objectClass="org.concord.otrunk.script.js.OTJavascript" engineClass="org.concord.otrunk.script.js.OTJavascriptEngine" />
          </engines>
        </OTScriptEngineBundle>
      </bundles>
      <root>
        <OTCompoundDoc local_id="page-1" name="1">
          <bodyText>
<!--                <object refid="${pedigreeView}" editable="true" /><br/>
                <object refid="${test_pedigree_view_script}" />
                <object refid="${button_width_script_pedigree}" /><br/>
-->								<object refid="${test_xhtml_script}" />
          </bodyText>
        </OTCompoundDoc>
      </root>
      <library>
	
				<OTXHTMLScript local_id="test_xhtml_script" name="Test XHTML Script">
					<script>
						<OTJRuby src="scripts/ruby_erb_dragon_test.rb" />
					</script>
					<variables>
						<OTScriptVariable name="template">
							<reference>
								<OTBlob src="scripts/ruby_erb_dragon_test.html.erb" />
							</reference>
						</OTScriptVariable>
            <OTScriptVariableComponent name="pedigreeView">
              <reference>
                <object refid="${pedigreeView}" />
              </reference>
            </OTScriptVariableComponent>
						<OTScriptVariableComponent name="newMotherComp">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariableComponent>
						<OTScriptVariableRealObject name="newMotherObj">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariableRealObject>
						<OTScriptVariable name="newMother">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariable>
						<OTScriptVariable name="staticOrganism1">
							<reference>
								<object refid="${staticOrganismContainer}"/>
							</reference>
						</OTScriptVariable>
						<OTScriptVariable name="staticOrganism1b">
							<reference>
								<object refid="${staticOrganismContainer}"/>
							</reference>
						</OTScriptVariable>
						<OTScriptVariable name="staticOrganism2">
							<reference>
								<object refid="${staticOrganismContainer2}"/>
							</reference>
						</OTScriptVariable>
          </variables>
				</OTXHTMLScript>
				
				
        <OTScriptObject local_id="test_sex_view_script" name="Sex view script">
          <script>
            <OTJRuby src="scripts/ruby_meiosis_script.rb" />
          </script>
          <variables>
            <OTScriptVariableComponent name="meiosisView">
              <reference>
                <object refid="${meiosisView}" />
              </reference>
           </OTScriptVariableComponent>
          </variables>
          <scriptState />
        </OTScriptObject>
        <OTScriptObject local_id="test_pedigree_view_script" name="Pedigree view script">
          <script>
            <OTJRuby src="scripts/ruby_pedigree_script.rb" />
          </script>
					<variables>
            <OTScriptVariableComponent name="pedigreeView">
              <reference>
                <object refid="${pedigreeView}" />
              </reference>
            </OTScriptVariableComponent>
          </variables>
          <scriptState />
        </OTScriptObject>
        <OTScriptButton local_id="button_width_script" name="Button Width script" text="Change width">
          <script>
            <OTJRuby src="scripts/button_width_script.rb" />
          </script>
          <scriptVariables>
            <OTScriptVariable name="meiosisViewVar">
              <reference>
                <object refid="${meiosisView}" />
              </reference>
            </OTScriptVariable>
						<OTScriptVariableView name="meiosisView">
              <reference>
                <object refid="${meiosisView}" />
              </reference>
            </OTScriptVariableView>
						<OTScriptVariableComponent name="meiosisViewComp">
              <reference>
                <object refid="${meiosisView}" />
              </reference>
            </OTScriptVariableComponent>
						<OTScriptVariable name="oldMotherVar">
							<reference>
								<object refid="${femaleOrganism}" />
							</reference>
						</OTScriptVariable>
						<OTScriptVariableComponent name="oldMotherComp">
							<reference>
								<object refid="${femaleOrganism}" />
							</reference>
						</OTScriptVariableComponent>
						<OTScriptVariableRealObject name="oldMotherObj">
							<reference>
								<object refid="${femaleOrganism}" />
							</reference>
						</OTScriptVariableRealObject>
						<OTScriptVariable name="newMotherVar">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariable>
						<OTScriptVariableComponent name="newMotherComp">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariableComponent>
						<OTScriptVariableRealObject name="newMotherObj">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariableRealObject>
						<OTScriptVariable name="newMother">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariable>
          </scriptVariables>
        </OTScriptButton>
<!-- Separate copy of button for pedigree view -->
        <OTScriptButton local_id="button_width_script_pedigree" name="Display selected organisms" text="Change width">
          <script>
            <OTJRuby src="scripts/button_width_script_pedigree.rb" />
          </script>
          <scriptVariables>
            <OTScriptVariable name="pedigreeViewVar">
              <reference>
                <object refid="${pedigreeView}" />
              </reference>
            </OTScriptVariable>
						<OTScriptVariableView name="pedigreeView">
              <reference>
                <object refid="${pedigreeView}" />
              </reference>
            </OTScriptVariableView>
						<OTScriptVariableComponent name="pedigreeViewComp">
              <reference>
                <object refid="${pedigreeView}" />
              </reference>
            </OTScriptVariableComponent>
<!--						<OTScriptVariableComponent name="multipleOrganismComp">
							<reference>
								<object refid="${multipleOrganism}"/>
							</reference>
						</OTScriptVariableComponent>
-->						<OTScriptVariable name="oldMotherVar">
							<reference>
								<object refid="${femaleOrganism}" />
							</reference>
						</OTScriptVariable>
						<OTScriptVariableComponent name="oldMotherComp">
							<reference>
								<object refid="${femaleOrganism}" />
							</reference>
						</OTScriptVariableComponent>
						<OTScriptVariableRealObject name="oldMotherObj">
							<reference>
								<object refid="${femaleOrganism}" />
							</reference>
						</OTScriptVariableRealObject>
						<OTScriptVariable name="newMotherVar">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariable>
						<OTScriptVariableComponent name="newMotherComp">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariableComponent>
						<OTScriptVariableRealObject name="newMotherObj">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariableRealObject>
						<OTScriptVariable name="newMother">
							<reference>
								<object refid="${newMother}" />
							</reference>
						</OTScriptVariable>
          </scriptVariables>
        </OTScriptButton>
				
				<OTStaticOrganism local_id="staticOrganismContainer">
				</OTStaticOrganism>
				<OTStaticOrganism local_id="staticOrganismContainer2">
				</OTStaticOrganism>				
        <OTPedigree local_id="pedigreeView" height="500" width="400">
            <organisms>
                <object refid="${maleOrganism}" />
                <object refid="${femaleOrganism}" />
            </organisms>
        </OTPedigree>
				<OTMultipleOrganism local_id="multipleOrganism">
				</OTMultipleOrganism>
        <OTSex local_id="meiosisView" replayButtonEnabled="false" width="800" height="600">
          <motherOrganism>
            <object refid="${femaleOrganism}" />
          </motherOrganism>
          <fatherOrganism>
            <object refid="${maleOrganism}" />
          </fatherOrganism>
        </OTSex>
        <OTOrganism local_id="femaleOrganism">
          <name>Mom</name>
          <sex>1</sex>
          <world>
            <object refid="${dragon_world}" />
          </world>
          <alleles>b:h,a:h,b:S,a:S,b:W,a:W,b:l,a:L,b:t,a:T,b:p,a:p,b:F,a:F,b:A,a:a,b:B,a:B</alleles>
        </OTOrganism>
        <OTOrganism local_id="maleOrganism">
          <name>male</name>
          <sex>0</sex>
          <world>
            <object refid="${dragon_world}" />
          </world>
          <alleles>b:h,a:h,b:S,a:S,b:W,a:w,b:l,a:L,b:t,a:t,a:p,a:f,a:a,a:B</alleles>
        </OTOrganism>
        <OTOrganism local_id="newMother">
          <name>New Mom</name>
          <sex>1</sex>
          <world>
            <object refid="${dragon_world}" />
          </world>
          <alleles>b:H,a:H,b:S,a:S,b:W,a:W,b:l,a:L,b:t,a:T,b:p,a:p,b:F,a:F,b:A,a:A,b:B,a:B</alleles>
        </OTOrganism>
        <OTWorld local_id="dragon_world" speciesPath="org/concord/biologica/worlds/dragonmarkers.xml" />
      </library>
    </OTSystem>
  </objects>
</otrunk>

