<?xml version="1.0" encoding="UTF-8"?>
<otrunk id="ee7a7352-b52f-4e20-95b8-f48af633be9f">
  <imports>
    <import class="org.concord.otrunk.OTSystem" />
    <import class="org.concord.otrunk.view.OTViewEntry" />
    <import class="org.concord.otrunk.view.OTViewBundle" />
    <import class="org.concord.otrunk.biologica.qtl.OTQTLSimulation" />
    <import class="org.concord.otrunk.biologica.qtl.OTQTL" />
    <import class="org.concord.datagraph.state.OTDataGraph"/>
    <import class="org.concord.datagraph.state.OTDataAxis"/>
    <import class="org.concord.otrunk.view.document.OTCompoundDoc" />
  </imports>

  <objects>
    <OTSystem>
      <bundles>
        <OTViewBundle showLeftPanel="false">
          <viewEntries>
            <OTViewEntry
              objectClass="org.concord.otrunk.biologica.qtl.OTQTLSimulation"
              viewClass="org.concord.otrunk.biologica.qtl.OTQTLSimulationView" />
            <OTViewEntry 
              objectClass="org.concord.datagraph.state.OTDataGraph" 
              viewClass="org.concord.datagraph.state.OTDataGraphView"/>
            <OTViewEntry
              objectClass="org.concord.otrunk.view.document.OTDocument"
              viewClass="org.concord.otrunk.view.document.OTDocumentView" />
          </viewEntries>
        </OTViewBundle>
      </bundles>

      <root>
        <OTCompoundDoc name="QTL">
          <bodyText>
            <object refid="${sim}" /><br/>
            <object refid="${graph}" />
          </bodyText>
          <documentRefs>
            <OTQTLSimulation local_id="sim" numberOfIndividuals="200" numberOfMarkersPerChromosome="200" method="em">
              <chromosomeLengths>
                <int>100</int>
                <int>100</int>
                <int>30</int>
              </chromosomeLengths>
              <thresholdValues>
                <double>0.01</double>
                <double>0.10</double>
                <double>0.35</double>
              </thresholdValues>
              <locations>
                <OTQTL chromosome="1" locationInCM="24" additiveEffect="0.5" dominanceDeviation="-0.5" />
                <OTQTL chromosome="2" locationInCM="67" additiveEffect="0.7" dominanceDeviation="0.5" />
                <!-- OTQTL chromosome="2" locationInCM="10" additiveEffect="0.7" dominanceDeviation="0.5" /> -->
              </locations>
              <dataGraph>
                <object refid="${graph}" />
              </dataGraph>
            </OTQTLSimulation>
            <OTDataGraph local_id="graph" name="LOD Scores">
              <xDataAxis>
                <OTDataAxis min="0" max="100" label="Position" units="cM" />
              </xDataAxis>
              <yDataAxis>
                <OTDataAxis min="0" max="10" label="LOD" units="" />
              </yDataAxis>
            </OTDataGraph>
          </documentRefs>
        </OTCompoundDoc>

      </root>

    </OTSystem>
  </objects>
</otrunk>