<?xml version="1.0" encoding="UTF-8"?>
<?eclipse version="3.4"?>
<plugin>
   <extension
         id="application"
         point="org.eclipse.core.runtime.applications">
      <application
            icon="distributionResources/appIcon.icns"
            visible="true">
         <run
               class="rulebender.Application">
         </run>
      </application>
   </extension>
   <extension
         point="org.eclipse.ui.perspectives">
      <perspective
            class="rulebender.Perspective"
            icon="icons/views/CMap.png"
            id="rulebender.perspective"
            name="Default">
      </perspective>
      <perspective
            class="rulebender.perspective.Custom2Perspective"
            id="rulebender.perspective.custom2perspective"
            name="Custom2">
      </perspective>      
   </extension>
   <extension
         point="org.eclipse.ui.perspectiveExtensions">
      <perspectiveExtension
            targetID="rulebender.perspective">
		<view
               closeable="true"
               id="rulebender.cnf.CommonNavigator"
               minimized="false"
               moveable="true"
               ratio="0.3f"
               relationship="left"
               relative="org.eclipse.ui.editorss"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.contactmap.view.ContactMapView"
               minimized="false"
               moveable="true"
               ratio="0.6f"
               relationship="right"
               relative="org.eclipse.ui.editorss"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.views.Console"
               minimized="false"
               moveable="true"
               ratio="0.7f"
               relationship="bottom"
               relative="org.eclipse.ui.editorss"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.properties.view.PropertiesSheetView"
               minimized="false"
               moveable="true"
               relationship="bottom"
               relative="rulebender.contactmap.view.ContactMapView"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.views.problemview"
               minimized="false"
               moveable="true"
               relationship="stack"
               relative="rulebender.views.Console"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.simulationjournaling.views.timelineview"
               minimized="false"
               moveable="true"
               relationship="stack"
               relative="rulebender.views.Console"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.speciesgraph.SpeciesGraphView"
               minimized="false"
               moveable="true"
               relationship="stack"
               relative="rulebender.contactmap.view.ContactMapView"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.simulate.view.SimulateView"
               minimized="false"
               moveable="true"
               ratio="0.3f"
               relationship="stack"
               relative="rulebender.contactmap.view.ContactMapView"
               showTitle="true"
               standalone="false"
               visible="true">
         </view>
         <view
               closeable="true"
               id="org.eclipse.ui.views.ProgressView"
               minimized="false"
               moveable="true"
               relationship="stack"
               relative="rulebender.properties.view.PropertiesSheetView"
               visible="true">
         </view>
      </perspectiveExtension>
      <perspectiveExtension
            targetID="rulebender.perspective.custom2perspective">
		<view
               closeable="true"
               id="rulebender.cnf.CommonNavigator"
               minimized="false"
               moveable="true"
               ratio="0.2f"
               relationship="left"
               relative="org.eclipse.ui.editorss"
               visible="true">
         </view>         
         <view
         	   closeable="true"
               id="rulebender.simulationjournaling.view.smallmultiplesview"
               minimized="false"
               moveable="true"
               ratio="0.8f"
               relationship="right"
               relative="org.eclipse.ui.editorss"
               visible="true">
         </view>
         <view
               closeable="true"
               id="rulebender.simulationjournaling.view.timelineview"
               minimized="false"
               moveable="true"
               ratio="0.8f"
               relationship="bottom"
               relative="rulebender.simulationjournaling.view.smallmultiplesview"
               visible="true">
         </view>
      </perspectiveExtension>
   </extension>
   <extension
         point="org.eclipse.ui.views">
      <view
            allowMultiple="false"
            class="org.eclipse.ui.internal.console.ConsoleView"
            icon="icons/views/console_view.png"
            id="rulebender.views.Console"
            name="Console"
            restorable="true">
      </view>
      <view
            allowMultiple="false"
            class="rulebender.simulationjournaling.view.TimelineView"
            icon="icons/views/timeline.png"
            id="rulebender.simulationjournaling.views.timelineview"
            name="Timeline"
            restorable="true">
      </view>
      <view
            class="rulebender.contactmap.view.ContactMapView"
            icon="icons/views/CMap.png"
            id="rulebender.contactmap.view.ContactMapView"
            name="Contact Map"
            restorable="true">
      </view>
      <view
            class="rulebender.speciesgraph.view.SpeciesGraphView"
            icon="icons/views/speciesGraph.png"
            id="rulebender.speciesgraph.SpeciesGraphView"
            name="Species Graph"
            restorable="true">
      </view>
      <view
            class="rulebender.specieslist.view.SpeciesListView"
            id="rulebender.specieslist.view.SpeciesListView"
            name="Species List"
            restorable="true">
      </view>
      <view
            class="rulebender.influencegraph.view.InfluenceGraphView"
            icon="icons/views/IGraph.png"
            id="rulebender.influencegraph.view.InfluenceGraphView"
            name="InfluenceGraph"
            restorable="true">
      </view>
      <view
            class="org.eclipse.ui.views.properties.PropertySheet"
            icon="icons/views/properties.png"
            id="rulebender.properties.view.PropertiesSheetView"
            name="Properties"
            restorable="true">
      </view>
      <view
            class="rulebender.simulate.view.SimulateView"
            icon="icons/views/run.png"
            id="rulebender.simulate.view.SimulateView"
            name="Simulation"
            restorable="true">
      </view>
      <view
            class="org.eclipse.ui.navigator.CommonNavigator"
            icon="icons/views/tree_explorer.png"
            id="rulebender.cnf.CommonNavigator"
            name="Navigator"
            restorable="true">
      </view>
      <view
            category="org.eclipse.ui"
            class="org.eclipse.ui.ExtensionFactory:progressView"
            icon="icons/views/pview.png"
            id="org.eclipse.ui.views.ProgressView"
            name="Progress View">
      </view>
      <view
            class="org.eclipse.ui.internal.views.markers.ProblemsView"
            icon="icons/views/problems_view.png"
            id="rulebender.views.problemview"
            name="Problems"
            restorable="true">
      </view>
      <view
            class="rulebender.simulationjournaling.view.SmallMultiplesView"
            id="rulebender.simulationjournaling.view.smallmultiplesview"
            name="Small Multiples"
            restorable="true">
      </view>
      <view
            class="rulebender.simulationjournaling.view.TimelineView"
            id="rulebender.simulationjournaling.view.timelineview"
            name="Timeline"
            restorable="true">
      </view>      
      <view
            class="rulebender.example.ExampleView"
            icon="icons/views/example.png"
            id="rulebender.example.exampleview"
            name="Example View Extension"
            restorable="true">
      </view>
   </extension>
   <extension
         point="org.eclipse.ui.menus">
      <menuContribution
            locationURI="menu:org.eclipse.ui.main.menu">
         <menu
               label="File">
            <command
                  commandId="rulebender.commands.SampleProjects"
                  label="New  BioNetGen  Project"
                  style="push">
            </command>
            <separator
                  name="rulebender.separator1"
                  visible="true">
            </separator>
            <command
                  commandId="org.eclipse.ui.newWizard"
                  label="New..."
                  style="push">
            </command>
            <command
                  commandId="org.eclipse.ui.file.save"
                  label="Save"
                  mnemonic="s">
            </command>
            <command
                  commandId="org.eclipse.ui.file.saveAll"
                  label="Save All">
            </command>
            <separator
                  name="rulebender.separator2">
            </separator>
            <command
                  commandId="org.eclipse.ui.file.print"
                  label="Print"
                  style="push">
            </command>
            <separator
                  name="rulebender.separator3">
            </separator>
            <command
                  commandId="org.eclipse.ui.file.exit"
                  label="Exit"
                  style="push">
            </command>
         </menu>
         <menu
               label="Edit">
            <command
                  commandId="org.eclipse.ui.edit.cut"
                  label="Cut"
                  mnemonic="x"
                  style="push">
            </command>
            <command
                  commandId="org.eclipse.ui.edit.copy"
                  label="Copy"
                  mnemonic="c"
                  style="push">
            </command>
            <command
                  commandId="org.eclipse.ui.edit.paste"
                  label="Paste"
                  mnemonic="v"
                  style="push">
            </command>
            <separator
                  name="rulebender.separator1">
            </separator>
            <command
                  commandId="org.eclipse.ui.edit.undo"
                  label="Undo"
                  mnemonic="z"
                  style="push">
            </command>
            <command
                  commandId="org.eclipse.ui.edit.redo"
                  label="Redo"
                  mnemonic="y"
                  style="push">
            </command>
            <separator
                  name="rulebender.separator2">
            </separator>
            <command
                  commandId="org.eclipse.ui.edit.findReplace"
                  label="Find &amp;&amp; Replace..."
                  mnemonic="f"
                  style="push">
            </command>
            <separator
                  name="rulebender.separator3">
            </separator>
            <command
                  commandId="org.eclipse.ui.edit.selectAll"
                  label="Select All"
                  mnemonic="a"
                  style="push">
            </command>
         </menu>
         <menu
               label="Window">
            <command
                  commandId="org.eclipse.ui.window.preferences"
                  label="Preferences..."
                  style="push">
            </command>
            <command
                  commandId="rulebender.commands.SwitchWorkspace"
                  label="Switch Workspace (restart required)"
                  style="push">
            </command>
            <command
                  commandId="rulebender.commands.CleanWorkspace"
                  label="Recover Workspace (restart required)"
                  style="push">
            </command>
            <command
                  commandId="org.eclipse.ui.help.aboutAction"
                  label="About..."
                  style="push">
            </command>
            <menu
                  label="Show View...">
               <dynamic
                     class="rulebender.ui.menu.ShowViewContributionItem"
                     id="rulebendender.ui.menu.showViewMenu">
               </dynamic>
            </menu>
         </menu>
      </menuContribution>
      <menuContribution
            locationURI="toolbar:org.eclipse.ui.main.toolbar">
         <toolbar
               id="rulebender.toolbars.main">
         </toolbar>
      </menuContribution>
   </extension>
       <extension
         point="org.eclipse.ui.navigator.viewer">
       <viewerContentBinding 
            viewerId="rulebender.cnf.CommonNavigator">
          <includes>
       	     <contentExtension pattern="org.eclipse.ui.navigator.resourceContent" />		       	      
	     <contentExtension pattern="org.eclipse.ui.navigator.resources.filters.*"/>
          </includes>
       </viewerContentBinding>
       <viewerActionBinding
             viewerId="rulebender.cnf.CommonNavigator">
          <includes>
             <actionExtension
                   pattern="org.eclipse.ui.navigator.resources.*">
             </actionExtension>
          </includes>
       </viewerActionBinding>
   </extension>
  <extension
         point="org.eclipse.ui.commands">
      <command
            defaultHandler="rulebender.core.commands.OpenFileHandler"
            id="rulebender.commands.OpenFile"
            name="OpenFile">
      </command>
      <command
            defaultHandler="rulebender.core.commands.SwitchWorkspace"
            id="rulebender.commands.SwitchWorkspace"
            name="Switch Workspace">
      </command>
      <command
            defaultHandler="rulebender.core.commands.CleanWorkspace"
            id="rulebender.commands.CleanWorkspace"
            name="Recover Workspace">
      </command>
      <command
            defaultHandler="rulebender.core.commands.SampleProjects"
            id="rulebender.commands.SampleProjects"
            name="Create rhc Sample">
      </command>
      <command
            defaultHandler="rulebender.core.commands.CloseTopConsole"
            id="rulebender.core.commands.CloseTopConsole"
            name="Close Console">
      </command>
   </extension>
   <extension
         point="org.eclipse.ui.preferencePages">
      <page
            class="rulebender.preferences.views.MyFieldEditorPreferencePage"
            id="rulebender.views.preferences.preferencePage"
            name="Simulator">
      </page>
      <page
            class="rulebender.preferences.views.MySettingsPreferencePage"
            id="rulebender.views.preferences.preferencePage"
            name="Settings">
      </page>
   </extension>
   <extension
         point="org.eclipse.ui.editors">
      <editor
            class="rulebender.editors.simple.SimpleEditor"
            contributorClass="org.eclipse.ui.texteditor.BasicTextEditorActionContributor"
            default="true"
            extensions="txt, log"
            id="rulebender.editors.simple"
            name="Simple Editor">
      </editor>
      <editor
            class="org.eclipse.ui.editors.text.TextEditor"
            contributorClass="org.eclipse.ui.texteditor.BasicTextEditorActionContributor"
            default="false"
            extensions="pos"
            icon="icons/views/pos.png"
            id="rulebender.editors.position"
            name="Position Editor">
      </editor>
      <editor
            class="rulebender.editors.bngl.BNGLEditor"
            contributorClass="org.eclipse.ui.texteditor.BasicTextEditorActionContributor"
            default="false"
            extensions="bngl"
            icon="/icons/views/CMap.png"
            id="rulebender.editors.bngl"
            name="BNGL Editor">
      </editor>
      <editor
            class="rulebender.editors.net.NETEditor"
            contributorClass="org.eclipse.ui.texteditor.BasicTextEditorActionContributor"
            default="false"
            extensions="net"
            id="rulebender.editors.net"
            name="NET File Editor">
      </editor>
      <editor
            class="rulebender.editors.bnga.BNGAMultiPageEditor"
            contributorClass="rulebender.editors.bnga.BNGAMultiPageEditorContributor"
            extensions="bnga"
            icon="icons/sample.png"
            id="rulebender.editors.bnga.BNGAMultiPageEditor"
            name="BioNetGen Actions Editor">
      </editor>
      <editor
            class="rulebender.editors.dat.DATMultiPageEditor"
            default="false"
            extensions="gdat, cdat, scan"
            icon="icons/views/Results.png"
            id="rulebender.editors.dat"
            name="Results File">
      </editor>
   </extension>
   <extension
         id="product"
         point="org.eclipse.core.runtime.products">
      <product
            application="rulebender.application"
            name="RuleBender">
         <property
               name="preferenceCustomization"
               value="plugin_customization.ini">
         </property>
         <property
               name="appName"
               value="RuleBender">
         </property>
         <property
               name="aboutText"
               value="RuleBender 2.1.0&#x0A;&#x0A;RuleBender was developed in collaboration between the groups of Dr. James R. Faeder and Dr. Elisabeta G. Marai at the University of Pittsburgh. It is currently maintained by the Faeder Lab in the Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh.&#x0A;&#x0A;Please send all feedback and questions to help@rulebender.org.">
         </property>
         <property
               name="startupProgressRect"
               value="5,275,445,15">
         </property>
      </product>
   </extension>
  
 <extension 
 		id="rulebender.markers.bnglerrormarker"
 		name="BNGL Error"
 		point= "org.eclipse.core.resources.markers"> 
	<super
         type="org.eclipse.core.resources.problemmarker">
   	</super>
   <super
         type="org.eclipse.core.resources.textmarker">
   </super>
   <persistent
         value="false">
   	</persistent>
 </extension>
 



  <extension
        id="rulebender.markers.textinstance"
        name="Text"
        point="org.eclipse.core.resources.markers">
     <persistent
           value="false">
     </persistent>
     <super
           type="org.eclipse.core.resources.textmarker">
     </super>
  </extension>
  <extension
        point="org.eclipse.ui.editors.annotationTypes">
     <type
           markerType="rulebender.markers.textinstance"
           name="rulebender.annotations.textinstance">
     </type>
  </extension>

<extension
      point="org.eclipse.ui.editors.markerAnnotationSpecification">
   <specification
         annotationType="rulebender.annotations.textinstance"
         colorPreferenceKey="rulebender.annotations.textinstance.color"
         colorPreferenceValue="155, 255, 155"
         contributesToHeader="false"
         highlightPreferenceKey="rulebender.annotations.textinstance.highlight"
         highlightPreferenceValue="true"
         includeOnPreferencePage="true"
         label="Text Instance Marker"
         overviewRulerPreferenceKey="rulebender.annotations.textinstance.overview"
         overviewRulerPreferenceValue="true"
         presentationLayer="0"
         textPreferenceKey="rulebender.annotations.textinstance.text"
         textPreferenceValue="true"
         textStylePreferenceValue="BOX"
         verticalRulerPreferenceKey="rulebender.annotations.textinstance.ruler"
         verticalRulerPreferenceValue="true">
   </specification>
</extension>
<extension
      point="org.eclipse.ui.startup">
   <startup
         class="rulebender.core.utility.Console">
   </startup>
</extension>
<extension
      id="TestRuleBenderProduct"
      point="org.eclipse.core.runtime.products">
   <product
         application="rulebender.application"
         name="RuleBender">
      <property
            name="appName"
            value="RuleBender">
      </property>
   </product>
</extension>
<extension
      point="org.eclipse.ui.console.consolePatternMatchListeners">
   <consolePatternMatchListener
         class="rulebender.core.utility.ConsolePatternMatchListenerDelegate"
         id="rulebender.core.utility.consolePatternMatchListener"
         regex="ABORT:\s+.*\s+at line \d+">
      <enablement></enablement>
   </consolePatternMatchListener>
</extension>

</plugin>