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JWS-114 Bumping varied config files and jetbrains xmls. Also adding some java classes...
[jabaws.git] / .idea / workspace.xml
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index 863a1f6..3169d8a 100644 (file)
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -6,11 +6,9 @@
   </component>
   <component name="ChangeListManager">
     <list default="true" id="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" name="Default" comment="">
-      <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/.idea/deployment.xml" />
-      <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/.idea/webServers.xml" />
-      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.gitignore" afterPath="$PROJECT_DIR$/.gitignore" />
-      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/ant.xml" afterPath="$PROJECT_DIR$/.idea/ant.xml" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.classpath" afterPath="$PROJECT_DIR$/.classpath" />
       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/build.xml" afterPath="$PROJECT_DIR$/build.xml" />
     </list>
     <ignored path="jabaws-dev.iws" />
     <ignored path=".idea/workspace.xml" />
@@ -79,81 +77,85 @@
   </component>
   <component name="FileEditorManager">
     <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
-      <file leaf-file-name="build.xml" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/build.xml">
+      <file leaf-file-name="template_header.jsp" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/website/template_header.jsp">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="328">
-              <caret line="564" column="68" lean-forward="true" selection-start-line="564" selection-start-column="68" selection-end-line="564" selection-end-column="68" />
-              <folding />
+            <state relative-caret-position="278">
+              <caret line="121" column="28" lean-forward="false" selection-start-line="121" selection-start-column="28" selection-end-line="121" selection-end-column="28" />
+              <folding>
+                <marker date="1491927253000" expanded="true" signature="6644:6648" ph="..." />
+              </folding>
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name=".gitignore" pinned="false" current-in-tab="true">
-        <entry file="file://$PROJECT_DIR$/.gitignore">
+      <file leaf-file-name="Joblist.jsp" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/website/statpages/Joblist.jsp">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="0">
+            <state relative-caret-position="-846">
               <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
               <folding />
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="RegistryWS.java" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/RegistryWS.java">
+      <file leaf-file-name="MonthlySummary.jsp" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/website/statpages/MonthlySummary.jsp">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="705">
-              <caret line="47" column="13" lean-forward="false" selection-start-line="47" selection-start-column="13" selection-end-line="47" selection-end-column="13" />
+            <state relative-caret-position="650">
+              <caret line="99" column="143" lean-forward="false" selection-start-line="99" selection-start-column="143" selection-end-line="99" selection-end-column="143" />
               <folding />
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="HttpCodeResponseServiceStatus.java" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/webservices/compbio/stat/servlet/HttpCodeResponseServiceStatus.java">
+      <file leaf-file-name="download.jsp" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/website/download.jsp">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="1035">
-              <caret line="69" column="28" lean-forward="false" selection-start-line="69" selection-start-column="28" selection-end-line="69" selection-end-column="28" />
-              <folding />
+            <state relative-caret-position="276">
+              <caret line="174" column="167" lean-forward="false" selection-start-line="174" selection-start-column="167" selection-end-line="174" selection-end-column="167" />
+              <folding>
+                <marker date="1491927221000" expanded="true" signature="12213:12354" ph="..." />
+              </folding>
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="WSTester.java" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/client/WSTester.java">
+      <file leaf-file-name="Executable.properties" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/conf/Executable.properties">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="6720">
-              <caret line="448" column="60" lean-forward="false" selection-start-line="448" selection-start-column="60" selection-end-line="448" selection-end-column="60" />
+            <state relative-caret-position="-1988">
+              <caret line="64" column="78" lean-forward="false" selection-start-line="64" selection-start-column="29" selection-end-line="64" selection-end-column="78" />
               <folding />
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="WSTesterTester.java" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/testsrc/compbio/ws/client/WSTesterTester.java">
+      <file leaf-file-name="Executable.properties.dundee" pinned="false" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/conf/Executable.properties.dundee">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="510">
-              <caret line="34" column="32" lean-forward="false" selection-start-line="34" selection-start-column="32" selection-end-line="34" selection-end-column="32" />
+            <state relative-caret-position="-2948">
+              <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
               <folding />
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="Alignment.java" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
+      <file leaf-file-name="Engine.cluster.properties" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/conf/Engine.cluster.properties">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="645">
-              <caret line="43" column="20" lean-forward="false" selection-start-line="43" selection-start-column="15" selection-end-line="43" selection-end-column="20" />
+            <state relative-caret-position="255">
+              <caret line="17" column="24" lean-forward="true" selection-start-line="17" selection-start-column="24" selection-end-line="17" selection-end-column="24" />
               <folding />
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="SequenceUtil.java" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/SequenceUtil.java">
+      <file leaf-file-name="template_footer.jsp" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/website/template_footer.jsp">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="912">
-              <caret line="504" column="56" lean-forward="false" selection-start-line="504" selection-start-column="56" selection-end-line="504" selection-end-column="56" />
+            <state relative-caret-position="264">
+              <caret line="68" column="28" lean-forward="false" selection-start-line="68" selection-start-column="28" selection-end-line="68" selection-end-column="28" />
               <folding />
             </state>
           </provider>
@@ -163,21 +165,48 @@
   </component>
   <component name="FindInProjectRecents">
     <findStrings>
-      <find>&lt;target name=</find>
-      <find>jabaws</find>
-      <find>2.1</find>
-      <find>jpred</find>
-      <find>http://localhost:8080/jabaws/RegistryWS?wsdl</find>
-      <find>RegistryWS?wsdl</find>
-      <find>RegistryWS</find>
-      <find>8080</find>
-      <find>project</find>
+      <find>http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws/ProbconsWS?wsdl</find>
+      <find>http://webserv1.cluster.lifesci.dundee.ac.uk:8089S?wsdl</find>
+      <find>http://webserv1.cluster.lifesci.dundee.ac.uk:8089</find>
+      <find>localhost</find>
+      <find>http://localhost:8080</find>
+      <find>Preset Huge alignments</find>
+      <find>Huge alignments</find>
+      <find>with</find>
+      <find>ResultNotAvailableException</find>
+      <find>test_outfile</find>
+      <find>FileNotFoundException</find>
+      <find>PStruct</find>
+      <find>mode</find>
+      <find>readStatisticsClusterExecution</find>
+      <find>testsrc</find>
+      <find>c</find>
+      <find>test_group_runner</find>
+      <find>singleTest</find>
+      <find>test_group_runner2</find>
+      <find>-c</find>
+      <find>test.</find>
+      <find>jaba.war</find>
+      <find>website</find>
+      <find>js</find>
+      <find>man_</find>
+      <find>man</find>
+      <find>ma</find>
+      <find>m</find>
+      <find>j</find>
+      <find>jsp</find>
     </findStrings>
     <replaceStrings>
       <replace>2.2</replace>
+      <replace>target=&quot;1.8&quot;</replace>
+      <replace>webapps/jabaws</replace>
+      <replace>test_group_runner</replace>
+      <replace>test_group_runner2</replace>
     </replaceStrings>
     <dirStrings>
       <dir>$PROJECT_DIR$</dir>
+      <dir>$PROJECT_DIR$/testsrc</dir>
+      <dir>$PROJECT_DIR$/website/statpages</dir>
     </dirStrings>
   </component>
   <component name="FindManager">
@@ -202,15 +231,6 @@
   <component name="IdeDocumentHistory">
     <option name="CHANGED_PATHS">
       <list>
-        <option value="$PROJECT_DIR$/wsbuild.xml" />
-        <option value="$PROJECT_DIR$/website/about.jsp" />
-        <option value="$PROJECT_DIR$/website/template_header.jsp" />
-        <option value="$PROJECT_DIR$/website/template_footer.jsp" />
-        <option value="$PROJECT_DIR$/website/statpages/ServicesStatus.jsp" />
-        <option value="$PROJECT_DIR$/website/statpages/MonthlySummary.jsp" />
-        <option value="$PROJECT_DIR$/website/statpages/Joblist.jsp" />
-        <option value="$PROJECT_DIR$/.gitignore" />
-        <option value="$PROJECT_DIR$/build.xml" />
         <option value="$PROJECT_DIR$/webservices/compbio/data/msa/Category.java" />
         <option value="$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java" />
         <option value="$PROJECT_DIR$/datamodel/compbio/data/sequence/Program.java" />
@@ -228,6 +248,40 @@
         <option value="$PROJECT_DIR$/webservices/compbio/ws/server/resource/JpredWS.wsdl" />
         <option value="$PROJECT_DIR$/webservices/compbio/ws/client/Services.java" />
         <option value="$PROJECT_DIR$/website/man_docs.jsp" />
+        <option value="$PROJECT_DIR$/conf/Engine.cluster.properties" />
+        <option value="$PROJECT_DIR$/conf/Engine.local.properties" />
+        <option value="$PROJECT_DIR$/webservices/compbio/ws/client/AAConClient.java" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/ws/server/RegistryWSTester.java" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/ws/client/WSTesterTester.java" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/ws/client/TestRNAalifoldWS.java" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/ws/client/TestIUPredWS.java" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/ws/client/TestAAConWS.java" />
+        <option value="$PROJECT_DIR$/testsrc/testdata/MuscleLimits.xml" />
+        <option value="$PROJECT_DIR$/datamodel/compbio/data/sequence/RNAStructReader.java" />
+        <option value="$PROJECT_DIR$/conf/settings/RNAalifoldParameters.xml" />
+        <option value="$PROJECT_DIR$/conf/settings/TcoffeeParameters.xml" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java" />
+        <option value="$PROJECT_DIR$/conf/settings/TcoffeePresets.xml" />
+        <option value="$PROJECT_DIR$/binaries/src/setexecflag.sh" />
+        <option value="$PROJECT_DIR$/conf/Executable.properties" />
+        <option value="$PROJECT_DIR$/binaries/src/compilebin.sh" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/runner/msa/ClustalOTester.java" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/runner/msa/TcoffeeParametersTester.java" />
+        <option value="$PROJECT_DIR$/testsrc/compbio/metadata/AllTestSuit.java" />
+        <option value="$PROJECT_DIR$/docs/generate_man.sh" />
+        <option value="$PROJECT_DIR$/website/man_serverwar.jsp" />
+        <option value="$PROJECT_DIR$/website/man_pages_old/man_stats.jsp" />
+        <option value="$PROJECT_DIR$/website/man_about.jsp" />
+        <option value="$PROJECT_DIR$/website/man_pages_old/man_about.jsp" />
+        <option value="$PROJECT_DIR$/website/index.jsp" />
+        <option value="$PROJECT_DIR$/website/about.jsp" />
+        <option value="$PROJECT_DIR$/website/getting_started.jsp" />
+        <option value="$PROJECT_DIR$/website/template_footer.jsp" />
+        <option value="$PROJECT_DIR$/build.xml" />
+        <option value="$PROJECT_DIR$/website/statpages/ServicesStatus.jsp" />
+        <option value="$PROJECT_DIR$/website/statpages/MonthlySummary.jsp" />
+        <option value="$PROJECT_DIR$/website/template_header.jsp" />
+        <option value="$PROJECT_DIR$/website/download.jsp" />
       </list>
     </option>
   </component>
@@ -238,10 +292,10 @@
     <sorting>DEFINITION_ORDER</sorting>
   </component>
   <component name="ProjectFrameBounds">
-    <option name="x" value="1440" />
+    <option name="x" value="1439" />
     <option name="y" value="23" />
     <option name="width" value="1920" />
-    <option name="height" value="1139" />
+    <option name="height" value="1140" />
   </component>
   <component name="ProjectInspectionProfilesVisibleTreeState">
     <entry key="Project Default">
@@ -280,8 +334,7 @@
       <foldersAlwaysOnTop value="true" />
     </navigator>
     <panes>
-      <pane id="Scratches" />
-      <pane id="Scope" />
+      <pane id="PackagesPane" />
       <pane id="ProjectPane">
         <subPane>
           <PATH>
@@ -294,9 +347,38 @@
               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
             </PATH_ELEMENT>
           </PATH>
+          <PATH>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="jabaws-dev" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="jabaws" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="website" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+          </PATH>
+          <PATH>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="jabaws-dev" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="jabaws" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="conf" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+          </PATH>
         </subPane>
       </pane>
-      <pane id="PackagesPane" />
+      <pane id="Scratches" />
+      <pane id="Scope" />
     </panes>
   </component>
   <component name="PropertiesComponent">
@@ -338,12 +420,28 @@
     <property name="settings.editor.selected.configurable" value="web.server" />
   </component>
   <component name="RecentsManager">
+    <key name="MoveFile.RECENT_KEYS">
+      <recent name="$PROJECT_DIR$/website/man_pages_old" />
+      <recent name="$PROJECT_DIR$/website" />
+    </key>
     <key name="CopyFile.RECENT_KEYS">
       <recent name="$PROJECT_DIR$/website" />
       <recent name="$PROJECT_DIR$/website/static/css" />
       <recent name="$PROJECT_DIR$/website/static/img" />
     </key>
   </component>
+  <component name="RunDashboard">
+    <option name="ruleStates">
+      <list>
+        <RuleState>
+          <option name="name" value="ConfigurationTypeDashboardGroupingRule" />
+        </RuleState>
+        <RuleState>
+          <option name="name" value="StatusDashboardGroupingRule" />
+        </RuleState>
+      </list>
+    </option>
+  </component>
   <component name="RunManager">
     <configuration default="true" type="#org.jetbrains.idea.devkit.run.PluginConfigurationType" factoryName="Plugin">
       <module name="" />
@@ -490,6 +588,17 @@
       <listeners />
       <method />
     </configuration>
+    <configuration default="true" type="BashConfigurationType" factoryName="Bash">
+      <option name="INTERPRETER_OPTIONS" value="" />
+      <option name="INTERPRETER_PATH" value="/bin/bash" />
+      <option name="WORKING_DIRECTORY" value="" />
+      <option name="PARENT_ENVS" value="true" />
+      <option name="SCRIPT_NAME" value="" />
+      <option name="PARAMETERS" value="" />
+      <module name="" />
+      <envs />
+      <method />
+    </configuration>
     <configuration default="true" type="Cold Fusion runner description" factoryName="Cold Fusion" custom_browser="" web_path="">
       <method />
     </configuration>
@@ -512,26 +621,6 @@
       <envs />
       <method />
     </configuration>
-    <configuration default="true" type="DjangoTestsConfigurationType" factoryName="Django tests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs>
-        <env name="PYTHONUNBUFFERED" value="1" />
-      </envs>
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="TARGET" value="" />
-      <option name="SETTINGS_FILE" value="" />
-      <option name="CUSTOM_SETTINGS" value="false" />
-      <option name="USE_OPTIONS" value="false" />
-      <option name="OPTIONS" value="" />
-      <method />
-    </configuration>
     <configuration default="true" type="FlashRunConfigurationType" factoryName="Flash App">
       <option name="BCName" value="" />
       <option name="IOSSimulatorSdkPath" value="" />
@@ -648,6 +737,13 @@
       <envs />
       <method />
     </configuration>
+    <configuration default="true" type="JavaScriptTestRunnerJest" factoryName="Jest">
+      <node-interpreter value="project" />
+      <working-dir value="" />
+      <envs />
+      <scope-kind value="ALL" />
+      <method />
+    </configuration>
     <configuration default="true" type="JavaScriptTestRunnerProtractor" factoryName="Protractor">
       <config-file value="" />
       <node-interpreter value="project" />
@@ -682,55 +778,6 @@
       <envs />
       <method />
     </configuration>
-    <configuration default="true" type="NodeJSConfigurationType" factoryName="Node.js" path-to-node="project" working-dir="">
-      <method />
-    </configuration>
-    <configuration default="true" type="PyBehaveRunConfigurationType" factoryName="Behave">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="ADDITIONAL_ARGS" value="" />
-      <method />
-    </configuration>
-    <configuration default="true" type="PyLettuceRunConfigurationType" factoryName="Lettuce">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="ADDITIONAL_ARGS" value="" />
-      <method />
-    </configuration>
-    <configuration default="true" type="PythonConfigurationType" factoryName="Python">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs>
-        <env name="PYTHONUNBUFFERED" value="1" />
-      </envs>
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="PARAMETERS" value="" />
-      <option name="SHOW_COMMAND_LINE" value="false" />
-      <method />
-    </configuration>
     <configuration default="true" type="Remote" factoryName="Remote">
       <option name="USE_SOCKET_TRANSPORT" value="true" />
       <option name="SERVER_MODE" value="false" />
@@ -739,40 +786,6 @@
       <option name="PORT" value="5005" />
       <method />
     </configuration>
-    <configuration default="true" type="ScalaTestRunConfiguration" factoryName="ScalaTest">
-      <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
-      <module name="" />
-      <setting name="path" value="" />
-      <setting name="package" value="" />
-      <setting name="vmparams" value="" />
-      <setting name="params" value="" />
-      <setting name="workingDirectory" value="" />
-      <setting name="searchForTest" value="Across module dependencies" />
-      <setting name="testName" value="" />
-      <setting name="testKind" value="Class" />
-      <setting name="showProgressMessages" value="true" />
-      <classRegexps />
-      <testRegexps />
-      <envs />
-      <method />
-    </configuration>
-    <configuration default="true" type="Specs2RunConfiguration" factoryName="Specs2">
-      <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
-      <module name="" />
-      <setting name="path" value="" />
-      <setting name="package" value="" />
-      <setting name="vmparams" value="" />
-      <setting name="params" value="" />
-      <setting name="workingDirectory" value="" />
-      <setting name="searchForTest" value="Across module dependencies" />
-      <setting name="testName" value="" />
-      <setting name="testKind" value="Class" />
-      <setting name="showProgressMessages" value="true" />
-      <classRegexps />
-      <testRegexps />
-      <envs />
-      <method />
-    </configuration>
     <configuration default="true" type="SpringBootApplicationConfigurationType" factoryName="Spring Boot">
       <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
       <module name="" />
@@ -807,19 +820,6 @@
       <listeners />
       <method />
     </configuration>
-    <configuration default="true" type="Tox" factoryName="Tox">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <module name="jabaws-dev" />
-      <method />
-    </configuration>
     <configuration default="true" type="js.build_tools.gulp" factoryName="Gulp.js">
       <node-interpreter>project</node-interpreter>
       <node-options />
@@ -836,152 +836,12 @@
       <envs />
       <method />
     </configuration>
-    <configuration default="true" type="mocha-javascript-test-runner" factoryName="Mocha">
-      <node-interpreter>project</node-interpreter>
-      <node-options />
-      <working-directory />
-      <pass-parent-env>true</pass-parent-env>
-      <envs />
-      <ui />
-      <extra-mocha-options />
-      <test-kind>DIRECTORY</test-kind>
-      <test-directory />
-      <recursive>false</recursive>
-      <method />
-    </configuration>
     <configuration default="true" type="osgi.bnd.run" factoryName="Run Launcher">
       <method />
     </configuration>
     <configuration default="true" type="osgi.bnd.run" factoryName="Test Launcher (JUnit)">
       <method />
     </configuration>
-    <configuration default="true" type="tests" factoryName="Attests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="Doctests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="Nosetests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <option name="PARAMS" value="" />
-      <option name="USE_PARAM" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="Unittests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <option name="PUREUNITTEST" value="true" />
-      <option name="PARAMS" value="" />
-      <option name="USE_PARAM" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="py.test">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="jabaws-dev" />
-      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <option name="testToRun" value="" />
-      <option name="keywords" value="" />
-      <option name="params" value="" />
-      <option name="USE_PARAM" value="false" />
-      <option name="USE_KEYWORD" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="uTestRunConfiguration" factoryName="utest">
-      <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
-      <module name="" />
-      <setting name="path" value="" />
-      <setting name="package" value="" />
-      <setting name="vmparams" value="" />
-      <setting name="params" value="" />
-      <setting name="workingDirectory" value="" />
-      <setting name="searchForTest" value="Across module dependencies" />
-      <setting name="testName" value="" />
-      <setting name="testKind" value="Class" />
-      <setting name="showProgressMessages" value="true" />
-      <classRegexps />
-      <testRegexps />
-      <envs />
-      <method />
-    </configuration>
     <configuration name="&lt;template&gt;" type="WebApp" default="true" selected="false">
       <Host>localhost</Host>
       <Port>5050</Port>
@@ -1034,11 +894,32 @@
       <workItem from="1488379246606" duration="1813000" />
       <workItem from="1488465570952" duration="1210000" />
       <workItem from="1488793686482" duration="4738000" />
+      <workItem from="1488993581303" duration="2096000" />
+      <workItem from="1489054273480" duration="14478000" />
+      <workItem from="1489083059587" duration="197000" />
+      <workItem from="1489140248528" duration="5292000" />
+      <workItem from="1489399347089" duration="8523000" />
+      <workItem from="1489487518570" duration="568000" />
+      <workItem from="1489576926071" duration="308000" />
+      <workItem from="1490604978271" duration="567000" />
+      <workItem from="1491214270330" duration="475000" />
+      <workItem from="1491295038045" duration="3347000" />
+      <workItem from="1491304154631" duration="589000" />
+      <workItem from="1491395781492" duration="12000" />
+      <workItem from="1491395838802" duration="22000" />
+      <workItem from="1491396051400" duration="60000" />
+      <workItem from="1491396130484" duration="17581000" />
+      <workItem from="1491419018389" duration="234000" />
+      <workItem from="1491422575753" duration="2626000" />
+      <workItem from="1491468765003" duration="11402000" />
+      <workItem from="1491554212248" duration="1423000" />
+      <workItem from="1491814142568" duration="6739000" />
+      <workItem from="1491900607240" duration="2564000" />
     </task>
     <servers />
   </component>
   <component name="TimeTrackingManager">
-    <option name="totallyTimeSpent" value="37407000" />
+    <option name="totallyTimeSpent" value="129320000" />
   </component>
   <component name="TodoView" selected-index="0">
     <todo-panel id="selected-file">
@@ -1061,12 +942,12 @@
     </todo-panel>
   </component>
   <component name="ToolWindowManager">
-    <frame x="1440" y="23" width="1920" height="1139" extended-state="6" />
-    <editor active="false" />
+    <frame x="1439" y="23" width="1920" height="1140" extended-state="6" />
+    <editor active="true" />
     <layout>
       <window_info id="Palette" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
       <window_info id="Nl-Palette" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
-      <window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32908913" sideWeight="0.5042598" order="7" side_tool="true" content_ui="tabs" />
+      <window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.3297456" sideWeight="0.5042598" order="7" side_tool="true" content_ui="tabs" />
       <window_info id="Maven Projects" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
       <window_info id="Properties" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
       <window_info id="Capture Tool" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
@@ -1081,27 +962,53 @@
       <window_info id="Image Layers" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
       <window_info id="Java Enterprise" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
       <window_info id="Capture Analysis" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
-      <window_info id="File Transfer" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.18021548" sideWeight="0.49520767" order="8" side_tool="false" content_ui="tabs" />
-      <window_info id="Version Control" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32804233" sideWeight="0.4969605" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="File Transfer" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.18003914" sideWeight="0.49520767" order="8" side_tool="false" content_ui="tabs" />
       <window_info id="Run" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
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+      <window_info id="Find" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32876712" sideWeight="0.49574015" order="1" side_tool="false" content_ui="tabs" />
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+      <window_info id="Palette" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
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+      <window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.3297456" sideWeight="0.5042598" order="7" side_tool="true" content_ui="tabs" />
+      <window_info id="Maven Projects" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Properties" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
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+      <window_info id="Capture Tool" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
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+      <window_info id="Designer" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
+      <window_info id="Database" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32994652" sideWeight="0.6556557" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="true" content_ui="tabs" />
+      <window_info id="Ant Build" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.24919786" sideWeight="0.6556557" order="1" side_tool="false" content_ui="tabs" />
+      <window_info id="UI Designer" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
+      <window_info id="Debug" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
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+      <window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32804233" sideWeight="0.4969605" order="6" side_tool="false" content_ui="tabs" />
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+      <window_info id="Image Layers" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
+      <window_info id="Java Enterprise" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Capture Analysis" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
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+      <window_info id="File Transfer" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.18003914" sideWeight="0.49520767" order="8" side_tool="false" content_ui="tabs" />
+      <window_info id="Version Control" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32804233" sideWeight="0.4969605" order="7" side_tool="false" content_ui="tabs" />
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+      <window_info id="Terminal" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Project" active="true" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.23003195" sideWeight="0.8368368" order="0" side_tool="false" content_ui="combo" />
+      <window_info id="Web" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="true" content_ui="tabs" />
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+      <window_info id="Find" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32876712" sideWeight="0.49574015" order="1" side_tool="false" content_ui="tabs" />
+      <window_info id="Theme Preview" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
+      <window_info id="Favorites" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.24544074" sideWeight="0.19223987" order="2" side_tool="true" content_ui="tabs" />
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   </component>
   <component name="TypeScriptGeneratedFilesManager">
@@ -1154,368 +1061,401 @@
     </buildFile>
   </component>
   <component name="editorHistoryManager">
-    <entry file="file://$PROJECT_DIR$/conf/GA.properties">
+    <entry file="file://$PROJECT_DIR$/conf/settings/ClustalParameters.xml">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="418">
+          <caret line="166" column="24" lean-forward="true" selection-start-line="166" selection-start-column="24" selection-end-line="166" selection-end-column="24" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/conf/Executable.properties.dundee">
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/ResultNotAvailableException.java">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="435">
+          <caret line="29" column="13" lean-forward="false" selection-start-line="29" selection-start-column="13" selection-end-line="29" selection-end-column="13" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/conf/Executable.properties">
+    <entry file="file://$PROJECT_DIR$/binaries/src/mafft/license.extensions" />
+    <entry file="file://$PROJECT_DIR$/binaries/src/mafft/core/Makefile">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="0">
+          <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
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-    <entry file="file://$PROJECT_DIR$/WEB-INF/classes/compbio/runner/predictors/Jpred.class" />
-    <entry file="file://$PROJECT_DIR$/runner/compbio/runner/RunnerUtil.java">
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/RunnerConfig.java">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="-56">
+          <caret line="44" column="13" lean-forward="false" selection-start-line="44" selection-start-column="13" selection-end-line="44" selection-end-column="13" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/runner/compbio/runner/package-info.java">
+    <entry file="file://$PROJECT_DIR$/webservices/compbio/stat/servlet/DownloadRedirector.java">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="135">
+          <caret line="9" column="13" lean-forward="false" selection-start-line="9" selection-start-column="13" selection-end-line="9" selection-end-column="13" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/runner/compbio/runner/OptionCombinator.java">
+    <entry file="file://$PROJECT_DIR$/conf/settings/MuscleLimits.xml">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="510">
+          <caret line="34" column="0" lean-forward="false" selection-start-line="34" selection-start-column="0" selection-end-line="34" selection-end-column="0" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/client/CmdHelper.java">
+    <entry file="file://$PROJECT_DIR$/testsrc/testdata/MuscleLimits.xml">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="210">
+          <caret line="14" column="8" lean-forward="true" selection-start-line="14" selection-start-column="8" selection-end-line="14" selection-end-column="8" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/client/Constraints.java">
+    <entry file="file://$PROJECT_DIR$/conf/settings/ClustalPresets.xml">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="0">
+          <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/client/IOHelper.java">
+    <entry file="file://$PROJECT_DIR$/conf/settings/AAConPresets.xml">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="0">
+          <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/client/MetadataHelper.java">
+    <entry file="file://$PROJECT_DIR$/conf/settings/MusclePresets.xml">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="0">
+          <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/webservices/compbio/data/msa/RegistryWS.java">
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/RNAStructReader.java">
       <provider selected="true" editor-type-id="text-editor">
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+        <state relative-caret-position="240">
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