Add intelliJ configuration files
[jabaws.git] / .idea / workspace.xml
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
new file mode 100644 (file)
index 0000000..c4b4cc6
--- /dev/null
@@ -0,0 +1,751 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ChangeListManager">
+    <list default="true" id="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" name="Default" comment="">
+      <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/.idea/ant.xml" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/website/archive/full-jaba-client-2.0.jar" afterPath="$PROJECT_DIR$/website/archive/full-jaba-client-2.0.jar" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/website/archive/jaba-no-binaries.war" afterPath="$PROJECT_DIR$/website/archive/jaba-no-binaries.war" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/website/archive/jaba.war" afterPath="$PROJECT_DIR$/website/archive/jaba.war" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/ExecutionStatistic/log/log.ctrl" afterPath="$PROJECT_DIR$/ExecutionStatistic/log/log.ctrl" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/ExecutionStatistic/log/log10.dat" afterPath="$PROJECT_DIR$/ExecutionStatistic/log/log10.dat" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/ExecutionStatistic/log/logmirror.ctrl" afterPath="$PROJECT_DIR$/ExecutionStatistic/log/logmirror.ctrl" />
+    </list>
+    <ignored path="jabaws-dev.iws" />
+    <ignored path=".idea/workspace.xml" />
+    <file path="/Dummy.txt" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364571839570" ignored="false" />
+    <file path="$PROJECT_DIR$/web/WEB-INF/web.xml" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364569053673" ignored="false" />
+    <file path="$PROJECT_DIR$/../../jaba-git2/jabaws-dev/webservices/compbio/ws/server/JronnWS.java" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364571910193" ignored="false" />
+    <file path="$PROJECT_DIR$/../../jaba-git2/jabaws-dev/testsrc/compbio/runner/msa/ClustalOTester.java" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364569115977" ignored="false" />
+    <option name="TRACKING_ENABLED" value="true" />
+    <option name="SHOW_DIALOG" value="false" />
+    <option name="HIGHLIGHT_CONFLICTS" value="true" />
+    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
+    <option name="LAST_RESOLUTION" value="IGNORE" />
+  </component>
+  <component name="ChangesViewManager" flattened_view="true" show_ignored="false" />
+  <component name="CreatePatchCommitExecutor">
+    <option name="PATCH_PATH" value="" />
+  </component>
+  <component name="DaemonCodeAnalyzer">
+    <disable_hints />
+  </component>
+  <component name="DebuggerManager">
+    <ui_properties default_suspend_policy="SuspendAll" default_condition_enabled="true" />
+    <breakpoint_any default_suspend_policy="SuspendAll" default_condition_enabled="true">
+      <breakpoint>
+        <option name="NOTIFY_CAUGHT" value="true" />
+        <option name="NOTIFY_UNCAUGHT" value="true" />
+        <option name="ENABLED" value="false" />
+        <option name="LOG_ENABLED" value="false" />
+        <option name="LOG_EXPRESSION_ENABLED" value="false" />
+        <option name="SUSPEND_POLICY" value="SuspendAll" />
+        <option name="SUSPEND" value="true" />
+        <option name="COUNT_FILTER_ENABLED" value="false" />
+        <option name="COUNT_FILTER" value="0" />
+        <option name="CONDITION_ENABLED" value="true" />
+        <option name="CLASS_FILTERS_ENABLED" value="false" />
+        <option name="INSTANCE_FILTERS_ENABLED" value="false" />
+        <option name="CONDITION" value="" />
+        <option name="LOG_MESSAGE" value="" />
+      </breakpoint>
+      <breakpoint>
+        <option name="NOTIFY_CAUGHT" value="true" />
+        <option name="NOTIFY_UNCAUGHT" value="true" />
+        <option name="ENABLED" value="false" />
+        <option name="LOG_ENABLED" value="false" />
+        <option name="LOG_EXPRESSION_ENABLED" value="false" />
+        <option name="SUSPEND_POLICY" value="SuspendAll" />
+        <option name="SUSPEND" value="true" />
+        <option name="COUNT_FILTER_ENABLED" value="false" />
+        <option name="COUNT_FILTER" value="0" />
+        <option name="CONDITION_ENABLED" value="true" />
+        <option name="CLASS_FILTERS_ENABLED" value="false" />
+        <option name="INSTANCE_FILTERS_ENABLED" value="false" />
+        <option name="CONDITION" value="" />
+        <option name="LOG_MESSAGE" value="" />
+      </breakpoint>
+    </breakpoint_any>
+    <breakpoint_rules />
+    <ui_properties />
+  </component>
+  <component name="ExecutionTargetManager" SELECTED_TARGET="default_target" />
+  <component name="FavoritesManager">
+    <favorites_list name="jabaws-dev" />
+  </component>
+  <component name="FileEditorManager">
+    <leaf>
+      <file leaf-file-name="LimitsManager.java" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="27" column="19" selection-start="1057" selection-end="1057" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="Configurator.java" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/engine/compbio/engine/Configurator.java">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="50" column="59" selection-start="1937" selection-end="1937" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="RegistryWS.java" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/RegistryWS.java">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="29" column="25" selection-start="1110" selection-end="1110" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="AnnualStat.java" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/webservices/compbio/stat/servlet/AnnualStat.java">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="38" column="27" selection-start="1385" selection-end="1385" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="MafftTester.java" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/testsrc/compbio/runner/msa/MafftTester.java">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="20" column="22" selection-start="851" selection-end="851" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="JronnWS.java" pinned="false" current="true" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/JronnWS.java">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="34" column="48" selection-start="1369" selection-end="1369" vertical-scroll-proportion="0.21212122">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="Alignment.java" pinned="false" current="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
+          <provider selected="true" editor-type-id="text-editor">
+            <state line="43" column="7" selection-start="1409" selection-end="1409" vertical-scroll-proportion="0.0">
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+    </leaf>
+  </component>
+  <component name="FindManager">
+    <FindUsagesManager>
+      <setting name="OPEN_NEW_TAB" value="false" />
+    </FindUsagesManager>
+  </component>
+  <component name="Git.Settings">
+    <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
+  </component>
+  <component name="GitLogSettings">
+    <option name="myDateState">
+      <MyDateState />
+    </option>
+  </component>
+  <component name="ProjectFrameBounds">
+    <option name="x" value="1946" />
+    <option name="width" value="1920" />
+    <option name="height" value="1152" />
+  </component>
+  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
+    <OptionsSetting value="true" id="Add" />
+    <OptionsSetting value="true" id="Remove" />
+    <OptionsSetting value="true" id="Checkout" />
+    <OptionsSetting value="true" id="Update" />
+    <OptionsSetting value="true" id="Status" />
+    <OptionsSetting value="true" id="Edit" />
+    <OptionsSetting value="true" id="Undo Check Out" />
+    <OptionsSetting value="true" id="Get Latest Version" />
+    <ConfirmationsSetting value="1" id="Add" />
+    <ConfirmationsSetting value="0" id="Remove" />
+  </component>
+  <component name="ProjectReloadState">
+    <option name="STATE" value="0" />
+  </component>
+  <component name="ProjectView">
+    <navigator currentView="ProjectPane" proportions="" version="1" splitterProportion="0.5">
+      <flattenPackages />
+      <showMembers />
+      <showModules />
+      <showLibraryContents />
+      <hideEmptyPackages />
+      <abbreviatePackageNames />
+      <autoscrollToSource />
+      <autoscrollFromSource />
+      <sortByType />
+    </navigator>
+    <panes>
+      <pane id="PackagesPane" />
+      <pane id="Scope" />
+      <pane id="ProjectPane">
+        <subPane>
+          <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="External Libraries" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ExternalLibrariesNode" />
+            </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-dev" />
+              <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-dev" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="webservices" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="compbio" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="ws" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="server" />
+              <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-dev" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="webservices" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="compbio" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="ws" />
+              <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-dev" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="webservices" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="compbio" />
+              <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-dev" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="engine" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+            <PATH_ELEMENT>
+              <option name="myItemId" value="engine" />
+              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
+            </PATH_ELEMENT>
+          </PATH>
+        </subPane>
+      </pane>
+    </panes>
+  </component>
+  <component name="PropertiesComponent">
+    <property name="project.structure.last.edited" value="Modules" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth0" value="214" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth1" value="233" />
+    <property name="project.structure.proportion" value="0.15" />
+    <property name="options.splitter.main.proportions" value="0.3" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth0" value="214" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder1" value="1" />
+    <property name="MemberChooser.sorted" value="false" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder0" value="0" />
+    <property name="last_opened_file_path" value="$PROJECT_DIR$/../../jaba-git2/jabaws-dev" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth2" value="240" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth3" value="1138" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth3" value="1138" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth2" value="240" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth1" value="233" />
+    <property name="GoToClass.toSaveIncludeLibraries" value="false" />
+    <property name="WebServerToolWindowFactoryState" value="false" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder2" value="2" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder3" value="3" />
+    <property name="MemberChooser.showClasses" value="true" />
+    <property name="GoToClass.includeLibraries" value="false" />
+    <property name="options.splitter.details.proportions" value="0.2" />
+    <property name="GoToFile.includeJavaFiles" value="false" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder0" value="0" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder3" value="3" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder1" value="1" />
+    <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder2" value="2" />
+    <property name="options.lastSelected" value="project.propVCSSupport.Mappings" />
+    <property name="project.structure.side.proportion" value="0.2" />
+    <property name="MemberChooser.copyJavadoc" value="false" />
+    <property name="options.searchVisible" value="true" />
+  </component>
+  <component name="RunManager">
+    <configuration default="true" type="#org.jetbrains.idea.devkit.run.PluginConfigurationType" factoryName="Plugin">
+      <module name="" />
+      <option name="VM_PARAMETERS" value="-Xmx512m -Xms256m -XX:MaxPermSize=250m" />
+      <option name="PROGRAM_PARAMETERS" />
+      <method />
+    </configuration>
+    <configuration default="true" type="Remote" factoryName="Remote">
+      <option name="USE_SOCKET_TRANSPORT" value="true" />
+      <option name="SERVER_MODE" value="false" />
+      <option name="SHMEM_ADDRESS" value="javadebug" />
+      <option name="HOST" value="localhost" />
+      <option name="PORT" value="5005" />
+      <method />
+    </configuration>
+    <configuration default="true" type="Applet" factoryName="Applet">
+      <module name="" />
+      <option name="MAIN_CLASS_NAME" />
+      <option name="HTML_FILE_NAME" />
+      <option name="HTML_USED" value="false" />
+      <option name="WIDTH" value="400" />
+      <option name="HEIGHT" value="300" />
+      <option name="POLICY_FILE" value="$APPLICATION_HOME_DIR$/bin/appletviewer.policy" />
+      <option name="VM_PARAMETERS" />
+      <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
+      <option name="ALTERNATIVE_JRE_PATH" />
+      <method />
+    </configuration>
+    <configuration default="true" type="TestNG" factoryName="TestNG">
+      <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
+      <module name="" />
+      <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
+      <option name="ALTERNATIVE_JRE_PATH" />
+      <option name="SUITE_NAME" />
+      <option name="PACKAGE_NAME" />
+      <option name="MAIN_CLASS_NAME" />
+      <option name="METHOD_NAME" />
+      <option name="GROUP_NAME" />
+      <option name="TEST_OBJECT" value="CLASS" />
+      <option name="VM_PARAMETERS" value="-ea" />
+      <option name="PARAMETERS" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
+      <option name="OUTPUT_DIRECTORY" />
+      <option name="ANNOTATION_TYPE" />
+      <option name="ENV_VARIABLES" />
+      <option name="PASS_PARENT_ENVS" value="true" />
+      <option name="TEST_SEARCH_SCOPE">
+        <value defaultName="moduleWithDependencies" />
+      </option>
+      <option name="USE_DEFAULT_REPORTERS" value="false" />
+      <option name="PROPERTIES_FILE" />
+      <envs />
+      <properties />
+      <listeners />
+      <method />
+    </configuration>
+    <configuration default="true" type="Application" factoryName="Application">
+      <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
+      <option name="MAIN_CLASS_NAME" />
+      <option name="VM_PARAMETERS" />
+      <option name="PROGRAM_PARAMETERS" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
+      <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
+      <option name="ALTERNATIVE_JRE_PATH" />
+      <option name="ENABLE_SWING_INSPECTOR" value="false" />
+      <option name="ENV_VARIABLES" />
+      <option name="PASS_PARENT_ENVS" value="true" />
+      <module name="" />
+      <envs />
+      <method />
+    </configuration>
+    <configuration default="true" type="JUnit" factoryName="JUnit">
+      <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
+      <module name="" />
+      <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
+      <option name="ALTERNATIVE_JRE_PATH" />
+      <option name="PACKAGE_NAME" />
+      <option name="MAIN_CLASS_NAME" />
+      <option name="METHOD_NAME" />
+      <option name="TEST_OBJECT" value="class" />
+      <option name="VM_PARAMETERS" value="-ea" />
+      <option name="PARAMETERS" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
+      <option name="ENV_VARIABLES" />
+      <option name="PASS_PARENT_ENVS" value="true" />
+      <option name="TEST_SEARCH_SCOPE">
+        <value defaultName="moduleWithDependencies" />
+      </option>
+      <envs />
+      <patterns />
+      <method />
+    </configuration>
+    <list size="0" />
+    <configuration name="&lt;template&gt;" type="WebApp" default="true" selected="false">
+      <Host>localhost</Host>
+      <Port>5050</Port>
+    </configuration>
+  </component>
+  <component name="ShelveChangesManager" show_recycled="false" />
+  <component name="SvnConfiguration" maxAnnotateRevisions="500" myUseAcceleration="nothing" myAutoUpdateAfterCommit="false" cleanupOnStartRun="false">
+    <option name="USER" value="" />
+    <option name="PASSWORD" value="" />
+    <option name="mySSHConnectionTimeout" value="30000" />
+    <option name="mySSHReadTimeout" value="30000" />
+    <option name="LAST_MERGED_REVISION" />
+    <option name="MERGE_DRY_RUN" value="false" />
+    <option name="MERGE_DIFF_USE_ANCESTRY" value="true" />
+    <option name="UPDATE_LOCK_ON_DEMAND" value="false" />
+    <option name="IGNORE_SPACES_IN_MERGE" value="false" />
+    <option name="DETECT_NESTED_COPIES" value="true" />
+    <option name="CHECK_NESTED_FOR_QUICK_MERGE" value="false" />
+    <option name="IGNORE_SPACES_IN_ANNOTATE" value="true" />
+    <option name="SHOW_MERGE_SOURCES_IN_ANNOTATE" value="true" />
+    <option name="FORCE_UPDATE" value="false" />
+    <option name="IGNORE_EXTERNALS" value="false" />
+    <myIsUseDefaultProxy>false</myIsUseDefaultProxy>
+  </component>
+  <component name="TaskManager">
+    <task active="true" id="Default" summary="Default task">
+      <changelist id="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" name="Default" comment="" />
+      <created>1364568968761</created>
+      <updated>1364568968761</updated>
+    </task>
+    <servers />
+  </component>
+  <component name="TodoView" selected-index="0">
+    <todo-panel id="selected-file">
+      <are-packages-shown value="false" />
+      <are-modules-shown value="false" />
+      <flatten-packages value="false" />
+      <is-autoscroll-to-source value="true" />
+    </todo-panel>
+    <todo-panel id="all">
+      <are-packages-shown value="true" />
+      <are-modules-shown value="false" />
+      <flatten-packages value="false" />
+      <is-autoscroll-to-source value="true" />
+    </todo-panel>
+    <todo-panel id="default-changelist">
+      <are-packages-shown value="false" />
+      <are-modules-shown value="false" />
+      <flatten-packages value="false" />
+      <is-autoscroll-to-source value="false" />
+    </todo-panel>
+  </component>
+  <component name="ToolWindowManager">
+    <frame x="1946" y="0" width="1920" height="1152" extended-state="0" />
+    <editor active="false" />
+    <layout>
+      <window_info id="Changes" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.3296593" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="JetGradle" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Palette" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Database" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Ant Build" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.24946466" sideWeight="0.6713427" order="1" side_tool="false" content_ui="tabs" />
+      <window_info id="Debug" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.4" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="IDEtalk Messages" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="7" 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" weight="0.33" sideWeight="0.5" order="7" side_tool="true" content_ui="tabs" />
+      <window_info id="Favorites" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="2" side_tool="true" content_ui="tabs" />
+      <window_info id="IDEtalk" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="3" 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" weight="0.3296593" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Messages" active="true" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" weight="0.47394788" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Web" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="2" side_tool="true" content_ui="tabs" />
+      <window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.3296593" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
+      <window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.25" sideWeight="0.5" order="1" 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" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Commander" active="false" anchor="right" auto_hide="false" internal_type="SLIDING" type="SLIDING" visible="false" weight="0.4" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" />
+      <window_info id="Application Servers" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" weight="0.23554604" sideWeight="0.5260521" order="0" side_tool="false" content_ui="combo" />
+      <window_info id="Run" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
+      <window_info id="Hierarchy" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.25" sideWeight="0.5" order="2" side_tool="false" content_ui="combo" />
+      <window_info id="Cvs" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.25" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
+      <window_info id="Message" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" />
+      <window_info id="Find" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
+      <window_info id="Inspection" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.4" sideWeight="0.5" order="5" side_tool="false" content_ui="tabs" />
+    </layout>
+  </component>
+  <component name="VcsContentAnnotationSettings">
+    <option name="myLimit" value="2678400000" />
+  </component>
+  <component name="VcsManagerConfiguration">
+    <option name="OFFER_MOVE_TO_ANOTHER_CHANGELIST_ON_PARTIAL_COMMIT" value="true" />
+    <option name="CHECK_CODE_SMELLS_BEFORE_PROJECT_COMMIT" value="true" />
+    <option name="CHECK_NEW_TODO" value="true" />
+    <option name="myTodoPanelSettings">
+      <value>
+        <are-packages-shown value="false" />
+        <are-modules-shown value="false" />
+        <flatten-packages value="false" />
+        <is-autoscroll-to-source value="false" />
+      </value>
+    </option>
+    <option name="PERFORM_UPDATE_IN_BACKGROUND" value="true" />
+    <option name="PERFORM_COMMIT_IN_BACKGROUND" value="true" />
+    <option name="PERFORM_EDIT_IN_BACKGROUND" value="true" />
+    <option name="PERFORM_CHECKOUT_IN_BACKGROUND" value="true" />
+    <option name="PERFORM_ADD_REMOVE_IN_BACKGROUND" value="true" />
+    <option name="PERFORM_ROLLBACK_IN_BACKGROUND" value="false" />
+    <option name="CHECK_LOCALLY_CHANGED_CONFLICTS_IN_BACKGROUND" value="false" />
+    <option name="CHANGED_ON_SERVER_INTERVAL" value="60" />
+    <option name="SHOW_ONLY_CHANGED_IN_SELECTION_DIFF" value="true" />
+    <option name="CHECK_COMMIT_MESSAGE_SPELLING" value="true" />
+    <option name="DEFAULT_PATCH_EXTENSION" value="patch" />
+    <option name="SHORT_DIFF_HORISONTALLY" value="true" />
+    <option name="SHORT_DIFF_EXTRA_LINES" value="2" />
+    <option name="SOFT_WRAPS_IN_SHORT_DIFF" value="true" />
+    <option name="INCLUDE_TEXT_INTO_PATCH" value="false" />
+    <option name="INCLUDE_TEXT_INTO_SHELF" value="false" />
+    <option name="SHOW_FILE_HISTORY_DETAILS" value="true" />
+    <option name="SHOW_VCS_ERROR_NOTIFICATIONS" value="true" />
+    <option name="SHOW_DIRTY_RECURSIVELY" value="false" />
+    <option name="LIMIT_HISTORY" value="true" />
+    <option name="MAXIMUM_HISTORY_ROWS" value="1000" />
+    <option name="FORCE_NON_EMPTY_COMMENT" value="false" />
+    <option name="CLEAR_INITIAL_COMMIT_MESSAGE" value="false" />
+    <option name="LAST_COMMIT_MESSAGE" />
+    <option name="MAKE_NEW_CHANGELIST_ACTIVE" value="false" />
+    <option name="OPTIMIZE_IMPORTS_BEFORE_PROJECT_COMMIT" value="false" />
+    <option name="CHECK_FILES_UP_TO_DATE_BEFORE_COMMIT" value="false" />
+    <option name="REFORMAT_BEFORE_PROJECT_COMMIT" value="false" />
+    <option name="REFORMAT_BEFORE_FILE_COMMIT" value="false" />
+    <option name="FILE_HISTORY_DIALOG_COMMENTS_SPLITTER_PROPORTION" value="0.8" />
+    <option name="FILE_HISTORY_DIALOG_SPLITTER_PROPORTION" value="0.5" />
+    <option name="ACTIVE_VCS_NAME" />
+    <option name="UPDATE_GROUP_BY_PACKAGES" value="false" />
+    <option name="UPDATE_GROUP_BY_CHANGELIST" value="false" />
+    <option name="SHOW_FILE_HISTORY_AS_TREE" value="false" />
+    <option name="FILE_HISTORY_SPLITTER_PROPORTION" value="0.6" />
+  </component>
+  <component name="XDebuggerManager">
+    <breakpoint-manager />
+  </component>
+  <component name="antWorkspaceConfiguration">
+    <option name="IS_AUTOSCROLL_TO_SOURCE" value="false" />
+    <option name="FILTER_TARGETS" value="false" />
+    <buildFile url="file://$PROJECT_DIR$/build.xml">
+      <antCommandLine value="" />
+      <runInBackground value="true" />
+      <targetFilters />
+      <treeView value="true" />
+      <verbose value="true" />
+      <viewClosedWhenNoErrors value="false" />
+      <expanded value="true" />
+    </buildFile>
+  </component>
+  <component name="editorHistoryManager">
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="27" column="19" selection-start="1057" selection-end="1057" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/engine/compbio/engine/Configurator.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="50" column="59" selection-start="1937" selection-end="1937" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="43" column="7" selection-start="1409" selection-end="1409" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="27" column="17" selection-start="1055" selection-end="1055" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="41" column="40" selection-start="1363" selection-end="1363" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="43" column="7" selection-start="1409" selection-end="1409" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="27" column="19" selection-start="1057" selection-end="1057" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/engine/compbio/engine/Configurator.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="50" column="59" selection-start="1937" selection-end="1937" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/RegistryWS.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="29" column="25" selection-start="1110" selection-end="1110" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/webservices/compbio/stat/servlet/AnnualStat.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="38" column="27" selection-start="1385" selection-end="1385" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/testsrc/compbio/runner/msa/MafftTester.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="20" column="22" selection-start="851" selection-end="851" vertical-scroll-proportion="0.0">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/JronnWS.java">
+      <provider selected="true" editor-type-id="text-editor">
+        <state line="34" column="48" selection-start="1369" selection-end="1369" vertical-scroll-proportion="0.21212122">
+          <folding />
+        </state>
+      </provider>
+    </entry>
+  </component>
+  <component name="masterDetails">
+    <states>
+      <state key="ArtifactsStructureConfigurable.UI">
+        <settings>
+          <artifact-editor />
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="FacetStructureConfigurable.UI">
+        <settings>
+          <last-edited>Web</last-edited>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="GlobalLibrariesConfigurable.UI">
+        <settings>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="JdkListConfigurable.UI">
+        <settings>
+          <last-edited>1.6</last-edited>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="ModuleStructureConfigurable.UI">
+        <settings>
+          <last-edited>jabaws-dev</last-edited>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="ProjectJDKs.UI">
+        <settings>
+          <last-edited>1.6</last-edited>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="ProjectLibrariesConfigurable.UI">
+        <settings>
+          <last-edited>lib</last-edited>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+    </states>
+  </component>
+</project>
+