Add intelliJ configuration files
[jabaws.git] / .idea / workspace.xml
1 <?xml version="1.0" encoding="UTF-8"?>
2 <project version="4">
3   <component name="ChangeListManager">
4     <list default="true" id="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" name="Default" comment="">
5       <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/.idea/ant.xml" />
6       <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" />
7       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/website/archive/jaba-no-binaries.war" afterPath="$PROJECT_DIR$/website/archive/jaba-no-binaries.war" />
8       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/website/archive/jaba.war" afterPath="$PROJECT_DIR$/website/archive/jaba.war" />
9       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/ExecutionStatistic/log/log.ctrl" afterPath="$PROJECT_DIR$/ExecutionStatistic/log/log.ctrl" />
10       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/ExecutionStatistic/log/log10.dat" afterPath="$PROJECT_DIR$/ExecutionStatistic/log/log10.dat" />
11       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/ExecutionStatistic/log/logmirror.ctrl" afterPath="$PROJECT_DIR$/ExecutionStatistic/log/logmirror.ctrl" />
12     </list>
13     <ignored path="jabaws-dev.iws" />
14     <ignored path=".idea/workspace.xml" />
15     <file path="/Dummy.txt" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364571839570" ignored="false" />
16     <file path="$PROJECT_DIR$/web/WEB-INF/web.xml" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364569053673" ignored="false" />
17     <file path="$PROJECT_DIR$/../../jaba-git2/jabaws-dev/webservices/compbio/ws/server/JronnWS.java" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364571910193" ignored="false" />
18     <file path="$PROJECT_DIR$/../../jaba-git2/jabaws-dev/testsrc/compbio/runner/msa/ClustalOTester.java" changelist="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" time="1364569115977" ignored="false" />
19     <option name="TRACKING_ENABLED" value="true" />
20     <option name="SHOW_DIALOG" value="false" />
21     <option name="HIGHLIGHT_CONFLICTS" value="true" />
22     <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
23     <option name="LAST_RESOLUTION" value="IGNORE" />
24   </component>
25   <component name="ChangesViewManager" flattened_view="true" show_ignored="false" />
26   <component name="CreatePatchCommitExecutor">
27     <option name="PATCH_PATH" value="" />
28   </component>
29   <component name="DaemonCodeAnalyzer">
30     <disable_hints />
31   </component>
32   <component name="DebuggerManager">
33     <ui_properties default_suspend_policy="SuspendAll" default_condition_enabled="true" />
34     <breakpoint_any default_suspend_policy="SuspendAll" default_condition_enabled="true">
35       <breakpoint>
36         <option name="NOTIFY_CAUGHT" value="true" />
37         <option name="NOTIFY_UNCAUGHT" value="true" />
38         <option name="ENABLED" value="false" />
39         <option name="LOG_ENABLED" value="false" />
40         <option name="LOG_EXPRESSION_ENABLED" value="false" />
41         <option name="SUSPEND_POLICY" value="SuspendAll" />
42         <option name="SUSPEND" value="true" />
43         <option name="COUNT_FILTER_ENABLED" value="false" />
44         <option name="COUNT_FILTER" value="0" />
45         <option name="CONDITION_ENABLED" value="true" />
46         <option name="CLASS_FILTERS_ENABLED" value="false" />
47         <option name="INSTANCE_FILTERS_ENABLED" value="false" />
48         <option name="CONDITION" value="" />
49         <option name="LOG_MESSAGE" value="" />
50       </breakpoint>
51       <breakpoint>
52         <option name="NOTIFY_CAUGHT" value="true" />
53         <option name="NOTIFY_UNCAUGHT" value="true" />
54         <option name="ENABLED" value="false" />
55         <option name="LOG_ENABLED" value="false" />
56         <option name="LOG_EXPRESSION_ENABLED" value="false" />
57         <option name="SUSPEND_POLICY" value="SuspendAll" />
58         <option name="SUSPEND" value="true" />
59         <option name="COUNT_FILTER_ENABLED" value="false" />
60         <option name="COUNT_FILTER" value="0" />
61         <option name="CONDITION_ENABLED" value="true" />
62         <option name="CLASS_FILTERS_ENABLED" value="false" />
63         <option name="INSTANCE_FILTERS_ENABLED" value="false" />
64         <option name="CONDITION" value="" />
65         <option name="LOG_MESSAGE" value="" />
66       </breakpoint>
67     </breakpoint_any>
68     <breakpoint_rules />
69     <ui_properties />
70   </component>
71   <component name="ExecutionTargetManager" SELECTED_TARGET="default_target" />
72   <component name="FavoritesManager">
73     <favorites_list name="jabaws-dev" />
74   </component>
75   <component name="FileEditorManager">
76     <leaf>
77       <file leaf-file-name="LimitsManager.java" pinned="false" current="false" current-in-tab="false">
78         <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
79           <provider selected="true" editor-type-id="text-editor">
80             <state line="27" column="19" selection-start="1057" selection-end="1057" vertical-scroll-proportion="0.0">
81               <folding />
82             </state>
83           </provider>
84         </entry>
85       </file>
86       <file leaf-file-name="Configurator.java" pinned="false" current="false" current-in-tab="false">
87         <entry file="file://$PROJECT_DIR$/engine/compbio/engine/Configurator.java">
88           <provider selected="true" editor-type-id="text-editor">
89             <state line="50" column="59" selection-start="1937" selection-end="1937" vertical-scroll-proportion="0.0">
90               <folding />
91             </state>
92           </provider>
93         </entry>
94       </file>
95       <file leaf-file-name="RegistryWS.java" pinned="false" current="false" current-in-tab="false">
96         <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/RegistryWS.java">
97           <provider selected="true" editor-type-id="text-editor">
98             <state line="29" column="25" selection-start="1110" selection-end="1110" vertical-scroll-proportion="0.0">
99               <folding />
100             </state>
101           </provider>
102         </entry>
103       </file>
104       <file leaf-file-name="AnnualStat.java" pinned="false" current="false" current-in-tab="false">
105         <entry file="file://$PROJECT_DIR$/webservices/compbio/stat/servlet/AnnualStat.java">
106           <provider selected="true" editor-type-id="text-editor">
107             <state line="38" column="27" selection-start="1385" selection-end="1385" vertical-scroll-proportion="0.0">
108               <folding />
109             </state>
110           </provider>
111         </entry>
112       </file>
113       <file leaf-file-name="MafftTester.java" pinned="false" current="false" current-in-tab="false">
114         <entry file="file://$PROJECT_DIR$/testsrc/compbio/runner/msa/MafftTester.java">
115           <provider selected="true" editor-type-id="text-editor">
116             <state line="20" column="22" selection-start="851" selection-end="851" vertical-scroll-proportion="0.0">
117               <folding />
118             </state>
119           </provider>
120         </entry>
121       </file>
122       <file leaf-file-name="JronnWS.java" pinned="false" current="true" current-in-tab="true">
123         <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/JronnWS.java">
124           <provider selected="true" editor-type-id="text-editor">
125             <state line="34" column="48" selection-start="1369" selection-end="1369" vertical-scroll-proportion="0.21212122">
126               <folding />
127             </state>
128           </provider>
129         </entry>
130       </file>
131       <file leaf-file-name="Alignment.java" pinned="false" current="false" current-in-tab="false">
132         <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
133           <provider selected="true" editor-type-id="text-editor">
134             <state line="43" column="7" selection-start="1409" selection-end="1409" vertical-scroll-proportion="0.0">
135               <folding />
136             </state>
137           </provider>
138         </entry>
139       </file>
140     </leaf>
141   </component>
142   <component name="FindManager">
143     <FindUsagesManager>
144       <setting name="OPEN_NEW_TAB" value="false" />
145     </FindUsagesManager>
146   </component>
147   <component name="Git.Settings">
148     <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
149   </component>
150   <component name="GitLogSettings">
151     <option name="myDateState">
152       <MyDateState />
153     </option>
154   </component>
155   <component name="ProjectFrameBounds">
156     <option name="x" value="1946" />
157     <option name="width" value="1920" />
158     <option name="height" value="1152" />
159   </component>
160   <component name="ProjectLevelVcsManager" settingsEditedManually="false">
161     <OptionsSetting value="true" id="Add" />
162     <OptionsSetting value="true" id="Remove" />
163     <OptionsSetting value="true" id="Checkout" />
164     <OptionsSetting value="true" id="Update" />
165     <OptionsSetting value="true" id="Status" />
166     <OptionsSetting value="true" id="Edit" />
167     <OptionsSetting value="true" id="Undo Check Out" />
168     <OptionsSetting value="true" id="Get Latest Version" />
169     <ConfirmationsSetting value="1" id="Add" />
170     <ConfirmationsSetting value="0" id="Remove" />
171   </component>
172   <component name="ProjectReloadState">
173     <option name="STATE" value="0" />
174   </component>
175   <component name="ProjectView">
176     <navigator currentView="ProjectPane" proportions="" version="1" splitterProportion="0.5">
177       <flattenPackages />
178       <showMembers />
179       <showModules />
180       <showLibraryContents />
181       <hideEmptyPackages />
182       <abbreviatePackageNames />
183       <autoscrollToSource />
184       <autoscrollFromSource />
185       <sortByType />
186     </navigator>
187     <panes>
188       <pane id="PackagesPane" />
189       <pane id="Scope" />
190       <pane id="ProjectPane">
191         <subPane>
192           <PATH>
193             <PATH_ELEMENT>
194               <option name="myItemId" value="jabaws-dev" />
195               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
196             </PATH_ELEMENT>
197             <PATH_ELEMENT>
198               <option name="myItemId" value="External Libraries" />
199               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ExternalLibrariesNode" />
200             </PATH_ELEMENT>
201           </PATH>
202           <PATH>
203             <PATH_ELEMENT>
204               <option name="myItemId" value="jabaws-dev" />
205               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
206             </PATH_ELEMENT>
207             <PATH_ELEMENT>
208               <option name="myItemId" value="jabaws-dev" />
209               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
210             </PATH_ELEMENT>
211           </PATH>
212           <PATH>
213             <PATH_ELEMENT>
214               <option name="myItemId" value="jabaws-dev" />
215               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
216             </PATH_ELEMENT>
217             <PATH_ELEMENT>
218               <option name="myItemId" value="jabaws-dev" />
219               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
220             </PATH_ELEMENT>
221             <PATH_ELEMENT>
222               <option name="myItemId" value="webservices" />
223               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
224             </PATH_ELEMENT>
225             <PATH_ELEMENT>
226               <option name="myItemId" value="compbio" />
227               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
228             </PATH_ELEMENT>
229             <PATH_ELEMENT>
230               <option name="myItemId" value="ws" />
231               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
232             </PATH_ELEMENT>
233             <PATH_ELEMENT>
234               <option name="myItemId" value="server" />
235               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
236             </PATH_ELEMENT>
237           </PATH>
238           <PATH>
239             <PATH_ELEMENT>
240               <option name="myItemId" value="jabaws-dev" />
241               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
242             </PATH_ELEMENT>
243             <PATH_ELEMENT>
244               <option name="myItemId" value="jabaws-dev" />
245               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
246             </PATH_ELEMENT>
247             <PATH_ELEMENT>
248               <option name="myItemId" value="webservices" />
249               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
250             </PATH_ELEMENT>
251             <PATH_ELEMENT>
252               <option name="myItemId" value="compbio" />
253               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
254             </PATH_ELEMENT>
255             <PATH_ELEMENT>
256               <option name="myItemId" value="ws" />
257               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
258             </PATH_ELEMENT>
259           </PATH>
260           <PATH>
261             <PATH_ELEMENT>
262               <option name="myItemId" value="jabaws-dev" />
263               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
264             </PATH_ELEMENT>
265             <PATH_ELEMENT>
266               <option name="myItemId" value="jabaws-dev" />
267               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
268             </PATH_ELEMENT>
269             <PATH_ELEMENT>
270               <option name="myItemId" value="webservices" />
271               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
272             </PATH_ELEMENT>
273             <PATH_ELEMENT>
274               <option name="myItemId" value="compbio" />
275               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
276             </PATH_ELEMENT>
277           </PATH>
278           <PATH>
279             <PATH_ELEMENT>
280               <option name="myItemId" value="jabaws-dev" />
281               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
282             </PATH_ELEMENT>
283             <PATH_ELEMENT>
284               <option name="myItemId" value="jabaws-dev" />
285               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
286             </PATH_ELEMENT>
287             <PATH_ELEMENT>
288               <option name="myItemId" value="engine" />
289               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
290             </PATH_ELEMENT>
291             <PATH_ELEMENT>
292               <option name="myItemId" value="engine" />
293               <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
294             </PATH_ELEMENT>
295           </PATH>
296         </subPane>
297       </pane>
298     </panes>
299   </component>
300   <component name="PropertiesComponent">
301     <property name="project.structure.last.edited" value="Modules" />
302     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth0" value="214" />
303     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth1" value="233" />
304     <property name="project.structure.proportion" value="0.15" />
305     <property name="options.splitter.main.proportions" value="0.3" />
306     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth0" value="214" />
307     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder1" value="1" />
308     <property name="MemberChooser.sorted" value="false" />
309     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder0" value="0" />
310     <property name="last_opened_file_path" value="$PROJECT_DIR$/../../jaba-git2/jabaws-dev" />
311     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth2" value="240" />
312     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatWidth3" value="1138" />
313     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth3" value="1138" />
314     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth2" value="240" />
315     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeWidth1" value="233" />
316     <property name="GoToClass.toSaveIncludeLibraries" value="false" />
317     <property name="WebServerToolWindowFactoryState" value="false" />
318     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder2" value="2" />
319     <property name="FileHistory.git4idea.history.GitHistoryProvider_flatOrder3" value="3" />
320     <property name="MemberChooser.showClasses" value="true" />
321     <property name="GoToClass.includeLibraries" value="false" />
322     <property name="options.splitter.details.proportions" value="0.2" />
323     <property name="GoToFile.includeJavaFiles" value="false" />
324     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder0" value="0" />
325     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder3" value="3" />
326     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder1" value="1" />
327     <property name="FileHistory.git4idea.history.GitHistoryProvider_treeOrder2" value="2" />
328     <property name="options.lastSelected" value="project.propVCSSupport.Mappings" />
329     <property name="project.structure.side.proportion" value="0.2" />
330     <property name="MemberChooser.copyJavadoc" value="false" />
331     <property name="options.searchVisible" value="true" />
332   </component>
333   <component name="RunManager">
334     <configuration default="true" type="#org.jetbrains.idea.devkit.run.PluginConfigurationType" factoryName="Plugin">
335       <module name="" />
336       <option name="VM_PARAMETERS" value="-Xmx512m -Xms256m -XX:MaxPermSize=250m" />
337       <option name="PROGRAM_PARAMETERS" />
338       <method />
339     </configuration>
340     <configuration default="true" type="Remote" factoryName="Remote">
341       <option name="USE_SOCKET_TRANSPORT" value="true" />
342       <option name="SERVER_MODE" value="false" />
343       <option name="SHMEM_ADDRESS" value="javadebug" />
344       <option name="HOST" value="localhost" />
345       <option name="PORT" value="5005" />
346       <method />
347     </configuration>
348     <configuration default="true" type="Applet" factoryName="Applet">
349       <module name="" />
350       <option name="MAIN_CLASS_NAME" />
351       <option name="HTML_FILE_NAME" />
352       <option name="HTML_USED" value="false" />
353       <option name="WIDTH" value="400" />
354       <option name="HEIGHT" value="300" />
355       <option name="POLICY_FILE" value="$APPLICATION_HOME_DIR$/bin/appletviewer.policy" />
356       <option name="VM_PARAMETERS" />
357       <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
358       <option name="ALTERNATIVE_JRE_PATH" />
359       <method />
360     </configuration>
361     <configuration default="true" type="TestNG" factoryName="TestNG">
362       <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
363       <module name="" />
364       <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
365       <option name="ALTERNATIVE_JRE_PATH" />
366       <option name="SUITE_NAME" />
367       <option name="PACKAGE_NAME" />
368       <option name="MAIN_CLASS_NAME" />
369       <option name="METHOD_NAME" />
370       <option name="GROUP_NAME" />
371       <option name="TEST_OBJECT" value="CLASS" />
372       <option name="VM_PARAMETERS" value="-ea" />
373       <option name="PARAMETERS" />
374       <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
375       <option name="OUTPUT_DIRECTORY" />
376       <option name="ANNOTATION_TYPE" />
377       <option name="ENV_VARIABLES" />
378       <option name="PASS_PARENT_ENVS" value="true" />
379       <option name="TEST_SEARCH_SCOPE">
380         <value defaultName="moduleWithDependencies" />
381       </option>
382       <option name="USE_DEFAULT_REPORTERS" value="false" />
383       <option name="PROPERTIES_FILE" />
384       <envs />
385       <properties />
386       <listeners />
387       <method />
388     </configuration>
389     <configuration default="true" type="Application" factoryName="Application">
390       <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
391       <option name="MAIN_CLASS_NAME" />
392       <option name="VM_PARAMETERS" />
393       <option name="PROGRAM_PARAMETERS" />
394       <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
395       <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
396       <option name="ALTERNATIVE_JRE_PATH" />
397       <option name="ENABLE_SWING_INSPECTOR" value="false" />
398       <option name="ENV_VARIABLES" />
399       <option name="PASS_PARENT_ENVS" value="true" />
400       <module name="" />
401       <envs />
402       <method />
403     </configuration>
404     <configuration default="true" type="JUnit" factoryName="JUnit">
405       <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
406       <module name="" />
407       <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
408       <option name="ALTERNATIVE_JRE_PATH" />
409       <option name="PACKAGE_NAME" />
410       <option name="MAIN_CLASS_NAME" />
411       <option name="METHOD_NAME" />
412       <option name="TEST_OBJECT" value="class" />
413       <option name="VM_PARAMETERS" value="-ea" />
414       <option name="PARAMETERS" />
415       <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
416       <option name="ENV_VARIABLES" />
417       <option name="PASS_PARENT_ENVS" value="true" />
418       <option name="TEST_SEARCH_SCOPE">
419         <value defaultName="moduleWithDependencies" />
420       </option>
421       <envs />
422       <patterns />
423       <method />
424     </configuration>
425     <list size="0" />
426     <configuration name="&lt;template&gt;" type="WebApp" default="true" selected="false">
427       <Host>localhost</Host>
428       <Port>5050</Port>
429     </configuration>
430   </component>
431   <component name="ShelveChangesManager" show_recycled="false" />
432   <component name="SvnConfiguration" maxAnnotateRevisions="500" myUseAcceleration="nothing" myAutoUpdateAfterCommit="false" cleanupOnStartRun="false">
433     <option name="USER" value="" />
434     <option name="PASSWORD" value="" />
435     <option name="mySSHConnectionTimeout" value="30000" />
436     <option name="mySSHReadTimeout" value="30000" />
437     <option name="LAST_MERGED_REVISION" />
438     <option name="MERGE_DRY_RUN" value="false" />
439     <option name="MERGE_DIFF_USE_ANCESTRY" value="true" />
440     <option name="UPDATE_LOCK_ON_DEMAND" value="false" />
441     <option name="IGNORE_SPACES_IN_MERGE" value="false" />
442     <option name="DETECT_NESTED_COPIES" value="true" />
443     <option name="CHECK_NESTED_FOR_QUICK_MERGE" value="false" />
444     <option name="IGNORE_SPACES_IN_ANNOTATE" value="true" />
445     <option name="SHOW_MERGE_SOURCES_IN_ANNOTATE" value="true" />
446     <option name="FORCE_UPDATE" value="false" />
447     <option name="IGNORE_EXTERNALS" value="false" />
448     <myIsUseDefaultProxy>false</myIsUseDefaultProxy>
449   </component>
450   <component name="TaskManager">
451     <task active="true" id="Default" summary="Default task">
452       <changelist id="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" name="Default" comment="" />
453       <created>1364568968761</created>
454       <updated>1364568968761</updated>
455     </task>
456     <servers />
457   </component>
458   <component name="TodoView" selected-index="0">
459     <todo-panel id="selected-file">
460       <are-packages-shown value="false" />
461       <are-modules-shown value="false" />
462       <flatten-packages value="false" />
463       <is-autoscroll-to-source value="true" />
464     </todo-panel>
465     <todo-panel id="all">
466       <are-packages-shown value="true" />
467       <are-modules-shown value="false" />
468       <flatten-packages value="false" />
469       <is-autoscroll-to-source value="true" />
470     </todo-panel>
471     <todo-panel id="default-changelist">
472       <are-packages-shown value="false" />
473       <are-modules-shown value="false" />
474       <flatten-packages value="false" />
475       <is-autoscroll-to-source value="false" />
476     </todo-panel>
477   </component>
478   <component name="ToolWindowManager">
479     <frame x="1946" y="0" width="1920" height="1152" extended-state="0" />
480     <editor active="false" />
481     <layout>
482       <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" />
483       <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" />
484       <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" />
485       <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" />
486       <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" />
487       <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" />
488       <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" />
489       <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" />
490       <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" />
491       <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" />
492       <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" />
493       <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" />
494       <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" />
495       <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" />
496       <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" />
497       <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" />
498       <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" />
499       <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" />
500       <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" />
501       <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" />
502       <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" />
503       <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" />
504       <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" />
505       <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" />
506       <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" />
507     </layout>
508   </component>
509   <component name="VcsContentAnnotationSettings">
510     <option name="myLimit" value="2678400000" />
511   </component>
512   <component name="VcsManagerConfiguration">
513     <option name="OFFER_MOVE_TO_ANOTHER_CHANGELIST_ON_PARTIAL_COMMIT" value="true" />
514     <option name="CHECK_CODE_SMELLS_BEFORE_PROJECT_COMMIT" value="true" />
515     <option name="CHECK_NEW_TODO" value="true" />
516     <option name="myTodoPanelSettings">
517       <value>
518         <are-packages-shown value="false" />
519         <are-modules-shown value="false" />
520         <flatten-packages value="false" />
521         <is-autoscroll-to-source value="false" />
522       </value>
523     </option>
524     <option name="PERFORM_UPDATE_IN_BACKGROUND" value="true" />
525     <option name="PERFORM_COMMIT_IN_BACKGROUND" value="true" />
526     <option name="PERFORM_EDIT_IN_BACKGROUND" value="true" />
527     <option name="PERFORM_CHECKOUT_IN_BACKGROUND" value="true" />
528     <option name="PERFORM_ADD_REMOVE_IN_BACKGROUND" value="true" />
529     <option name="PERFORM_ROLLBACK_IN_BACKGROUND" value="false" />
530     <option name="CHECK_LOCALLY_CHANGED_CONFLICTS_IN_BACKGROUND" value="false" />
531     <option name="CHANGED_ON_SERVER_INTERVAL" value="60" />
532     <option name="SHOW_ONLY_CHANGED_IN_SELECTION_DIFF" value="true" />
533     <option name="CHECK_COMMIT_MESSAGE_SPELLING" value="true" />
534     <option name="DEFAULT_PATCH_EXTENSION" value="patch" />
535     <option name="SHORT_DIFF_HORISONTALLY" value="true" />
536     <option name="SHORT_DIFF_EXTRA_LINES" value="2" />
537     <option name="SOFT_WRAPS_IN_SHORT_DIFF" value="true" />
538     <option name="INCLUDE_TEXT_INTO_PATCH" value="false" />
539     <option name="INCLUDE_TEXT_INTO_SHELF" value="false" />
540     <option name="SHOW_FILE_HISTORY_DETAILS" value="true" />
541     <option name="SHOW_VCS_ERROR_NOTIFICATIONS" value="true" />
542     <option name="SHOW_DIRTY_RECURSIVELY" value="false" />
543     <option name="LIMIT_HISTORY" value="true" />
544     <option name="MAXIMUM_HISTORY_ROWS" value="1000" />
545     <option name="FORCE_NON_EMPTY_COMMENT" value="false" />
546     <option name="CLEAR_INITIAL_COMMIT_MESSAGE" value="false" />
547     <option name="LAST_COMMIT_MESSAGE" />
548     <option name="MAKE_NEW_CHANGELIST_ACTIVE" value="false" />
549     <option name="OPTIMIZE_IMPORTS_BEFORE_PROJECT_COMMIT" value="false" />
550     <option name="CHECK_FILES_UP_TO_DATE_BEFORE_COMMIT" value="false" />
551     <option name="REFORMAT_BEFORE_PROJECT_COMMIT" value="false" />
552     <option name="REFORMAT_BEFORE_FILE_COMMIT" value="false" />
553     <option name="FILE_HISTORY_DIALOG_COMMENTS_SPLITTER_PROPORTION" value="0.8" />
554     <option name="FILE_HISTORY_DIALOG_SPLITTER_PROPORTION" value="0.5" />
555     <option name="ACTIVE_VCS_NAME" />
556     <option name="UPDATE_GROUP_BY_PACKAGES" value="false" />
557     <option name="UPDATE_GROUP_BY_CHANGELIST" value="false" />
558     <option name="SHOW_FILE_HISTORY_AS_TREE" value="false" />
559     <option name="FILE_HISTORY_SPLITTER_PROPORTION" value="0.6" />
560   </component>
561   <component name="XDebuggerManager">
562     <breakpoint-manager />
563   </component>
564   <component name="antWorkspaceConfiguration">
565     <option name="IS_AUTOSCROLL_TO_SOURCE" value="false" />
566     <option name="FILTER_TARGETS" value="false" />
567     <buildFile url="file://$PROJECT_DIR$/build.xml">
568       <antCommandLine value="" />
569       <runInBackground value="true" />
570       <targetFilters />
571       <treeView value="true" />
572       <verbose value="true" />
573       <viewClosedWhenNoErrors value="false" />
574       <expanded value="true" />
575     </buildFile>
576   </component>
577   <component name="editorHistoryManager">
578     <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
579       <provider selected="true" editor-type-id="text-editor">
580         <state line="27" column="19" selection-start="1057" selection-end="1057" vertical-scroll-proportion="0.0">
581           <folding />
582         </state>
583       </provider>
584     </entry>
585     <entry file="file://$PROJECT_DIR$/engine/compbio/engine/Configurator.java">
586       <provider selected="true" editor-type-id="text-editor">
587         <state line="50" column="59" selection-start="1937" selection-end="1937" vertical-scroll-proportion="0.0">
588           <folding />
589         </state>
590       </provider>
591     </entry>
592     <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
593       <provider selected="true" editor-type-id="text-editor">
594         <state line="43" column="7" selection-start="1409" selection-end="1409" vertical-scroll-proportion="0.0">
595           <folding />
596         </state>
597       </provider>
598     </entry>
599     <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
600       <provider selected="true" editor-type-id="text-editor">
601         <state line="27" column="17" selection-start="1055" selection-end="1055" vertical-scroll-proportion="0.0">
602           <folding />
603         </state>
604       </provider>
605     </entry>
606     <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
607       <provider selected="true" editor-type-id="text-editor">
608         <state line="41" column="40" selection-start="1363" selection-end="1363" vertical-scroll-proportion="0.0">
609           <folding />
610         </state>
611       </provider>
612     </entry>
613     <entry file="file://$PROJECT_DIR$/datamodel/compbio/data/sequence/Alignment.java">
614       <provider selected="true" editor-type-id="text-editor">
615         <state line="43" column="7" selection-start="1409" selection-end="1409" vertical-scroll-proportion="0.0">
616           <folding />
617         </state>
618       </provider>
619     </entry>
620     <entry file="file://$PROJECT_DIR$/datamodel/compbio/metadata/LimitsManager.java">
621       <provider selected="true" editor-type-id="text-editor">
622         <state line="27" column="19" selection-start="1057" selection-end="1057" vertical-scroll-proportion="0.0">
623           <folding />
624         </state>
625       </provider>
626     </entry>
627     <entry file="file://$PROJECT_DIR$/engine/compbio/engine/Configurator.java">
628       <provider selected="true" editor-type-id="text-editor">
629         <state line="50" column="59" selection-start="1937" selection-end="1937" vertical-scroll-proportion="0.0">
630           <folding />
631         </state>
632       </provider>
633     </entry>
634     <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/RegistryWS.java">
635       <provider selected="true" editor-type-id="text-editor">
636         <state line="29" column="25" selection-start="1110" selection-end="1110" vertical-scroll-proportion="0.0">
637           <folding />
638         </state>
639       </provider>
640     </entry>
641     <entry file="file://$PROJECT_DIR$/webservices/compbio/stat/servlet/AnnualStat.java">
642       <provider selected="true" editor-type-id="text-editor">
643         <state line="38" column="27" selection-start="1385" selection-end="1385" vertical-scroll-proportion="0.0">
644           <folding />
645         </state>
646       </provider>
647     </entry>
648     <entry file="file://$PROJECT_DIR$/testsrc/compbio/runner/msa/MafftTester.java">
649       <provider selected="true" editor-type-id="text-editor">
650         <state line="20" column="22" selection-start="851" selection-end="851" vertical-scroll-proportion="0.0">
651           <folding />
652         </state>
653       </provider>
654     </entry>
655     <entry file="file://$PROJECT_DIR$/webservices/compbio/ws/server/JronnWS.java">
656       <provider selected="true" editor-type-id="text-editor">
657         <state line="34" column="48" selection-start="1369" selection-end="1369" vertical-scroll-proportion="0.21212122">
658           <folding />
659         </state>
660       </provider>
661     </entry>
662   </component>
663   <component name="masterDetails">
664     <states>
665       <state key="ArtifactsStructureConfigurable.UI">
666         <settings>
667           <artifact-editor />
668           <splitter-proportions>
669             <option name="proportions">
670               <list>
671                 <option value="0.2" />
672               </list>
673             </option>
674           </splitter-proportions>
675         </settings>
676       </state>
677       <state key="FacetStructureConfigurable.UI">
678         <settings>
679           <last-edited>Web</last-edited>
680           <splitter-proportions>
681             <option name="proportions">
682               <list>
683                 <option value="0.2" />
684               </list>
685             </option>
686           </splitter-proportions>
687         </settings>
688       </state>
689       <state key="GlobalLibrariesConfigurable.UI">
690         <settings>
691           <splitter-proportions>
692             <option name="proportions">
693               <list>
694                 <option value="0.2" />
695               </list>
696             </option>
697           </splitter-proportions>
698         </settings>
699       </state>
700       <state key="JdkListConfigurable.UI">
701         <settings>
702           <last-edited>1.6</last-edited>
703           <splitter-proportions>
704             <option name="proportions">
705               <list>
706                 <option value="0.2" />
707               </list>
708             </option>
709           </splitter-proportions>
710         </settings>
711       </state>
712       <state key="ModuleStructureConfigurable.UI">
713         <settings>
714           <last-edited>jabaws-dev</last-edited>
715           <splitter-proportions>
716             <option name="proportions">
717               <list>
718                 <option value="0.2" />
719               </list>
720             </option>
721           </splitter-proportions>
722         </settings>
723       </state>
724       <state key="ProjectJDKs.UI">
725         <settings>
726           <last-edited>1.6</last-edited>
727           <splitter-proportions>
728             <option name="proportions">
729               <list>
730                 <option value="0.2" />
731               </list>
732             </option>
733           </splitter-proportions>
734         </settings>
735       </state>
736       <state key="ProjectLibrariesConfigurable.UI">
737         <settings>
738           <last-edited>lib</last-edited>
739           <splitter-proportions>
740             <option name="proportions">
741               <list>
742                 <option value="0.2" />
743               </list>
744             </option>
745           </splitter-proportions>
746         </settings>
747       </state>
748     </states>
749   </component>
750 </project>
751