From 3b29344a55400698c1ab1f89ca2ae85caba1c69f Mon Sep 17 00:00:00 2001
From: Alexander Sherstnev <asherstnev@main-laptop2>
Date: Fri, 29 Mar 2013 15:47:36 +0000
Subject: [PATCH] Add intelliJ configuration files

---
 .idea/.name                           |    1 +
 .idea/ant.xml                         |   15 +
 .idea/compiler.xml                    |   23 +
 .idea/copyright/profiles_settings.xml |    5 +
 .idea/encodings.xml                   |    5 +
 .idea/libraries/archive.xml           |   15 +
 .idea/libraries/lib.xml               |   27 ++
 .idea/libraries/servlet_api.xml       |    9 +
 .idea/libraries/testng_5_10_jdk15.xml |    9 +
 .idea/misc.xml                        |   11 +
 .idea/modules.xml                     |    9 +
 .idea/scopes/scope_settings.xml       |    5 +
 .idea/uiDesigner.xml                  |  125 ++++++
 .idea/vcs.xml                         |    7 +
 .idea/workspace.xml                   |  751 +++++++++++++++++++++++++++++++++
 jabaws-dev.iml                        |   38 ++
 16 files changed, 1055 insertions(+)
 create mode 100644 .idea/.name
 create mode 100644 .idea/ant.xml
 create mode 100644 .idea/compiler.xml
 create mode 100644 .idea/copyright/profiles_settings.xml
 create mode 100644 .idea/encodings.xml
 create mode 100644 .idea/libraries/archive.xml
 create mode 100644 .idea/libraries/lib.xml
 create mode 100644 .idea/libraries/servlet_api.xml
 create mode 100644 .idea/libraries/testng_5_10_jdk15.xml
 create mode 100644 .idea/misc.xml
 create mode 100644 .idea/modules.xml
 create mode 100644 .idea/scopes/scope_settings.xml
 create mode 100644 .idea/uiDesigner.xml
 create mode 100644 .idea/vcs.xml
 create mode 100644 .idea/workspace.xml
 create mode 100644 jabaws-dev.iml

diff --git a/.idea/.name b/.idea/.name
new file mode 100644
index 0000000..dd6efff
--- /dev/null
+++ b/.idea/.name
@@ -0,0 +1 @@
+jabaws-dev
\ No newline at end of file
diff --git a/.idea/ant.xml b/.idea/ant.xml
new file mode 100644
index 0000000..4674eea
--- /dev/null
+++ b/.idea/ant.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="AntConfiguration">
+    <defaultAnt bundledAnt="true" />
+    <buildFile url="file://$PROJECT_DIR$/build.xml">
+      <additionalClassPath />
+      <antReference projectDefault="true" />
+      <customJdkName value="" />
+      <maximumHeapSize value="128" />
+      <maximumStackSize value="2" />
+      <properties />
+    </buildFile>
+  </component>
+</project>
+
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
new file mode 100644
index 0000000..217af47
--- /dev/null
+++ b/.idea/compiler.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="CompilerConfiguration">
+    <option name="DEFAULT_COMPILER" value="Javac" />
+    <resourceExtensions />
+    <wildcardResourcePatterns>
+      <entry name="!?*.java" />
+      <entry name="!?*.form" />
+      <entry name="!?*.class" />
+      <entry name="!?*.groovy" />
+      <entry name="!?*.scala" />
+      <entry name="!?*.flex" />
+      <entry name="!?*.kt" />
+      <entry name="!?*.clj" />
+    </wildcardResourcePatterns>
+    <annotationProcessing>
+      <profile default="true" name="Default" enabled="false">
+        <processorPath useClasspath="true" />
+      </profile>
+    </annotationProcessing>
+  </component>
+</project>
+
diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml
new file mode 100644
index 0000000..3572571
--- /dev/null
+++ b/.idea/copyright/profiles_settings.xml
@@ -0,0 +1,5 @@
+<component name="CopyrightManager">
+  <settings default="">
+    <module2copyright />
+  </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
new file mode 100644
index 0000000..e206d70
--- /dev/null
+++ b/.idea/encodings.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false" />
+</project>
+
diff --git a/.idea/libraries/archive.xml b/.idea/libraries/archive.xml
new file mode 100644
index 0000000..694c724
--- /dev/null
+++ b/.idea/libraries/archive.xml
@@ -0,0 +1,15 @@
+<component name="libraryTable">
+  <library name="archive">
+    <CLASSES>
+      <root url="jar://$PROJECT_DIR$/website/archive/datamodel-src-2.0.jar!/" />
+      <root url="jar://$PROJECT_DIR$/website/archive/jaba-client-src-2.0.jar!/" />
+      <root url="jar://$PROJECT_DIR$/website/archive/jabaws-src-2.0.jar!/" />
+      <root url="jar://$PROJECT_DIR$/website/archive/full-jaba-client-pack.zip!/" />
+      <root url="jar://$PROJECT_DIR$/website/archive/full-jaba-client-2.0.jar!/" />
+      <root url="jar://$PROJECT_DIR$/website/archive/datamodel-2.0.jar!/" />
+      <root url="jar://$PROJECT_DIR$/website/archive/min-jaba-client-2.0.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
\ No newline at end of file
diff --git a/.idea/libraries/lib.xml b/.idea/libraries/lib.xml
new file mode 100644
index 0000000..fd22c90
--- /dev/null
+++ b/.idea/libraries/lib.xml
@@ -0,0 +1,27 @@
+<component name="libraryTable">
+  <library name="lib">
+    <CLASSES>
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/itext-1.4.7.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/commons-collections-3.2.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/derby.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/compbio-util-1.4.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/log4j-1.2.15.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/commons-lang-2.3.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/webservices-api.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/poi-3.2-FINAL-20081019.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/displaytag-1.2.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/commons-logging-1.1.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/webservices-tools.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/displaytag-export-poi-1.2.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/webservices-rt.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/jstl-1.1.2.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/standard-1.1.2.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/drmaa.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/compbio-ga-1.0.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/commons-beanutils-1.7.0.jar!/" />
+      <root url="jar://$PROJECT_DIR$/WEB-INF/lib/compbio-annotations-1.0.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
\ No newline at end of file
diff --git a/.idea/libraries/servlet_api.xml b/.idea/libraries/servlet_api.xml
new file mode 100644
index 0000000..e05fc3c
--- /dev/null
+++ b/.idea/libraries/servlet_api.xml
@@ -0,0 +1,9 @@
+<component name="libraryTable">
+  <library name="servlet-api">
+    <CLASSES>
+      <root url="jar://$PROJECT_DIR$/lib/servlet-api.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
\ No newline at end of file
diff --git a/.idea/libraries/testng_5_10_jdk15.xml b/.idea/libraries/testng_5_10_jdk15.xml
new file mode 100644
index 0000000..57330cd
--- /dev/null
+++ b/.idea/libraries/testng_5_10_jdk15.xml
@@ -0,0 +1,9 @@
+<component name="libraryTable">
+  <library name="testng-5.10-jdk15">
+    <CLASSES>
+      <root url="jar://$PROJECT_DIR$/testsrc/lib/testng-5.10-jdk15.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..fae7daf
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="EntryPointsManager">
+    <entry_points version="2.0" />
+  </component>
+  <component name="IdProvider" IDEtalkID="3E79422D699ED7045D207DD2F7C5E9A0" />
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.6" project-jdk-type="JavaSDK">
+    <output url="file://$PROJECT_DIR$/../out-jabaws-dev" />
+  </component>
+</project>
+
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..5d191c6
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/jabaws-dev.iml" filepath="$PROJECT_DIR$/jabaws-dev.iml" />
+    </modules>
+  </component>
+</project>
+
diff --git a/.idea/scopes/scope_settings.xml b/.idea/scopes/scope_settings.xml
new file mode 100644
index 0000000..922003b
--- /dev/null
+++ b/.idea/scopes/scope_settings.xml
@@ -0,0 +1,5 @@
+<component name="DependencyValidationManager">
+  <state>
+    <option name="SKIP_IMPORT_STATEMENTS" value="false" />
+  </state>
+</component>
\ No newline at end of file
diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml
new file mode 100644
index 0000000..3b00020
--- /dev/null
+++ b/.idea/uiDesigner.xml
@@ -0,0 +1,125 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Palette2">
+    <group name="Swing">
+      <item class="com.intellij.uiDesigner.HSpacer" tooltip-text="Horizontal Spacer" icon="/com/intellij/uiDesigner/icons/hspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="1" hsize-policy="6" anchor="0" fill="1" />
+      </item>
+      <item class="com.intellij.uiDesigner.VSpacer" tooltip-text="Vertical Spacer" icon="/com/intellij/uiDesigner/icons/vspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="1" anchor="0" fill="2" />
+      </item>
+      <item class="javax.swing.JPanel" icon="/com/intellij/uiDesigner/icons/panel.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JScrollPane" icon="/com/intellij/uiDesigner/icons/scrollPane.png" removable="false" auto-create-binding="false" can-attach-label="true">
+        <default-constraints vsize-policy="7" hsize-policy="7" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JButton" icon="/com/intellij/uiDesigner/icons/button.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="0" fill="1" />
+        <initial-values>
+          <property name="text" value="Button" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JRadioButton" icon="/com/intellij/uiDesigner/icons/radioButton.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="RadioButton" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JCheckBox" icon="/com/intellij/uiDesigner/icons/checkBox.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="CheckBox" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JLabel" icon="/com/intellij/uiDesigner/icons/label.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="0" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="Label" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JTextField" icon="/com/intellij/uiDesigner/icons/textField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JPasswordField" icon="/com/intellij/uiDesigner/icons/passwordField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JFormattedTextField" icon="/com/intellij/uiDesigner/icons/formattedTextField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTextArea" icon="/com/intellij/uiDesigner/icons/textArea.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTextPane" icon="/com/intellij/uiDesigner/icons/textPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JEditorPane" icon="/com/intellij/uiDesigner/icons/editorPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JComboBox" icon="/com/intellij/uiDesigner/icons/comboBox.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="2" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JTable" icon="/com/intellij/uiDesigner/icons/table.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JList" icon="/com/intellij/uiDesigner/icons/list.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="2" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTree" icon="/com/intellij/uiDesigner/icons/tree.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTabbedPane" icon="/com/intellij/uiDesigner/icons/tabbedPane.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+          <preferred-size width="200" height="200" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JSplitPane" icon="/com/intellij/uiDesigner/icons/splitPane.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+          <preferred-size width="200" height="200" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JSpinner" icon="/com/intellij/uiDesigner/icons/spinner.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JSlider" icon="/com/intellij/uiDesigner/icons/slider.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JSeparator" icon="/com/intellij/uiDesigner/icons/separator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JProgressBar" icon="/com/intellij/uiDesigner/icons/progressbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1" />
+      </item>
+      <item class="javax.swing.JToolBar" icon="/com/intellij/uiDesigner/icons/toolbar.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1">
+          <preferred-size width="-1" height="20" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JToolBar$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
+      </item>
+      <item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
+      </item>
+    </group>
+  </component>
+</project>
+
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..275077f
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>
+
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
new file mode 100644
index 0000000..c4b4cc6
--- /dev/null
+++ b/.idea/workspace.xml
@@ -0,0 +1,751 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ChangeListManager">
+    <list default="true" id="e8b4b79e-8aed-4386-9e7f-8dda0becf4dd" name="Default" comment="">
+      <change type="NEW" beforePath="" afterPath="$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>
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+      <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>
+
diff --git a/jabaws-dev.iml b/jabaws-dev.iml
new file mode 100644
index 0000000..899703c
--- /dev/null
+++ b/jabaws-dev.iml
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="FacetManager">
+    <facet type="web" name="Web">
+      <configuration>
+        <descriptors>
+          <deploymentDescriptor name="web.xml" url="file://$MODULE_DIR$/WEB-INF/web.xml" />
+        </descriptors>
+        <webroots />
+        <sourceRoots>
+          <root url="file://$MODULE_DIR$/src" />
+          <root url="file://$MODULE_DIR$/datamodel" />
+          <root url="file://$MODULE_DIR$/engine" />
+          <root url="file://$MODULE_DIR$/runner" />
+          <root url="file://$MODULE_DIR$/webservices" />
+        </sourceRoots>
+      </configuration>
+    </facet>
+  </component>
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/datamodel" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/engine" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/runner" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/webservices" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/testsrc" isTestSource="true" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="lib" level="project" />
+    <orderEntry type="library" name="archive" level="project" />
+    <orderEntry type="library" name="servlet-api" level="project" />
+    <orderEntry type="library" scope="TEST" name="testng-5.10-jdk15" level="project" />
+  </component>
+</module>
+
-- 
1.7.10.2