Add IntelliJ project files

7edebc62 · bow · 0ba851aa · 7edebc62 · 7edebc62 · 7edebc62
Commit 7edebc62 authored 10 years ago by bow
--- a/.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml
+++ b/.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml
+<component name="libraryTable">
+  <library name="Maven: org.hamcrest:hamcrest-core:1.1">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scala_lang_modules_scala_parser_combinators_2_11_1_0_2.xml
+++ b/.idea/libraries/Maven__org_scala_lang_modules_scala_parser_combinators_2_11_1_0_2.xml
+<component name="libraryTable">
+  <library name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.2/scala-parser-combinators_2.11-1.0.2.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.2/scala-parser-combinators_2.11-1.0.2-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.2/scala-parser-combinators_2.11-1.0.2-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scala_lang_modules_scala_xml_2_11_1_0_2.xml
+++ b/.idea/libraries/Maven__org_scala_lang_modules_scala_xml_2_11_1_0_2.xml
+<component name="libraryTable">
+  <library name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_1.xml
+++ b/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_1.xml
+<component name="libraryTable">
+  <library name="Maven: org.scala-lang:scala-compiler-bundle:2.11.1">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-compiler/2.11.1/scala-compiler-2.11.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-library/2.11.1/scala-library-2.11.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-reflect/2.11.1/scala-reflect-2.11.1.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
+++ b/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
+<component name="libraryTable">
+  <library name="Maven: org.scala-lang:scala-compiler-bundle:2.11.2">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-compiler/2.11.2/scala-compiler-2.11.2.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
+++ b/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
+<component name="libraryTable">
+  <library name="Maven: org.scala-lang:scala-library:2.11.2">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_11_2.xml
+++ b/.idea/libraries/Maven__org_scala_lang_scala_reflect_2_11_2.xml
+<component name="libraryTable">
+  <library name="Maven: org.scala-lang:scala-reflect:2.11.2">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scalatest_scalatest_2_11_2_2_1.xml
+++ b/.idea/libraries/Maven__org_scalatest_scalatest_2_11_2_2_1.xml
+<component name="libraryTable">
+  <library name="Maven: org.scalatest:scalatest_2.11:2.2.1">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scalatest/scalatest_2.11/2.2.1/scalatest_2.11-2.2.1.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scalatest/scalatest_2.11/2.2.1/scalatest_2.11-2.2.1-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scalatest/scalatest_2.11/2.2.1/scalatest_2.11-2.2.1-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_scalaz_scalaz_core_2_11_7_1_0.xml
+++ b/.idea/libraries/Maven__org_scalaz_scalaz_core_2_11_7_1_0.xml
+<component name="libraryTable">
+  <library name="Maven: org.scalaz:scalaz-core_2.11:7.1.0">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scalaz/scalaz-core_2.11/7.1.0/scalaz-core_2.11-7.1.0.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scalaz/scalaz-core_2.11/7.1.0/scalaz-core_2.11-7.1.0-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/scalaz/scalaz-core_2.11/7.1.0/scalaz-core_2.11-7.1.0-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_testng_testng_6_8.xml
+++ b/.idea/libraries/Maven__org_testng_testng_6_8.xml
+<component name="libraryTable">
+  <library name="Maven: org.testng:testng:6.8">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8/testng-6.8.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8/testng-6.8-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8/testng-6.8-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
+++ b/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
+<component name="libraryTable">
+  <library name="Maven: org.yaml:snakeyaml:1.6">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/yaml/snakeyaml/1.6/snakeyaml-1.6-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__redis_clients_jedis_2_5_1.xml
+++ b/.idea/libraries/Maven__redis_clients_jedis_2_5_1.xml
+<component name="libraryTable">
+  <library name="Maven: redis.clients:jedis:2.5.1">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/redis/clients/jedis/2.5.1/jedis-2.5.1.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/redis/clients/jedis/2.5.1/jedis-2.5.1-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/redis/clients/jedis/2.5.1/jedis-2.5.1-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/gatk_protected.xml
+++ b/.idea/libraries/gatk_protected.xml
+<component name="libraryTable">
+  <library name="gatk-protected">
+    <CLASSES>
+      <root url="file://$PROJECT_DIR$/../gatk-protected" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES>
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/gatk-queue/src/main/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/gatk-utils/src/main/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/gatk-engine/src/main/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/external-example/src/main/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/external-example/src/test/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/gatk-tools-public/src/main/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/gatk-tools-public/src/test/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/public/gatk-queue-extensions-generator/src/main/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/protected/gatk-tools-protected/src/main/java" />
+      <root url="file://$PROJECT_DIR$/../gatk-protected/protected/gatk-tools-protected/src/test/java" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="EntryPointsManager">
+    <entry_points version="2.0" />
+  </component>
+  <component name="MavenProjectsManager">
+    <option name="originalFiles">
+      <list>
+        <option value="$PROJECT_DIR$/pom.xml" />
+      </list>
+    </option>
+  </component>
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.8" project-jdk-type="JavaSDK">
+    <output url="file://$PROJECT_DIR$/out" />
+  </component>
+</project>
--- a/.idea/modules.xml
+++ b/.idea/modules.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/Biopet.iml" filepath="$PROJECT_DIR$/Biopet.iml" />
+      <module fileurl="file://$PROJECT_DIR$/biopet-framework/BiopetFramework.iml" filepath="$PROJECT_DIR$/biopet-framework/BiopetFramework.iml" />
+    </modules>
+  </component>
+</project>
--- a/.idea/scala_settings.xml
+++ b/.idea/scala_settings.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ScalaProjectSettings">
+    <option name="inProcessMode" value="false" />
+    <option name="intInjectionMapping">
+      <map>
+        <entry key="xml" value="XML" />
+      </map>
+    </option>
+  </component>
+</project>
--- a/.idea/scopes/scope_settings.xml
+++ b/.idea/scopes/scope_settings.xml
+<component name="DependencyValidationManager">
+  <state>
+    <option name="SKIP_IMPORT_STATEMENTS" value="false" />
+  </state>
+</component>
\ No newline at end of file
--- a/.idea/uiDesigner.xml
+++ b/.idea/uiDesigner.xml
+<?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">
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+        </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">
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+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
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+          <preferred-size width="-1" height="20" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JToolBar$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
+      </item>
+      <item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
+      </item>
+    </group>
+  </component>
+</project>
--- a/.idea/vcs.xml
+++ b/.idea/vcs.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
--- a/Biopet.iml
+++ b/Biopet.iml
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="false">
+    <output url="file://$MODULE_DIR$/target/classes" />
+    <output-test url="file://$MODULE_DIR$/target/test-classes" />
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>