From b4d0e747600bde8a2021867fe86d7bc370db9f93 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 6 Nov 2014 10:39:45 +0100
Subject: [PATCH] Update project files to IntelliJ 14

---
 ...n__org_scala_lang_scala_library_2_11_2.xml |  9 ++-
 ...ven__org_scalaz_scalaz_core_2_11_7_1_0.xml |  1 +
 .idea/scala_compiler.xml                      | 11 ++++
 ...cala_lang_scala_compiler_bundle_2_11_2.xml | 11 ++++
 ...n__org_scala_lang_scala_library_2_11_2.xml | 13 +++++
 .../biopet-framework/BiopetFramework.iml      | 54 ++++++++++++++++++
 ...cala_lang_scala_compiler_bundle_2_11_2.xml | 11 ++++
 ...n__org_scala_lang_scala_library_2_11_2.xml | 13 +++++
 .../biopet-framework/BiopetFramework.iml      | 55 +++++++++++++++++++
 9 files changed, 177 insertions(+), 1 deletion(-)
 create mode 100644 .idea/scala_compiler.xml
 create mode 100644 projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
 create mode 100644 projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
 create mode 100644 projectFilesBackup/biopet-framework/BiopetFramework.iml
 create mode 100644 projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
 create mode 100644 projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
 create mode 100644 projectFilesBackup1/biopet-framework/BiopetFramework.iml

diff --git 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
index 497462405..c2e5403fc 100644
--- 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
@@ -1,5 +1,12 @@
 <component name="libraryTable">
-  <library name="Maven: org.scala-lang:scala-library:2.11.2">
+  <library name="Maven: org.scala-lang:scala-library:2.11.2" type="Scala">
+    <properties>
+      <compiler-classpath>
+        <root url="file://$MAVEN_REPOSITORY$/org/scala-lang/scala-compiler/2.11.2/scala-compiler-2.11.2.jar" />
+        <root url="file://$MAVEN_REPOSITORY$/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.jar" />
+        <root url="file://$MAVEN_REPOSITORY$/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2.jar" />
+      </compiler-classpath>
+    </properties>
     <CLASSES>
       <root url="jar://$MAVEN_REPOSITORY$/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.jar!/" />
     </CLASSES>
diff --git 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
index 3c580f059..8cd45ed1b 100644
--- 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
@@ -5,6 +5,7 @@
     </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!/" />
+      <root url="http://docs.typelevel.org/api/scalaz/stable/7.1.0-M3/doc/#package" />
     </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!/" />
diff --git a/.idea/scala_compiler.xml b/.idea/scala_compiler.xml
new file mode 100644
index 000000000..d79c187ea
--- /dev/null
+++ b/.idea/scala_compiler.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ScalaCompilerConfiguration">
+    <option name="deprecationWarnings" value="true" />
+    <parameters>
+      <parameter value="-dependencyfile" />
+      <parameter value="$MODULE_DIR$/target/.scala_dependencies" />
+      <parameter value="-feature" />
+    </parameters>
+  </component>
+</project>
\ No newline at end of file
diff --git a/projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml b/projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
new file mode 100644
index 000000000..2baaf4294
--- /dev/null
+++ b/projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
@@ -0,0 +1,11 @@
+<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
diff --git a/projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml b/projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
new file mode 100644
index 000000000..497462405
--- /dev/null
+++ b/projectFilesBackup/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
@@ -0,0 +1,13 @@
+<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
diff --git a/projectFilesBackup/biopet-framework/BiopetFramework.iml b/projectFilesBackup/biopet-framework/BiopetFramework.iml
new file mode 100644
index 000000000..3dcb6528e
--- /dev/null
+++ b/projectFilesBackup/biopet-framework/BiopetFramework.iml
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="FacetManager">
+    <facet type="scala" name="Scala">
+      <configuration>
+        <option name="compilerLibraryLevel" value="Project" />
+        <option name="compilerLibraryName" value="Maven: org.scala-lang:scala-compiler-bundle:2.11.2" />
+        <option name="compilerOptions" value="-dependencyfile $MODULE_DIR$/target/.scala_dependencies -feature" />
+        <option name="deprecationWarnings" value="true" />
+        <option name="languageLevel" value="Scala 2.11" />
+        <option name="vmOptions" value="" />
+      </configuration>
+    </facet>
+    <facet type="Python" name="Python">
+      <configuration sdkName="" />
+    </facet>
+  </component>
+  <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://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/scripts" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="com.twitter:algebird-core_2.10:0.8.1" level="project" />
+    <orderEntry type="library" name="gatk-protected" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: junit:junit:4.10" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.3" level="project" />
+    <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
+    <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
+    <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml b/projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
new file mode 100644
index 000000000..2baaf4294
--- /dev/null
+++ b/projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml
@@ -0,0 +1,11 @@
+<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
diff --git a/projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml b/projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
new file mode 100644
index 000000000..497462405
--- /dev/null
+++ b/projectFilesBackup1/.idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml
@@ -0,0 +1,13 @@
+<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
diff --git a/projectFilesBackup1/biopet-framework/BiopetFramework.iml b/projectFilesBackup1/biopet-framework/BiopetFramework.iml
new file mode 100644
index 000000000..e526de5bd
--- /dev/null
+++ b/projectFilesBackup1/biopet-framework/BiopetFramework.iml
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="FacetManager">
+    <facet type="scala" name="Scala">
+      <configuration>
+        <option name="compilerLibraryLevel" value="Project" />
+        <option name="compilerLibraryName" value="Maven: org.scala-lang:scala-compiler-bundle:2.11.2" />
+        <option name="compilerOptions" value="-dependencyfile $MODULE_DIR$/target/.scala_dependencies -feature" />
+        <option name="deprecationWarnings" value="true" />
+        <option name="languageLevel" value="Scala 2.11" />
+        <option name="vmOptions" value="" />
+      </configuration>
+    </facet>
+    <facet type="Python" name="Python">
+      <configuration sdkName="" />
+    </facet>
+  </component>
+  <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://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/scripts" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="com.twitter:algebird-core_2.10:0.8.1" level="project" />
+    <orderEntry type="library" name="gatk-protected" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: junit:junit:4.10" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.3" level="project" />
+    <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
+    <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
+    <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
+    <orderEntry type="library" name="scala-sdk-2.11.1" level="application" />
+  </component>
+</module>
\ No newline at end of file
-- 
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