From 7edebc6259addca4949f62630c3535c2ab71e3c7 Mon Sep 17 00:00:00 2001 From: bow <bow@bow.web.id> Date: Thu, 23 Oct 2014 10:36:03 +0200 Subject: [PATCH] Add IntelliJ project files --- .idea/.name | 1 + .idea/compiler.xml | 30 +++++ .idea/copyright/profiles_settings.xml | 3 + .idea/dictionaries/warindrarto.xml | 21 +++ .idea/encodings.xml | 7 + .idea/inspectionProfiles/Project_Default.xml | 16 +++ .../inspectionProfiles/profiles_settings.xml | 7 + .../Maven__com_baqend_bloom_filter_1_02.xml | 13 ++ .../Maven__com_beust_jcommander_1_27.xml | 13 ++ ...ulien_truffaut_monocle_core_2_11_0_5_0.xml | 13 ++ ...ven__com_github_scopt_scopt_2_10_3_2_0.xml | 13 ++ ...Maven__com_google_code_gson_gson_2_2_4.xml | 13 ++ .../Maven__com_google_guava_guava_17_0.xml | 13 ++ ...aven__io_argonaut_argonaut_2_11_6_1_M4.xml | 13 ++ .idea/libraries/Maven__junit_junit_4_10.xml | 13 ++ ...__org_apache_commons_commons_pool2_2_2.xml | 13 ++ .../Maven__org_beanshell_bsh_2_0b4.xml | 13 ++ ...Maven__org_biojava_biojava3_core_3_1_0.xml | 13 ++ ..._org_biojava_biojava3_sequencing_3_1_0.xml | 13 ++ ...tk_gatk_queue_package_distribution_3_2.xml | 15 +++ .../Maven__org_hamcrest_hamcrest_core_1_1.xml | 13 ++ ...es_scala_parser_combinators_2_11_1_0_2.xml | 13 ++ ...cala_lang_modules_scala_xml_2_11_1_0_2.xml | 13 ++ ...cala_lang_scala_compiler_bundle_2_11_1.xml | 11 ++ ...cala_lang_scala_compiler_bundle_2_11_2.xml | 11 ++ ...n__org_scala_lang_scala_library_2_11_2.xml | 13 ++ ...n__org_scala_lang_scala_reflect_2_11_2.xml | 13 ++ ...en__org_scalatest_scalatest_2_11_2_2_1.xml | 13 ++ ...ven__org_scalaz_scalaz_core_2_11_7_1_0.xml | 13 ++ .../Maven__org_testng_testng_6_8.xml | 13 ++ .../Maven__org_yaml_snakeyaml_1_6.xml | 13 ++ .../Maven__redis_clients_jedis_2_5_1.xml | 13 ++ .idea/libraries/gatk_protected.xml | 20 +++ .idea/misc.xml | 17 +++ .idea/modules.xml | 10 ++ .idea/scala_settings.xml | 12 ++ .idea/scopes/scope_settings.xml | 5 + .idea/uiDesigner.xml | 125 ++++++++++++++++++ .idea/vcs.xml | 7 + Biopet.iml | 13 ++ biopet-framework/BiopetFramework.iml | 56 ++++++++ 41 files changed, 673 insertions(+) create mode 100644 .idea/.name create mode 100644 .idea/compiler.xml create mode 100644 .idea/copyright/profiles_settings.xml create mode 100644 .idea/dictionaries/warindrarto.xml create mode 100644 .idea/encodings.xml create mode 100644 .idea/inspectionProfiles/Project_Default.xml create mode 100644 .idea/inspectionProfiles/profiles_settings.xml create mode 100644 .idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml create mode 100644 .idea/libraries/Maven__com_beust_jcommander_1_27.xml create mode 100644 .idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml create mode 100644 .idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml create mode 100644 .idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml create mode 100644 .idea/libraries/Maven__com_google_guava_guava_17_0.xml create mode 100644 .idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml create mode 100644 .idea/libraries/Maven__junit_junit_4_10.xml create mode 100644 .idea/libraries/Maven__org_apache_commons_commons_pool2_2_2.xml create mode 100644 .idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml create mode 100644 .idea/libraries/Maven__org_biojava_biojava3_core_3_1_0.xml create mode 100644 .idea/libraries/Maven__org_biojava_biojava3_sequencing_3_1_0.xml create mode 100644 .idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_package_distribution_3_2.xml create mode 100644 .idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml create mode 100644 .idea/libraries/Maven__org_scala_lang_modules_scala_parser_combinators_2_11_1_0_2.xml create mode 100644 .idea/libraries/Maven__org_scala_lang_modules_scala_xml_2_11_1_0_2.xml create mode 100644 .idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_1.xml create mode 100644 .idea/libraries/Maven__org_scala_lang_scala_compiler_bundle_2_11_2.xml create mode 100644 .idea/libraries/Maven__org_scala_lang_scala_library_2_11_2.xml create mode 100644 .idea/libraries/Maven__org_scala_lang_scala_reflect_2_11_2.xml create mode 100644 .idea/libraries/Maven__org_scalatest_scalatest_2_11_2_2_1.xml create mode 100644 .idea/libraries/Maven__org_scalaz_scalaz_core_2_11_7_1_0.xml create mode 100644 .idea/libraries/Maven__org_testng_testng_6_8.xml create mode 100644 .idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml create mode 100644 .idea/libraries/Maven__redis_clients_jedis_2_5_1.xml create mode 100644 .idea/libraries/gatk_protected.xml create mode 100644 .idea/misc.xml create mode 100644 .idea/modules.xml create mode 100644 .idea/scala_settings.xml create mode 100644 .idea/scopes/scope_settings.xml create mode 100644 .idea/uiDesigner.xml create mode 100644 .idea/vcs.xml create mode 100644 Biopet.iml create mode 100644 biopet-framework/BiopetFramework.iml diff --git a/.idea/.name b/.idea/.name new file mode 100644 index 000000000..4b5075762 --- /dev/null +++ b/.idea/.name @@ -0,0 +1 @@ +Biopet \ No newline at end of file diff --git a/.idea/compiler.xml b/.idea/compiler.xml new file mode 100644 index 000000000..48ac3c04c --- /dev/null +++ b/.idea/compiler.xml @@ -0,0 +1,30 @@ +<?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> + <profile default="false" name="Maven default annotation processors profile" enabled="false"> + <sourceOutputDir name="target/generated-sources/annotations" /> + <sourceTestOutputDir name="target/generated-test-sources/test-annotations" /> + <outputRelativeToContentRoot value="true" /> + <processorPath useClasspath="true" /> + <module name="BiopetFramework" /> + </profile> + </annotationProcessing> + </component> +</project> + diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml new file mode 100644 index 000000000..e7bedf337 --- /dev/null +++ b/.idea/copyright/profiles_settings.xml @@ -0,0 +1,3 @@ +<component name="CopyrightManager"> + <settings default="" /> +</component> \ No newline at end of file diff --git a/.idea/dictionaries/warindrarto.xml b/.idea/dictionaries/warindrarto.xml new file mode 100644 index 000000000..89d157168 --- /dev/null +++ b/.idea/dictionaries/warindrarto.xml @@ -0,0 +1,21 @@ +<component name="ProjectDictionaryState"> + <dictionary name="warindrarto"> + <words> + <w>arindrarto</w> + <w>biopet</w> + <w>chrom</w> + <w>cufflinks</w> + <w>exon</w> + <w>fastq</w> + <w>gentrap</w> + <w>gsnap</w> + <w>snvmix</w> + <w>tophat</w> + <w>transcriptome</w> + <w>varcaller</w> + <w>varscan</w> + <w>warindrarto</w> + <w>wibowo</w> + </words> + </dictionary> +</component> \ No newline at end of file diff --git a/.idea/encodings.xml b/.idea/encodings.xml new file mode 100644 index 000000000..2aa2187f2 --- /dev/null +++ b/.idea/encodings.xml @@ -0,0 +1,7 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project version="4"> + <component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false"> + <file url="file://$PROJECT_DIR$/biopet-framework" charset="UTF-8" /> + </component> +</project> + diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml new file mode 100644 index 000000000..dcf891305 --- /dev/null +++ b/.idea/inspectionProfiles/Project_Default.xml @@ -0,0 +1,16 @@ +<component name="InspectionProjectProfileManager"> + <profile version="1.0" is_locked="false"> + <option name="myName" value="Project Default" /> + <option name="myLocal" value="false" /> + <inspection_tool class="LoggerInitializedWithForeignClass" enabled="false" level="WARNING" enabled_by_default="false"> + <option name="loggerClassName" value="org.apache.log4j.Logger,org.slf4j.LoggerFactory,org.apache.commons.logging.LogFactory,java.util.logging.Logger" /> + <option name="loggerFactoryMethodName" value="getLogger,getLogger,getLog,getLogger" /> + </inspection_tool> + <inspection_tool class="MatchToPartialFunction" enabled="false" level="WARNING" enabled_by_default="false" /> + <inspection_tool class="SpellCheckingInspection" enabled="false" level="TYPO" enabled_by_default="false"> + <option name="processCode" value="true" /> + <option name="processLiterals" value="true" /> + <option name="processComments" value="true" /> + </inspection_tool> + </profile> +</component> \ No newline at end of file diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml new file mode 100644 index 000000000..3b312839b --- /dev/null +++ b/.idea/inspectionProfiles/profiles_settings.xml @@ -0,0 +1,7 @@ +<component name="InspectionProjectProfileManager"> + <settings> + <option name="PROJECT_PROFILE" value="Project Default" /> + <option name="USE_PROJECT_PROFILE" value="true" /> + <version value="1.0" /> + </settings> +</component> \ No newline at end of file diff --git a/.idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml b/.idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml new file mode 100644 index 000000000..a08d14f4e --- /dev/null +++ b/.idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml @@ -0,0 +1,13 @@ +<component name="libraryTable"> + <library name="Maven: com.baqend:bloom-filter:1.02"> + <CLASSES> + <root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02.jar!/" /> + </CLASSES> + <JAVADOC> + <root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02-javadoc.jar!/" /> + </JAVADOC> + <SOURCES> + <root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02-sources.jar!/" /> + </SOURCES> + </library> +</component> \ No newline at end of file diff --git a/.idea/libraries/Maven__com_beust_jcommander_1_27.xml b/.idea/libraries/Maven__com_beust_jcommander_1_27.xml new file mode 100644 index 000000000..f0f9060d9 --- /dev/null +++ b/.idea/libraries/Maven__com_beust_jcommander_1_27.xml @@ -0,0 +1,13 @@ +<component name="libraryTable"> + <library name="Maven: com.beust:jcommander:1.27"> + <CLASSES> + <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27.jar!/" /> + </CLASSES> + <JAVADOC> + <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27-javadoc.jar!/" /> + </JAVADOC> + <SOURCES> + <root url="jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27-sources.jar!/" /> + </SOURCES> + </library> +</component> \ No newline at end of file diff --git a/.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml b/.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml new file mode 100644 index 000000000..4a6e5b1ee --- /dev/null +++ b/.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml @@ -0,0 +1,13 @@ +<component name="libraryTable"> + <library name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0"> + <CLASSES> + <root url="jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0.jar!/" /> + </CLASSES> + <JAVADOC> + <root url="jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0-javadoc.jar!/" /> + </JAVADOC> + <SOURCES> + <root url="jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0-sources.jar!/" /> + </SOURCES> + </library> +</component> \ No newline at end of file diff --git a/.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml b/.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml new file mode 100644 index 000000000..adf0f2cb7 --- /dev/null +++ b/.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml @@ -0,0 +1,13 @@ +<component name="libraryTable"> + <library name="Maven: com.github.scopt:scopt_2.10:3.2.0"> + <CLASSES> + <root url="jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0.jar!/" /> + </CLASSES> + <JAVADOC> + <root url="jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0-javadoc.jar!/" /> + </JAVADOC> + <SOURCES> + <root url="jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0-sources.jar!/" /> + </SOURCES> + </library> +</component> \ No newline at end of file diff --git a/.idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml b/.idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml new file mode 100644 index 000000000..4533c1ba7 --- 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url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0.jar!/" /> + </CLASSES> + <JAVADOC> + <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0-javadoc.jar!/" /> + </JAVADOC> + <SOURCES> + <root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0-sources.jar!/" /> + </SOURCES> + </library> +</component> \ No newline at end of file diff --git a/.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml b/.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml new file mode 100644 index 000000000..fa8e4d1d2 --- /dev/null +++ b/.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml @@ -0,0 +1,13 @@ +<component name="libraryTable"> + <library name="Maven: io.argonaut:argonaut_2.11:6.1-M4"> + <CLASSES> + <root url="jar://$MAVEN_REPOSITORY$/io/argonaut/argonaut_2.11/6.1-M4/argonaut_2.11-6.1-M4.jar!/" /> + </CLASSES> + <JAVADOC> + <root 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