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eugenefischer
2025-04-10 11:05:08 -05:00
parent 81d8a12765
commit bcf5a4c749
3 changed files with 47 additions and 60 deletions
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28
.idea/artifacts/BiGpairSEQ_Sim_jar.xml generated
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@@ -1,27 +1,27 @@
<component name="ArtifactManager"> <component name="ArtifactManager">
<artifact type="jar" name="BiGpairSEQ_Sim:jar"> <artifact type="jar" name="BiGpairSEQ_Sim:jar">
<output-path>$PROJECT_DIR$/out/artifacts/BiGpairSEQ_Sim_jar</output-path> <output-path>$PROJECT_DIR$/out/artifacts/BiGpairSEQ_Sim_jar</output-path>
<root id="archive" name="TCellSim.jar"> <root id="archive" name="BiGpairSEQ_Sim.jar">
<element id="directory" name="META-INF"> <element id="directory" name="META-INF">
<element id="file-copy" path="$PROJECT_DIR$/META-INF/MANIFEST.MF" /> <element id="file-copy" path="$PROJECT_DIR$/META-INF/MANIFEST.MF" />
</element> </element>
<element id="module-output" name="TCellSim" /> <element id="module-output" name="BiGpairSEQ_Sim" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-client-api/1.6/commons-rng-client-api-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.14.0/commons-csv-1.14.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-io/commons-io/2.18.0/commons-io-2.18.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.18.0/commons-codec-1.18.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-sampling/1.6/commons-rng-sampling-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.2/jgrapht-io-1.5.2.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-sampling/1.6/commons-rng-sampling-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.14.0/commons-csv-1.14.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.12.0/antlr4-runtime-4.12.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.10.0/commons-text-1.10.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jetbrains/annotations/26.0.2/annotations-26.0.2.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jetbrains/annotations/26.0.2/annotations-26.0.2.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.2/jgrapht-io-1.5.2.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-simple/1.6/commons-rng-simple-1.6.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-simple/1.6/commons-rng-simple-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.9.0/commons-cli-1.9.0.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-io/commons-io/2.18.0/commons-io-2.18.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-core/1.6/commons-rng-core-1.6.jar" path-in-jar="/" /> <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-core/1.6/commons-rng-core-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.18.0/commons-codec-1.18.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-client-api/1.6/commons-rng-client-api-1.6.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.9.0/commons-cli-1.9.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.12.0/antlr4-runtime-4.12.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.10.0/commons-text-1.10.0.jar" path-in-jar="/" />
<element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar" path-in-jar="/" />
</root> </root>
</artifact> </artifact>
</component> </component>

2
.idea/compiler.xml generated
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@@ -6,8 +6,8 @@
<sourceOutputDir name="target/generated-sources/annotations" /> <sourceOutputDir name="target/generated-sources/annotations" />
<sourceTestOutputDir name="target/generated-test-sources/test-annotations" /> <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
<outputRelativeToContentRoot value="true" /> <outputRelativeToContentRoot value="true" />
<module name="TCellSim" />
<module name="BigPairSEQ" /> <module name="BigPairSEQ" />
<module name="BiGpairSEQ_Sim" />
</profile> </profile>
</annotationProcessing> </annotationProcessing>
</component> </component>

77
pom.xml
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@@ -5,7 +5,7 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>org.example</groupId> <groupId>org.example</groupId>
<artifactId>TCellSim</artifactId> <artifactId>BiGpairSEQ_Sim</artifactId>
<version>1.0-SNAPSHOT</version> <version>1.0-SNAPSHOT</version>
<build> <build>
<plugins> <plugins>
@@ -26,60 +26,47 @@
<version>RELEASE</version> <version>RELEASE</version>
<scope>compile</scope> <scope>compile</scope>
</dependency> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/org.apache.commons/commons-rng-simple &ndash;&gt;--> <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-rng-simple -->
<dependency> <dependency>
<groupId>org.apache.commons</groupId> <groupId>org.apache.commons</groupId>
<artifactId>commons-rng-simple</artifactId> <artifactId>commons-rng-simple</artifactId>
<version>1.6</version> <version>1.6</version>
</dependency> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/org.apache.commons/commons-rng-core &ndash;&gt;-->
<!-- <dependency>-->
<!-- <groupId>org.apache.commons</groupId>-->
<!-- <artifactId>commons-rng-core</artifactId>-->
<!-- <version>1.6</version>-->
<!-- </dependency>-->
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-rng-sampling -->
<dependency> <dependency>
<groupId>org.apache.commons</groupId> <groupId>org.apache.commons</groupId>
<artifactId>commons-rng-sampling</artifactId> <artifactId>commons-rng-sampling</artifactId>
<version>1.6</version> <version>1.6</version>
</dependency> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/org.apache.commons/commons-rng-client-api &ndash;&gt;--> <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
<!-- <dependency>--> <dependency>
<!-- <groupId>org.apache.commons</groupId>--> <groupId>org.apache.commons</groupId>
<!-- <artifactId>commons-rng-client-api</artifactId>--> <artifactId>commons-csv</artifactId>
<!-- <version>1.6</version>--> <version>1.14.0</version>
<!-- </dependency>--> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/org.apache.commons/commons-csv &ndash;&gt;--> <!-- https://mvnrepository.com/artifact/org.jgrapht/jgrapht-core -->
<!-- <dependency>--> <dependency>
<!-- <groupId>org.apache.commons</groupId>--> <groupId>org.jgrapht</groupId>
<!-- <artifactId>commons-csv</artifactId>--> <artifactId>jgrapht-core</artifactId>
<!-- <version>1.14.0</version>--> <version>1.5.2</version>
<!-- </dependency>--> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/org.jgrapht/jgrapht-core &ndash;&gt;--> <!-- https://mvnrepository.com/artifact/org.jgrapht/jgrapht-io -->
<!-- <dependency>--> <dependency>
<!-- <groupId>org.jgrapht</groupId>--> <groupId>org.jgrapht</groupId>
<!-- <artifactId>jgrapht-core</artifactId>--> <artifactId>jgrapht-io</artifactId>
<!-- <version>1.5.2</version>--> <version>1.5.2</version>
<!-- </dependency>--> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/org.jgrapht/jgrapht-io &ndash;&gt;--> <!-- https://mvnrepository.com/artifact/org.jheaps/jheaps -->
<!-- <dependency>--> <dependency>
<!-- <groupId>org.jgrapht</groupId>--> <groupId>org.jheaps</groupId>
<!-- <artifactId>jgrapht-io</artifactId>--> <artifactId>jheaps</artifactId>
<!-- <version>1.5.2</version>--> <version>0.14</version>
<!-- </dependency>--> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/org.jheaps/jheaps &ndash;&gt;--> <!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
<!-- <dependency>--> <dependency>
<!-- <groupId>org.jheaps</groupId>--> <groupId>commons-cli</groupId>
<!-- <artifactId>jheaps</artifactId>--> <artifactId>commons-cli</artifactId>
<!-- <version>0.14</version>--> <version>1.9.0</version>
<!-- </dependency>--> </dependency>
<!-- &lt;!&ndash; https://mvnrepository.com/artifact/commons-cli/commons-cli &ndash;&gt;-->
<!-- <dependency>-->
<!-- <groupId>commons-cli</groupId>-->
<!-- <artifactId>commons-cli</artifactId>-->
<!-- <version>1.9.0</version>-->
<!-- </dependency>-->
</dependencies> </dependencies>
<properties> <properties>
<maven.compiler.source>11</maven.compiler.source> <maven.compiler.source>11</maven.compiler.source>