pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <groupId>com.eljaguar</groupId>
    <artifactId>loopmatcher</artifactId>
    <version>1.3.3</version>
    <packaging>jar</packaging>
    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <maven.compiler.source>1.8</maven.compiler.source>
        <maven.compiler.target>1.8</maven.compiler.target>
    </properties>
    <dependencies>
        <dependency>
            <groupId>org.biojava</groupId>
            <artifactId>biojava-core</artifactId>
            <version>7.1.1</version>
        </dependency>
        <!-- other biojava jars as needed -->
        <!-- https://mvnrepository.com/artifact/com.opencsv/opencsv -->
        <!-- https://mvnrepository.com/artifact/org.netbeans.modules/org-netbeans-modules-web-inspect -->
        <dependency>
            <groupId>com.opencsv</groupId>
            <artifactId>opencsv</artifactId>
            <version>5.9</version>
        </dependency>
        <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-io -->
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-io</artifactId>
            <version>1.3.2</version>
        </dependency>
        <dependency>
            <groupId>org.jetbrains</groupId>
            <artifactId>annotations</artifactId>
            <version>24.1.0</version>
            <scope>compile</scope>
        </dependency>
    </dependencies>
    <name>LoopMatcher (LAZLO)</name>
    
    <build>
      <plugins>
        <plugin>
          <artifactId>maven-assembly-plugin</artifactId>
          <configuration>
            <archive>
              <manifest>
                <mainClass>com.eljaguar.mvnlaslo.gui.GUIFrame</mainClass>
              </manifest>
            </archive>
            <descriptorRefs>
              <descriptorRef>jar-with-dependencies</descriptorRef>
            </descriptorRefs>
          </configuration>
        </plugin>
         <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-compiler-plugin</artifactId>
            <version>3.13.0</version>
            <configuration>
               <debug>true</debug>
               <showDeprecation>true</showDeprecation>
                <source>11</source>
                <target>11</target>
            </configuration>
         </plugin>
      </plugins>
    </build>
    <description>Search for hairpin structures with specific loop patterns</description>
</project>