<commit_before><?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/maven-v4_0_0.xsd">
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>5.2.2-SNAPSHOT</version>
	</parent>
	<modelVersion>4.0.0</modelVersion>
	<artifactId>biojava-genome</artifactId>
	<name>biojava-genome</name>

	<licenses>
		<license>
			<name>GNU LGPL v2</name>
			<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

	<repositories>
		<repository>
			<id>biojava-maven-repo</id>
			<name>BioJava repository</name>
			<url>http://www.biojava.org/download/maven/</url>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
			<releases>
				<enabled>true</enabled>
			</releases>
		</repository>
	</repositories>
	<url>http://maven.apache.org</url>
	<build>
		<plugins>

			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <excludes>
                        <exclude>demo/**</exclude>
                    </excludes>
                </configuration>
            </plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>

				<configuration>
					<debug>true</debug>
				</configuration>
			</plugin>

			<plugin>
				<artifactId>maven-clean-plugin</artifactId>
				<configuration>
					<filesets>
						<fileset>
							<directory>${basedir}/src/test/resources/testoutput</directory>
							<includes>
								<include>**/volvox_all.faa</include>
							</includes>
						</fileset>
					</filesets>
				</configuration>
			</plugin>

		</plugins>
	</build>
	<dependencies>
		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<scope>compile</scope>
			<version>24.0-jre</version>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>5.2.2-SNAPSHOT</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId><commit_msg>Bump guava dependency version to 28.1-jre.<commit_after><?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/maven-v4_0_0.xsd">
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>5.2.2-SNAPSHOT</version>
	</parent>
	<modelVersion>4.0.0</modelVersion>
	<artifactId>biojava-genome</artifactId>
	<name>biojava-genome</name>

	<licenses>
		<license>
			<name>GNU LGPL v2</name>
			<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

	<repositories>
		<repository>
			<id>biojava-maven-repo</id>
			<name>BioJava repository</name>
			<url>http://www.biojava.org/download/maven/</url>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
			<releases>
				<enabled>true</enabled>
			</releases>
		</repository>
	</repositories>
	<url>http://maven.apache.org</url>
	<build>
		<plugins>

			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <excludes>
                        <exclude>demo/**</exclude>
                    </excludes>
                </configuration>
            </plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>

				<configuration>
					<debug>true</debug>
				</configuration>
			</plugin>

			<plugin>
				<artifactId>maven-clean-plugin</artifactId>
				<configuration>
					<filesets>
						<fileset>
							<directory>${basedir}/src/test/resources/testoutput</directory>
							<includes>
								<include>**/volvox_all.faa</include>
							</includes>
						</fileset>
					</filesets>
				</configuration>
			</plugin>

		</plugins>
	</build>
	<dependencies>
		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<scope>compile</scope>
			<version>28.1-jre</version>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>5.2.2-SNAPSHOT</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
{'fraction_non_alphanumeric': 0.16887608069164264, 'fraction_numerical': 0.014024975984630164, 'mean_word_length': 2.983167559296098, 'pattern_counts': {'":': 0, '<': 245, '<?xml version=': 2, '>': 245, 'https://': 0, 'lorem ipsum': 0, 'www.': 6, 'xml': 6}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '78318', 'n_tokens_mistral': 2214, 'n_tokens_neox': 1715, 'n_words': 234}