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Merge pull request #996 from sbliven/fix-jaxb
Change JAXB implementation for better java version compatibility
2 parents baefba4 + a35d0b6 commit ebb6eb0

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6 files changed

+220
-208
lines changed

6 files changed

+220
-208
lines changed

‎biojava-aa-prop/pom.xml‎

Lines changed: 35 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -20,15 +20,15 @@
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<build>
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<plugins>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
@@ -80,28 +80,37 @@
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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</dependency>
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<!-- binding for log4j2, scope=runTime set in parent pom -->
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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</dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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</dependency>
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<!-- binding for log4j2, scope=runTime set in parent pom -->
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>javax.xml.bind</groupId>
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<artifactId>jaxb-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>
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</dependency>
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</dependencies>
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</project>
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</project>

‎biojava-core/pom.xml‎

Lines changed: 46 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -26,15 +26,15 @@
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<plugins>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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</plugins>
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</build>
@@ -43,35 +43,43 @@
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-engine</artifactId>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-params</artifactId>
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</dependency>
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<dependency>
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<groupId>org.junit.vintage</groupId>
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<artifactId>junit-vintage-engine</artifactId>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-engine</artifactId>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-params</artifactId>
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</dependency>
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<dependency>
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<groupId>org.junit.vintage</groupId>
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<artifactId>junit-vintage-engine</artifactId>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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</dependency>
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<!-- binding for log4j2, scope=runTime set in parent pom -->
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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</dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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</dependency>
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<!-- binding for log4j2, scope=runTime set in parent pom -->
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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</dependency>
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<dependency>
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<groupId>javax.xml.bind</groupId>
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<artifactId>jaxb-api</artifactId>
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</dependency>
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<dependency>
81+
<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>
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</dependency>
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</dependencies>
77-
</project>
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</project>

‎biojava-modfinder/pom.xml‎

Lines changed: 78 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -1,80 +1,88 @@
11
<?xml version="1.0"?>
22
<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">
3-
<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>6.0.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-modfinder</artifactId>
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<name>biojava-modfinder</name>
11-
<url>http://www.biojava.org</url>
3+
<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>6.0.1-SNAPSHOT</version>
8+
</parent>
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<artifactId>biojava-modfinder</artifactId>
10+
<name>biojava-modfinder</name>
11+
<url>http://www.biojava.org</url>
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<licenses>
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<license>
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<name>GNU LGPL v2</name>
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<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
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<distribution>repo</distribution>
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</license>
19-
</licenses>
13+
<licenses>
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<license>
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<name>GNU LGPL v2</name>
16+
<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
2020

21-
<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
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</properties>
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<dependencies>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>6.0.1-SNAPSHOT</version>
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<type>jar</type>
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<scope>compile</scope>
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</dependency>
24+
</properties>
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<dependencies>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
32+
<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>6.0.1-SNAPSHOT</version>
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<type>jar</type>
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<scope>compile</scope>
37+
</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>
40-
<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
42-
</dependency>
43-
<!-- binding for log4j2, scope=runTime set in parent pom -->
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
46-
<artifactId>log4j-slf4j-impl</artifactId>
47-
</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
51-
</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
55-
</dependency>
56-
</dependencies>
57-
<build>
58-
<plugins>
40+
<groupId>org.slf4j</groupId>
41+
<artifactId>slf4j-api</artifactId>
42+
</dependency>
43+
<!-- binding for log4j2, scope=runTime set in parent pom -->
44+
<dependency>
45+
<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
47+
</dependency>
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<dependency>
49+
<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
51+
</dependency>
52+
<dependency>
53+
<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
55+
</dependency>
56+
<dependency>
57+
<groupId>javax.xml.bind</groupId>
58+
<artifactId>jaxb-api</artifactId>
59+
</dependency>
60+
<dependency>
61+
<groupId>org.glassfish.jaxb</groupId>
62+
<artifactId>jaxb-runtime</artifactId>
63+
</dependency>
64+
</dependencies>
65+
<build>
66+
<plugins>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
62-
<groupId>org.apache.maven.plugins</groupId>
63-
<artifactId>maven-jar-plugin</artifactId>
64-
<configuration>
65-
<excludes>
66-
<exclude>demo/**</exclude>
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</excludes>
68-
</configuration>
69-
</plugin>
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<plugin>
70+
<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
75+
</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<debug>true</debug>
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</configuration>
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</plugin>
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</plugins>
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</build>
80-
</project>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<debug>true</debug>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>

‎biojava-protein-disorder/pom.xml‎

Lines changed: 11 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -23,17 +23,17 @@
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
2525
<debug>true</debug>
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</configuration>
26+
</configuration>
2727
</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
34-
<excludes>
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<exclude>demo/**</exclude>
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</excludes>
34+
<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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<descriptorRefs>
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<descriptorRef>bin</descriptorRef>
@@ -85,13 +85,17 @@
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<artifactId>log4j-core</artifactId>
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</dependency>
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<dependency>
88-
<groupId>javax.xml.bind</groupId>
89-
<artifactId>jaxb-api</artifactId>
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<groupId>javax.xml.bind</groupId>
89+
<artifactId>jaxb-api</artifactId>
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</dependency>
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<dependency>
92+
<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>
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</dependency>
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</dependencies>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
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</properties>
97-
</project>
101+
</project>

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