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Merge branch 'bugfixes-4.2' of github.com:biojava/biojava into bugfixes-4.2
* 'bugfixes-4.2' of github.com:biojava/biojava: Updating biojava-protein-comparison-tool dependencies Setting 4.2.1-SNAPSHOT in all other poms Logging and documentation Fix major bug with BIO: identifiers
2 parents aac75fe + eb0d536 commit d63491c

19 files changed

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‎biojava-aa-prop/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-aa-prop</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

‎biojava-alignment/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-alignment</artifactId>
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<name>biojava-alignment</name>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-phylo</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</dependency>
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</dependencies>
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</project>

‎biojava-core/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-core</artifactId>

‎biojava-genome/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-genome</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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<scope>compile</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-alignment</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-integrationtest/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-integrationtest</artifactId>
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<packaging>jar</packaging>
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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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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>

‎biojava-modfinder/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-modfinder</artifactId>
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<name>biojava-modfinder</name>
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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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<type>jar</type>
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<scope>compile</scope>
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</dependency>

‎biojava-ontology/pom.xml‎

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<parent>
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<groupId>org.biojava</groupId>
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<artifactId>biojava</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-ontology</artifactId>

‎biojava-phylo/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-phylo</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-protein-comparison-tool/pom.xml‎

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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>4.1.1-SNAPSHOT</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-protein-comparison-tool</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
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<version>4.1.1-SNAPSHOT</version>
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<version>4.2.1-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>4.1.1-SNAPSHOT</version>
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<version>4.2.1-SNAPSHOT</version>
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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>4.1.1-SNAPSHOT</version>
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<version>4.2.1-SNAPSHOT</version>
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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-gui</artifactId>
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<version>4.1.1-SNAPSHOT</version>
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<version>4.2.1-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>net.sourceforge.jmol</groupId>

‎biojava-protein-disorder/pom.xml‎

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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>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-protein-disorder</artifactId>
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<packaging>jar</packaging>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>4.2.0</version>
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<version>4.2.1-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or
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scopes here) -->

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