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Merge pull request #882 from josemduarte/remove-ava
Removing code that uses deprecated web service source.rcsb.org
2 parents c9474c7 + c76aca8 commit 2038cae

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‎CHANGELOG.md‎

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BioJava Changelog
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-----------------
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BioJava 6.0.0 (future release)
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==============================
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### Removed
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* All code related to All-vs-All structural alignments db calculation and access
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* JFatCatClient and all code depending on it
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* PDP domain providers (depended on JFatCatClient)
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* Support for retrieving structure data with prefix "PDP:" (AtomCache, StructureIO)
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* RemoteScopInstallation consuming data provided by source.rcsb.org
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BioJava 5.4.0
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=============
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### Added

‎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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/RemoteScopInstallationTest.java‎

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This file was deleted.

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopFactoryTest.java‎

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package org.biojava.nbio.structure.test.scop;
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import org.biojava.nbio.structure.scop.BerkeleyScopInstallation;
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import org.biojava.nbio.structure.scop.RemoteScopInstallation;
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import org.biojava.nbio.structure.scop.ScopDatabase;
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import org.biojava.nbio.structure.scop.ScopFactory;
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import org.junit.Before;
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scop = ScopFactory.getSCOP(ScopFactory.VERSION_1_75);
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assertEquals(ScopFactory.VERSION_1_75, scop.getScopVersion());
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ScopFactory.setScopDatabase(ScopFactory.VERSION_1_75, false);
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scop = ScopFactory.getSCOP();
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assertEquals(ScopFactory.VERSION_1_75, scop.getScopVersion());
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assertSame( RemoteScopInstallation.class,scop.getClass());
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ScopFactory.setScopDatabase(ScopFactory.VERSION_1_75, true);
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ScopFactory.setScopDatabase(ScopFactory.VERSION_1_75);
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scop = ScopFactory.getSCOP();
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assertEquals(ScopFactory.VERSION_1_75, scop.getScopVersion());
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assertSame( BerkeleyScopInstallation.class,scop.getClass());
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ScopFactory.setScopDatabase(ScopFactory.LATEST_VERSION, true);
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ScopFactory.setScopDatabase(ScopFactory.LATEST_VERSION);
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scop = ScopFactory.getSCOP();
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assertEquals(ScopFactory.LATEST_VERSION, scop.getScopVersion());
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assertSame( BerkeleyScopInstallation.class,scop.getClass());

‎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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-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>5.4.1-SNAPSHOT</version>
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<version>6.0.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-ontology</artifactId>

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