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Updating to biojava 4. Fixing biojava/bio/structure/* links to API docs
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‎alignment/installation.md‎

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@@ -6,22 +6,7 @@ BioJava is open source and you can get the code from [Github](https://github.com
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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```xml
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<dependencies>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-core</artifactId>
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<version>3.0.8</version>
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<artifactId>biojava-alignment</artifactId>
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<version>4.0.0</version>
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</dependency>
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‎core/installation.md‎

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@@ -6,22 +6,8 @@ BioJava is open source and you can get the code from [Github](https://github.com
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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```xml
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<dependencies>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-core</artifactId>
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<version>3.0.8</version>
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<artifactId>biojava-core</artifactId>
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<version>4.0.0</version>
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</dependency>
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‎installation.md‎

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Original file line numberDiff line numberDiff line change
@@ -6,22 +6,7 @@ BioJava is open source and you can get the code from [Github](https://github.com
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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```xml
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<dependencies>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-genomics</artifactId>
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<version>3.0.8</version>
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<artifactId>biojava-genomics</artifactId>
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<version>4.0.0</version>
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<!-- note: the genomics module depends on the BioJava-core module and will import it automatically -->
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-structure</artifactId>
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<version>3.0.8</version>
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<artifactId>biojava-structure</artifactId>
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<version>4.0.0</version>
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</dependency>
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</dependencies>
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```

‎structure/installation.md‎

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Original file line numberDiff line numberDiff line change
@@ -6,32 +6,23 @@ BioJava is open source and you can get the code from [Github](https://github.com
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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We are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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<dependencies>
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...
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<dependency>
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<!-- This imports the latest SNAPSHOT builds from the protein structure modules of BioJava.
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-->
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-structure</artifactId>
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<version>3.0.8</version>
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<artifactId>biojava-structure</artifactId>
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<version>4.0.0</version>
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</dependency>
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<!-- if you want to use the visualisation tools you need also this one: -->
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-structure-gui</artifactId>
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<version>3.0.8</version>
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<artifactId>biojava-structure-gui</artifactId>
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<version>4.0.0</version>
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</dependency>
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<!-- other biojava jars as needed -->
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</dependencies>

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