[Biojava-l] How to compile and run the demo in biojava3?

[Peng Yu]

Hi,

I see some demos in biojava3 source repository.

~/dvcs_src/biojava/biojava3-alignment/src/main/java/demo$ dir
CookbookMSA.java  DemoAlignProteins.java  DemoLoadSubstMax.java
TestDNANeedlemanWunsch.java

I just learned how to use mvn to start a new project and added biojava
info to pom.xml as in the following. But I'm not sure how to compile
the demo and run it. Could anybody show the detailed procedure on how
to use them? Thanks.

~/linux/test/java/maven/bin/mvn/my-app$ cat pom.xml
<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">
  <modelVersion>4.0.0</modelVersion>
  <groupId>com.mycompany.app</groupId>
  <artifactId>my-app</artifactId>
  <packaging>jar</packaging>
  <version>1.0-SNAPSHOT</version>
  <name>my-app</name>
  <url>http://maven.apache.org</url>
  <dependencies>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>3.8.1</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>biojava3-core</artifactId>
      <version>3.0.6</version>
    </dependency>
  </dependencies>
  <repositories>
    <repository>
      <id>biojava-maven-repo</id>
      <name>BioJava repository</name>
      <url>http://www.biojava.org/download/maven/</url>
    </repository>
  </repositories>
</project>

-- 
Regards,
Peng