[Biojava-l] How to compile and run the demo in biojava3?
Peng Yu
pengyu.ut at gmail.com
Tue Jul 23 16:17:24 UTC 2013
Hi,
I can't figure out how to use IDE with biojava as shown in other
emails in the thread.
But I copied DecoCE.java to a new project (created by 'mvn
archetype:generate -DgroupId=com.mycompany.app -DartifactId=my-app
-DarchetypeArtifactId=maven-archetype-quickstart
-DinteractiveMode=false').
~/linux/test/java/maven/bin/mvn/my-app$ ll
src/main/java/com/mycompany/app/DemoCE.java
-rw-r--r-- 1 py staff 3930 2013-07-23 00:23:44
src/main/java/com/mycompany/app/DemoCE.java
The pom.xml is the following. I then compiled the package and run
DemoCE. But it failed. Does anybody know what is wrong? 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>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-structure</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>
~/linux/test/java/maven/bin/mvn/my-app$ mvn package
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building my-app 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-resources-plugin:2.4.3:resources (default-resources)
@ my-app ---
[WARNING] Using platform encoding (MacRoman actually) to copy filtered
resources, i.e. build is platform dependent!
[INFO] skip non existing resourceDirectory
/Users/py/linux/test/java/maven/bin/mvn/my-app/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ my-app ---
[WARNING] File encoding has not been set, using platform encoding
MacRoman, i.e. build is platform dependent!
[INFO] Compiling 3 source files to
/Users/py/linux/test/java/maven/bin/mvn/my-app/target/classes
[INFO]
[INFO] --- maven-resources-plugin:2.4.3:testResources
(default-testResources) @ my-app ---
[WARNING] Using platform encoding (MacRoman actually) to copy filtered
resources, i.e. build is platform dependent!
[INFO] skip non existing resourceDirectory
/Users/py/linux/test/java/maven/bin/mvn/my-app/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:2.3.2:testCompile
(default-testCompile) @ my-app ---
[WARNING] File encoding has not been set, using platform encoding
MacRoman, i.e. build is platform dependent!
[INFO] Compiling 1 source file to
/Users/py/linux/test/java/maven/bin/mvn/my-app/target/test-classes
[INFO]
[INFO] --- maven-surefire-plugin:2.7.2:test (default-test) @ my-app ---
[INFO] Surefire report directory:
/Users/py/linux/test/java/maven/bin/mvn/my-app/target/surefire-reports
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running com.mycompany.app.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec
Results :
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO] --- maven-jar-plugin:2.3.1:jar (default-jar) @ my-app ---
[INFO] Building jar:
/Users/py/linux/test/java/maven/bin/mvn/my-app/target/my-app-1.0-SNAPSHOT.jar
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.838s
[INFO] Finished at: Tue Jul 23 11:15:30 CDT 2013
[INFO] Final Memory: 9M/81M
[INFO] ------------------------------------------------------------------------
~/linux/test/java/maven/bin/mvn/my-app$ java -cp
target/my-app-1.0-SNAPSHOT.jar com.mycompany.app.DemoCE
Exception in thread "main" java.lang.NoClassDefFoundError:
org/biojava/bio/structure/align/util/AtomCache
at com.mycompany.app.DemoCE.main(DemoCE.java:36)
Caused by: java.lang.ClassNotFoundException:
org.biojava.bio.structure.align.util.AtomCache
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 1 more
On Mon, Jul 22, 2013 at 11:25 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> 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
--
Regards,
Peng
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