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...@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 _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l