biojava package import error

Question

I have downloaded biojava jar files and kept in my classpath. I am trying example to test from : http://www.biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite

but, it gives me error :

error: package org.biojava3.core.sequence does not exist   
import org.biojava3.core.sequence.ProteinSequence;

I have 24 errors of the example file shown in site. I have kept jar files in class path. then why this gave me error? Did i miss any step?

Answer 1

Please check your classpath settings and biojava version.

I took the example from the webpage in combination with version 3.0.7 of biojava. Here is what I have done

• Download the biojava.jar

   wget http://biojava.org/download/maven/org/biojava/biojava3-core/3.0.7/biojava3-core-3.0.7.jar 

• Create a Java file FastaOpen.java containing the code taken from your link

• Compile

   javac -cp .:biojava3-core-3.0.7.jar FastaOpen.java 

• Execute

   java -cp .:biojava3-core-3.0.7.jar FastaOpen Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0 at FastaOpen.main(FastaOpen.java:20) 

The exception is OK, as I did not specify a filename. So, for me the example is working. And if I do not specify the classpath at compile time I get the same errors as you do, eg:

FastaOpen.java:5: error: package org.biojava3.core.sequence does not exist
import org.biojava3.core.sequence.ProteinSequence;

The description above works on Linux. On MS Windows you should try something similar to follwing commands (issued in Powershell)

• Compilation

   PS > & 'C:\\Program Files\\Java\\jdk1.7.0_45\\bin\\javac.exe' -cp "C:\\Users\\stefan\\Downloads\\biojava3-core-3.0.7.jar" .\\FastaOpen.java 

• Execution

   PS > & 'C:\\Program Files\\Java\\jdk1.7.0_45\\bin\\java.exe' -cp "C:\\Users\\stefan\\Downloads\\biojava3-core-3.0.7.jar;C:\\Users\\stefan\\Downloads" FastaOpen 

  (Both files, java source/class and jar reside in the Downloads directory.