Refresh old Java Project
Answered
I recently got my hands on an old java project from a classmate, he added all his dependencys in eclipse with an absolute path in the .classpath file, like:
<classpathentry kind="lib" path="A:/BioInfo/BioJava/biojava lib/biojava3-aa-prop-3.0.4.jar"/>
<classpathentry kind="lib" path="A:/BioInfo/BioJava/biojava lib/biojava3-alignment-3.0.4.jar"/>
<classpathentry kind="lib" path="A:/BioInfo/BioJava/biojava lib/biojava3-core-3.0.4.jar"/>
Now every import of the biojava lib fails, how can i fix this properly?
Erros are like:
Error:(3, 33) java: package org.biojava.bio.structure does not exist
Error:(9, 25) java: cannot find symbol
symbol: class AminoAcid
location: class model.SortableAminoAcid
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Add the jars manually: https://www.jetbrains.com/help/idea/2017.1/working-with-module-dependencies.html.
Thanks for you quick response Serge, but i do not have the jars. I added them using the build in maven. But this did not work =/
Not sure how we can help you obtaining the jars you don't have?
Well biojava3 is from 2010, and it's dead. biojava4 is the way to go now. So i added all biojava 4 equivalents of the librarys with maven but this does not work as i told you. So what would be the right way to Approach such a problem?
Find the original jars somewhere or rewrite your code to use the new API of biojava4.
OK, I did the work for you and found the deb package for biojava3 here https://debian.pkgs.org/7/debian-main-amd64/libbiojava3.0-java_3.0.4-1_all.deb.html.
I've downloaded the .deb file, unpacked it and extracted the jars.
You can find the zip with the jars here: biojava3.zip.
Thank you very much, your help is very appreciated!