BioJava Upgrade notes.

BioJava upgrade notes.

we upgraded from biojava 1.7.1 to biojava 4.2.0 [update jar, and classpath in bio/sources/fasta/.classpath]

For mines which have their custom fasta parsing:

you should update your FastaLoaderTask.java following what done in the intermine one, in particular in the processFile method use the new FastaReader [like here]

note a few name changes in methods, e.g. in the bioJavaSequence class

• .seqString() -> .getSequenceAsString()
• .length() -> .getLength()
• .getName -> .getAccession().getID() [e.g.]

If you were using the old Annotation class to get the header, like in

Annotation annotation = bioJavaSequence.getAnnotation();

you can now use directly something like

bioJavaSequence.getOriginalHeader() [e.g.]