added uniprot id pattern matching to fail-fast on wrong uniprot ids, added retrying netwrok request if id is not available immediately, bubbling-up the error codes in case uniprot servers are down
corrected the fetch url, not writing into cache when cache directory not specified and breaking correctly after fetching the entry xml
changed CompoundNotFoundException into IllegalArgumentException, removed MalFormedUrlException, added RemoteException when failing to fetch the uniprot entry
Fixing test to fail only if CompoundNotFound, otherwise will go to error
Merge pull request #2 from josemduarte/fixToTest

Fixing test to fail only if CompoundNotFound, otherwise will go to error
Merge pull request #200 from parit/uniprotRMI

Improvements in fetching uniprot entry using uniprot accession id
Fixing #202 . Doubles the memory requirement in alignments
Adding test for #202
Better test
Merge pull request #203 from josemduarte/master

Fixing #202
Making sure that the parent pom sets the jdk version for all children
Another fix for #193
Merge 'main/master' with 'sbliven/master'

This adds some pom cleanups:
- Use vecmath 1.3.1
- Take JDK version from the parent pom

Also some code changes:
- Improvements to CrystalTransform class & xtal package
- Warnings and logging improvements

Conflicts:
	biojava3-alignment/pom.xml
	biojava3-core/pom.xml
	biojava3-modfinder/pom.xml
	biojava3-phylo/pom.xml
	biojava3-protein-disorder/pom.xml