refactoring of annotationMethods
finished refactor
refatored experimentMethods
refactored fileMethods
added tests
Merge branch 'database' of https://github.com/genomizer/genomizer-server into database
refactored genomeMethods
Merge branch 'database' of https://github.com/genomizer/genomizer-server into database
refactored usermethods
Extra annotation tests.
Merge branch 'database' of
https://github.com/genomizer/genomizer-server.git into database

Conflicts:
	src/database/subClasses/GenomeMethods.java
Now catching SQLexceptions on close.
remove chainfile maybe working, not tested
Merge branch 'database' of https://github.com/genomizer/genomizer-server into database
added dataholder object for genome
new lines in genome methods
Merge branch 'database' of https://github.com/genomizer/genomizer-server into database
upadted method isPubMedStringValid
added new class to all tests
Now actually deleting files from disk!