Refactored the Parameters and ParameterParser classes for the age, dlrs, dltrs and pdlrs apps, creating super classes for these two, with each app implementing inherited versions of these. This clears up a lot of code duplication that was present in the code, where the majority of these classes were previously identical.
Fixed a number of problems with maven dependencies:
Maven was using JDK 1.6 whereas some of the dependencies it included required at least JDK 1.7 - now it uses JDK 1.8.
An old version of BioJava (3) was being retrieved through maven - now it retrieves BioJava 4 instead.
There were problems with Logback using a different version of log4j than BioJava 4, which is why exclusions have been added to the BioJava 4 dependencies to avoid collision with the version of log4j that Logback needs.
BioJava 4 retrieves Forester through maven, which is why it has been removed locally.
Refactored the Parameters and ParameterParser classes for the age, dlrs, dltrs and pdlrs apps, creating super classes for these two, with each app implementing inherited versions of these. This clears up a lot of code duplication that was present in the code, where the majority of these classes were previously identical.
Fixed a number of problems with maven dependencies:
Unused import statements were also removed.