- add features support for Genbank proxy parser
- add parent sequence parsing into ProteinSequence
- add DBReferneceInfo as Feature
Introducing slf4j #155
- added runTime scope binding for log4j2 since it's the one logger
framework that was used already elsewhere. We even had already some
config files for it in the structure module
- added the safe config to all poms of modules. Config files for log4j2
are only in the structure module. Other modules will have to add config
files if needed
- default level in config files set to: warn for run, info for test
- moved logging in the PDB parser to slf4j
Fixed issue: wasn't pointing to the right class in logger
Merge pull request #159 from josemduarte/master

Introducing slf4j #155
Some fixes for #111 and #155
Default log4j config now outputs to stderr
Important fix for #155, was not specifying runtime scope correctly
More on #155 and #111
Convert SimpleMMcifParser to use SLF4J logging
Changing logging configuration (#155)

Test configuration uses INFO and production uses WARN
More #111 and #155
add understanding non-standard DNA nucleotides
- add junit tests for GenbankProxySequenceReader and another LocationParserTest
- fixed problem with 'db_xref' parser in GenbankSequenceParser
Merge biojava/biojava branch
add log4j 2 config file
add slf4j logger to parsers
#155 and some #111
More logging #155
Better logging to debug #145
replaced "/tmp" path by more generic: System.getProperty("java.io.tempdir")