Fix problems exposed by using mmCIF files (towards #173)

Some test cases apply specifically to PDB files. There were also
a NullPointerException caused by differences between the PDB
and mmCIF parsers.
Fix #173. Use mmCIF as default structure format
Merge pull request #174 from sbliven/mmCIF

Fix #173: Use mmCIF as default structure format
Fix logger class name #155
Updated org.biojava3.modfinder package to use slf4j
Updated org.biojava3.ontology package to use slf4j #155
Updated org.biojava3.phylo package to use slf4j for logging #155
Modified class name (and references) from "ProgessListenerStub" to
"ProgressListenerStub"
Added log4j configuration to org.biojava3.modfinder,
org.biojava3.ontology, org.biojava3.phylo #155
Merge remote-tracking branch 'upstream/master'