Merge pull request #24 from biojava/master

Catch back up with Trunk
Merge pull request #25 from biojava/master

Catch back up with Trunk
Merge pull request #26 from biojava/master

Catch back up with Trunk
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
Towards fixing #148, compiles but some tests don't pass yet
- some exception handling fixes #111
- important bug fixed in alt loc handling, the lookup map for atom names wasn't properly reset when adding a new alt loc group
- fixed implementation of StructureTools.getBackboneAtomArray (was including CB atoms, and excluding all GLY groups)
- added some tests for the StructureTools methods
Full fix for #148, all tests pass
- some improvement in exceptions and logging #111 and #155
More #111 and #155
Adding a test for correct writing of atom names in PDB format
Merge pull request #174 from sbliven/mmCIF

Fix #173: Use mmCIF as default structure format
Adding some better javadoc to clarify ambiguity in atom names
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'
Merge pull request #177 from benjamintboyle/master

Updated packages to use slf4j for logging #155
Merge branch 'josemduarte-master'