Merge pull request #5 from biojava/master

update to latest master branch
working on validation file parser
new datamodel for parsing of validation reports
new datamodel for parsing of validation reports
updating to version 1.75C
Merge branch 'master' of github.com:andreasprlic/biojava into validation
Merge pull request #60 from emckee2006/master

Fix defect in format strings for formatter in GenBank Writer
Merge pull request #63 from aalhossary/master

update my fork to latest Biojava version
Merge pull request #6 from biojava/master

updating My Fork to latest BioJava master
Stockholm Parser is stateless now (more tolerant but less robust)
added getBioSequences(boolean ignoreCase, String forcedSequenceType) to
force returned type to either PFAM or RFAM.

Signed-off-by: aalhossary <amr_alhossary@hotmail.com>
Merge pull request #64 from aalhossary/master

Merge pull request #6 from biojava/master
updating
removing print
 demo of working with large structures
adding demo for cath domains
merging in new code for parsing upcoming wwPDB validation files
Merge branch 'master' of github.com:biojava/biojava
Refactored ModelTransformationMatrix and renamed to
BiologicalAssemblyTransformation. Fixed various classes to correct
generation of biological assemblies from PDB and mmCIF files.
Merge pull request #65 from pwrose/master

Refactored ModelTransformationMatrix and renamed to
Fixing #50 Error in RemoteScopInstallation

Fixes two bugs in RemoteScopInstallation (#50)
* Wrong Unmarshaller was used in XMLUtil
* The root node threw an Exception. Although not
  technically valid, it is common enough that returning
  null is better.