https://redmine.open-bio.org/issues/3364 representing nonstandard amino acids with X character. Also added a BioJava- style ProteinSequence entry point which gets converted to the FastaSequence that is used internally in the protein-disorder module 

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9759 7c6358e6-4a41-0410-a743-a5b2a554c398
fix for unit test failures, use proper temp directory for test output files

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9760 7c6358e6-4a41-0410-a743-a5b2a554c398
Added indexes into FeatureList and GFF3Reader classes.



git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9761 7c6358e6-4a41-0410-a743-a5b2a554c398
Removed the Log4j dependencies from the GFF3 parser.


git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9762 7c6358e6-4a41-0410-a743-a5b2a554c398
Fixed the compile error in Feature.java


git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9763 7c6358e6-4a41-0410-a743-a5b2a554c398
docu update and changing access for some fields

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9766 7c6358e6-4a41-0410-a743-a5b2a554c398
now really returning the first bio assembly, rather than the asym unit

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9767 7c6358e6-4a41-0410-a743-a5b2a554c398
extending test to compare with access of flat file downloads

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9768 7c6358e6-4a41-0410-a743-a5b2a554c398
fix wrongly formatted  groups names

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9769 7c6358e6-4a41-0410-a743-a5b2a554c398
adding new cif categories

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9770 7c6358e6-4a41-0410-a743-a5b2a554c398
fixing a bug with resetting a counter

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9771 7c6358e6-4a41-0410-a743-a5b2a554c398
new utility method to remove all models

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9772 7c6358e6-4a41-0410-a743-a5b2a554c398
making sure NMR structures with bio assemblies are dealt with correctly

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9773 7c6358e6-4a41-0410-a743-a5b2a554c398
making sure NMR structures with bio assemblies are dealt with correctly

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9774 7c6358e6-4a41-0410-a743-a5b2a554c398
improved comparisons between residueNumbers, as provided by Douglas

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9775 7c6358e6-4a41-0410-a743-a5b2a554c398
fixing failing unit test

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9776 7c6358e6-4a41-0410-a743-a5b2a554c398
not showing chain ID for now

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9779 7c6358e6-4a41-0410-a743-a5b2a554c398
transformations have higher precision...

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9780 7c6358e6-4a41-0410-a743-a5b2a554c398
Major bug fix for dealing with rare biological assemblies, such as 4A1I bio assembly 2

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9781 7c6358e6-4a41-0410-a743-a5b2a554c398
Major bug fix for dealing with rare biological assemblies, such as 4A1I bio assembly 2

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9782 7c6358e6-4a41-0410-a743-a5b2a554c398