Merge pull request #5 from biojava/master

update to latest master branch
Swapped expected and test values, and added comments.
Added caching using soft references in a multiton pattern. Commented.
Added two constructors for non-standard needs, allowing future ASTRAL
sets and parsing of local files.
Merge branch 'master' of https://github.com/dmyersturnbull/biojava.git
Critical null check of soft reference.
Some of the URLs and Ids were swapped; critical fix.
Made a general-purpose public method
getAminoAcidSubstitutionMatrix(String).
Ran cleanup on AtomCache.
Added simple Genbank reader. Update CommandPrompt to use the Genbank
reader for .gb files. The code is just done as a first pass for proof of
concept.
Updated GenbankReader and files to properly handle AbstractSequence and
Compound types. Added testcase for DNASequence/Nucleotide sequence.
Merge pull request #36 from dmyersturnbull/master

Small changes
adding support for different types of file access
Merge remote-tracking branch 'andreas/mmcif' into 'andreas/master'

Conflicts:
	biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java
Fixing formatting with biojava lGPL header
Add tests for atom bonds

This tests for intra-residue, peptide, disulfide, and LINK bonds. Tests
are done on PDB ID 1KH9, which has all of those.
Introduce a new Bond class

The previous Bond class was barely used, so this completely replaces it.

Bonds keep track of two atoms, their type (using BondType), and their
order.

Also included are a few utility methods, like those for getting
distances between the two atoms and getting the other atom in a bond,
given the first one.
Add a getBonds() method to Atoms and implement it.
Comment out StructureTools.findBonds

This code relies on an old version of Bonds.
ChempComp and ChemCompConsumer now use ChemCompBonds.
Add a utility method to convert a ChemCompBond's order into an int