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.
Added a GenbankProxySequenceReader class that takes an accessionid and
reads genbank data from either a file if it exists or the ncbi/eutils
web interface.
Merge remote-tracking branch 'updates/master'
Merge pull request #40 from dmyersturnbull/master

Changed Eclipse cleanup and formatter preferences to better reflect what's currently in Biojava.
Added GenbankParser and changed other Genbank code to use it.
More work on Genbank files, bringing them inline with interfaces.
Renamed FastaHeaderParserInterface to SequenceHeaderParserInterface.
Changed SequenceParserInterface to use BufferedReader instead of
DataInput to provide flexibility for GenbankParser. Updated
SequenceFileProxyLoader to BufferedReader.
Merge remote-tracking branch 'updates/master'
Fixed bug created in SequenceFile when converted to BufferedReader from
DataInput.
Remove BondType from Bond

All Bond objects are assumed to be covalent bonds
By default, Bonds will now add themselves to their Atoms' bond lists.
For LINK records, work strictly with atoms that aren't alt locs
Use the new bond constructor in PDBFileReader
Add a test making sure ligands get bonds too
Loop through all non-water groups for intra-residue bonds, not just sequence residues
By default, keep the bond arraylist as small as possible
Trim to size all bond arraylists after creating the bonds
Merge branch 'master' of github.com:biojava/biojava
Merge branch 'master' of https://github.com/karlnicholas/biojava into karl
Merge branch 'bond-efficiency' of https://github.com/ulyssecarion/biojava into ulyssecarion-bond-efficiency