Merge pull request #9 from sbliven/master

Non-unique selection in alignment jmol
Recalculate more AFPChain properties when the alignment changes.
update guava dependency version to 14.0.1
adding quality method to fastq variant
add null check to sequence and quality lengths match
Merge pull request #10 from heuermh/master

Minor updates to fastq package in sequencing module
updating maven plugin dependency versions
First commit trial using Git. Just some documentation decoration.

Signed-off-by: aalhossary <amr_alhossary@hotmail.com>
better use of StringBuilder

Signed-off-by: aalhossary <amr_alhossary@hotmail.com>
Added process(int max) which tries to parse maximum max records from the
open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method resumes parsing.
This is particularly useful when dealing with very big data files, (e.g.
NCBI nr database), which can't fit into memory and will take long time
before the first result is available.

Signed-off-by: aalhossary <amr_alhossary@hotmail.com>
fixing problems with unit test
Merge pull request #14 from andreasprlic/master

resolving issue #12
adding more verbosity during XML reading
Merge branch 'master' of https://github.com/biojava/biojava
Merge pull request #15 from andreasprlic/master

adding more verbosity during XML reading
Merge pull request #11 from heuermh/master

Update maven plugin dependency versions
more meaningful error messages
Merge pull request #16 from andreasprlic/master

more meaningful error messages
Merge branch 'master' of https://github.com/biojava/biojava