Ignoring calculation time in AFPChainTest
Ignoring some more temp files
Removing non-ascii characters from TestSECalignment.java

Some strings contained \0 characters so that they could be compared to a
raw char[]. Removed the delimiting characters and used the proper length
variable instead.

The binary problem was discussed in comments of pull #14
Removing debugging print statement in AFPChain
Merge pull request #4 from biojava/master

update to latest master branch
making access methods to inputstreams public, so the code to fetch the
files from the file system can be re-used
updating to latest branch.

MMergeerge branch 'master' of ssh://github.com/andreasprlic/biojava
Merge pull request #24 from andreasprlic/master

Making access methods to InputStreams public
Merge pull request #26 from aalhossary/master

update to latest master branch
Accept lower-case amino acid single-letter codes.
Accept lower-case amino acid single-letter codes.
less verbose
making inpustream access method public
Merge branch 'master' of github.com:andreasprlic/biojava
Merge branch 'master' of github.com:biojava/biojava
ResidueNumber.printFull() is missing an underscore after chainId.
Made ResidueRange more robust, and gave it some methods for iterating,
finding, and checking containment.
Added a method getSubstructureMatchingProteinSequence and a test case
for it. Added @Test annotations to tests in StructureSequenceMatcherTest
(why weren't they there?).
Do Smith-Waterman local alignment rather than global alignment (comment
says local, too). Also, skip null residues in
getSubstructureMatchingProteinSequence.
Adding header comment.