Added multiple test cases for various alignment bugs including #78
Merge branch 'master' of https://github.com/d-cameron/biojava
Alignments of zero length return a null Location instead of crashing during alignment
Refactored subproblem bounds from int[4] into a Subproblem class to improve code readability
Bug fix: Cut query positions are no longer outside the bounds of the subproblem
Additional GuanUberbacher test coverage
Refactored alignment to allow anchored compounds for all global alignments
Replaced setSteps(int[] anchor) algorithm due to design flaw (information lost in anchor conversion: not possible to get steps from anchors {(1,1), (3,3)} as alignment could 1-23 or 12-3)
Added aligner.addAnchor() for addition of single anchors
Refactored some alignment internal method signatures to improve code readability
Improved test coverage
Bug fix: #78