Compounds not included in the scoring matrix will default to the alternative case of the compound if it exists in the scoring matrix instead of the min matrix value
Added multiple test cases for various alignment bugs including #81
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
Merge pull request #84 from d-cameron/master

Fix for #78
Added getO3Prime(), getO5Prime(), and getP() methods.
Merge pull request #86 from pwrose/master

Added getO3Prime(), getO5Prime(), and getP() methods.
if params.setParseCAOnly(true) and params.setCreateAtomBonds(true) are
set, some bonds specified in LINK records or SSBOND records cannot be
set (atoms are not there). In these cases StructureException should not
be thrown.
Merge pull request #87 from pwrose/master

if params.setParseCAOnly(true) and params.setCreateAtomBonds(true) are
Merge branch 'master' of https://github.com/biojava/biojava
Fixed use of assertEquals() on doubles.
Added a caution note for StructureImpl.getHetGroups().