Protein Family Alignment Annotation Tool svncode

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added comments renamed some vars

For Dan

comment out part preventing compile

updated dependencies

updated to allow for GetCavity to properly work, allowing the following object relationship to hold:
GetCavity.main
-> PatchBuilder.buildPatchesCavity()
-> PatchBuilderForPathConnectedResiduesCavity

PatchBuilderForPathConnectedResiduesCavity contains the altered algorithm:
patches that are not within -D specified distance from the -O coordinate are not

For building patches within a cavity, instead of GetPatches being used as the main Java class, getCavity is used instead.
note: getCavity has two additional options:
[-D | maximum seed distance from 3d point] (GetCavity.seedDistance)
[-O | x:y:z coordinates for 3d point] (GetCavity.cavityPoint)
Object Dependencies:
GetCavity -> PatchBuilder -> PatchBuilderForPathConnectedResiduesCavity(new) -> PatchGraph

where PatchBuilderForPathConnectedResiduesCavity is a version of PatchBuilderForPathConnectedResidues with an altered algorithm that excludes patches from being seeds that are further than -D away from the -O specified point