org.forester.surfacing
Interfaces 
BinaryDomainCombination
CombinableDomains
Domain
DomainSimilarity
DomainSimilarityCalculator
GenomeWideCombinableDomains
PairwiseDomainSimilarity
PairwiseDomainSimilarityCalculator
Protein
Species
Classes 
AdjactantDirectedBinaryDomainCombination
AdjactantDirectedCombinableDomains
BasicBinaryDomainCombination
BasicCombinableDomains
BasicDomain
BasicDomainSimilarityCalculator
BasicGenomeWideCombinableDomains
BasicProtein
BasicSpecies
CombinationsBasedPairwiseDomainSimilarity
CombinationsBasedPairwiseDomainSimilarityCalculator
CountsBasedPairwiseDomainSimilarity
DirectedBinaryDomainCombination
DirectedCombinableDomains
DomainArchitectureBasedGenomeSimilarityCalculator
DomainCountsBasedPairwiseSimilarityCalculator
DomainCountsDifferenceUtil
DomainId
DomainLengths
DomainLengthsTable
DomainParsimonyCalculator
MappingResults
PairwiseGenomeComparator
PrintableDomainSimilarity
ProteinCountsBasedPairwiseDomainSimilarityCalculator
ProteinId
SimpleDomain
SurfacingConstants
SurfacingUtil
TestSurfacing
Enums 
BinaryDomainCombination.DomainCombinationType
BinaryDomainCombination.OutputFormat
DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
DomainSimilarity.DomainSimilarityScoring
DomainSimilarity.DomainSimilaritySortField
DomainSimilarityCalculator.Detailedness
DomainSimilarityCalculator.GoAnnotationOutput
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
PrintableDomainSimilarity.PRINT_OPTION