Package org.forester.surfacing

Interface Summary
BinaryDomainCombination  
CombinableDomains  
Domain  
DomainSimilarity  
DomainSimilarityCalculator  
GenomeWideCombinableDomains  
PairwiseDomainSimilarity  
PairwiseDomainSimilarityCalculator  
Protein  
Species  
 

Class Summary
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  
 

Enum Summary
BinaryDomainCombination.DomainCombinationType  
BinaryDomainCombination.OutputFormat  
DomainCountsDifferenceUtil.COPY_CALCULATION_MODE  
DomainSimilarity.DomainSimilarityScoring  
DomainSimilarity.DomainSimilaritySortField  
DomainSimilarityCalculator.Detailedness  
DomainSimilarityCalculator.GoAnnotationOutput  
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder  
PrintableDomainSimilarity.PRINT_OPTION