Uses of Interface
org.forester.protein.Domain

Packages that use Domain

Package	Description
org.forester.protein
org.forester.surfacing
org.forester.util

Uses of Domain in org.forester.protein

Classes in org.forester.protein that implement Domain

Modifier and Type	Class and Description
class	BasicDomain

Fields in org.forester.protein with type parameters of type Domain

Modifier and Type	Field and Description
static Comparator<Domain>	BasicProtein.DomainMidPositionComparator

Methods in org.forester.protein that return Domain

Modifier and Type	Method and Description
Domain	Protein.getProteinDomain(int index)
Domain	BasicProtein.getProteinDomain(int index)

Methods in org.forester.protein that return types with arguments of type Domain

Modifier and Type	Method and Description
List<Domain>	Protein.getDomainsSortedByPosition()
List<Domain>	BasicProtein.getDomainsSortedByPosition()
List<Domain>	Protein.getProteinDomains()
List<Domain>	BasicProtein.getProteinDomains()
List<Domain>	Protein.getProteinDomains(String domain_id)
List<Domain>	BasicProtein.getProteinDomains(String domain_id)

Methods in org.forester.protein with parameters of type Domain

Modifier and Type	Method and Description
void	Protein.addProteinDomain(Domain protein_domain)
void	BasicProtein.addProteinDomain(Domain protein_domain)
int	BasicDomain.compareTo(Domain domain) Basic domains are compared/sorted based upon their identifiers (case insensitive) and their numbers.

Uses of Domain in org.forester.surfacing

Classes in org.forester.surfacing that implement Domain

Modifier and Type	Class and Description
class	SimpleDomain

Methods in org.forester.surfacing that return types with arguments of type Domain

Modifier and Type	Method and Description
static List<Domain>	SurfacingUtil.sortDomainsWithAscendingConfidenceValues(Protein protein)

Methods in org.forester.surfacing with parameters of type Domain

Modifier and Type	Method and Description
int	SimpleDomain.compareTo(Domain domain)

Uses of Domain in org.forester.util

Methods in org.forester.util with parameters of type Domain

Modifier and Type	Method and Description
static int	ForesterUtil.calculateOverlap(Domain domain, List<Boolean> covered_positions)
static boolean	ForesterUtil.isEngulfed(Domain domain, List<Boolean> covered_positions) Returns true is Domain domain falls in an uninterrupted stretch of covered positions.