Uses of Interface
org.forester.protein.Domain
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Packages that use Domain Package Description org.forester.protein org.forester.surfacing org.forester.util -
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Uses of Domain in org.forester.protein
Classes in org.forester.protein that implement Domain Modifier and Type Class Description class
BasicDomain
Fields in org.forester.protein with type parameters of type Domain Modifier and Type Field Description static java.util.Comparator<Domain>
BasicProtein. DomainMidPositionComparator
Methods in org.forester.protein that return Domain Modifier and Type Method Description Domain
BasicProtein. getProteinDomain(int index)
Domain
Protein. getProteinDomain(int index)
Methods in org.forester.protein that return types with arguments of type Domain Modifier and Type Method Description java.util.List<Domain>
BasicProtein. getDomainsSortedByPosition()
java.util.List<Domain>
Protein. getDomainsSortedByPosition()
java.util.List<Domain>
BasicProtein. getProteinDomains()
java.util.List<Domain>
BasicProtein. getProteinDomains(java.lang.String domain_id)
java.util.List<Domain>
Protein. getProteinDomains()
java.util.List<Domain>
Protein. getProteinDomains(java.lang.String domain_id)
Methods in org.forester.protein with parameters of type Domain Modifier and Type Method Description void
BasicProtein. addProteinDomain(Domain protein_domain)
void
Protein. 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 Description class
SimpleDomain
Methods in org.forester.surfacing that return types with arguments of type Domain Modifier and Type Method Description static java.util.List<Domain>
SurfacingUtil. sortDomainsWithAscendingConfidenceValues(Protein protein)
Methods in org.forester.surfacing with parameters of type Domain Modifier and Type Method Description int
SimpleDomain. compareTo(Domain domain)
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Uses of Domain in org.forester.util
Methods in org.forester.util with parameters of type Domain Modifier and Type Method Description static int
ForesterUtil. calculateOverlap(Domain domain, java.util.List<java.lang.Boolean> covered_positions)
static boolean
ForesterUtil. isEngulfed(Domain domain, java.util.List<java.lang.Boolean> covered_positions)
Returns true is Domain domain falls in an uninterrupted stretch of covered positions.
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