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Packages that use ProteinSet | |
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data.complexes | |
data.networks | |
data.purifications | |
methods.scores | |
methods.scores.go |
Uses of ProteinSet in data.complexes |
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Classes in data.complexes that implement ProteinSet | |
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class |
Complex
Represents a complex of proteins. |
class |
ComplexSet
A complex set is a list of complexes. |
Methods in data.complexes with parameters of type ProteinSet | |
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ComplexSet |
ComplexSet.restrictToProteinSpace(ProteinSet proteins,
boolean fullCoverage)
Returns a new complex set containing only those complexes whose proteins are completely or partially contained in a given set of proteins. |
Uses of ProteinSet in data.networks |
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Classes in data.networks that implement ProteinSet | |
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class |
ProteinNetwork
Represents a network of binary protein interactions. |
Methods in data.networks with parameters of type ProteinSet | |
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ProteinNetwork |
ProteinNetwork.restrictToProteins(ProteinSet proteins,
boolean fullCoverage)
Returns a new network object which contains only those edges where one or both adjacent proteins are contained in a given set of proteins. |
Uses of ProteinSet in data.purifications |
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Classes in data.purifications that implement ProteinSet | |
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class |
PurificationData
A set of protein purification experiments where each experiment constists of a bait protein along with a list of prey proteins it purified. |
class |
PurificationExperiment
Represents a single purification experiment having a bait protein and a list of prey proteins which were purified by that bait. |
Uses of ProteinSet in methods.scores |
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Subinterfaces of ProteinSet in methods.scores | |
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interface |
ScoresCalculator
Implemented by all classes which calculate interaction scores between proteins based on experimental or other data. |
Classes in methods.scores that implement ProteinSet | |
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class |
HartCalculator
Calculates protein-protein interaction scores from purification data according to Hart, G. |
class |
PECalculator
Calculates Purification Enrichment scores according to Collins et al. |
class |
SocioAffinityCalculator
Calculates socio affinity scores according to Gavin et al. |
Uses of ProteinSet in methods.scores.go |
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Subinterfaces of ProteinSet in methods.scores.go | |
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interface |
FunctionalSimilarities
This interface is implemented by classes which calculate a semantic similarity score of two given proteins based on GO information. |
Classes in methods.scores.go that implement ProteinSet | |
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class |
FunctionalSimilaritiesSchlicker
Implements the calculation of functional similarites between proteins as described in Schlicker, A.; Domingues, F. |
class |
GOAnnotations
Represents a set of gene-product to GO-term annotations which are normally read from a file. |
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