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Packages that use ProteinSet | |
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procope.data.complexes | |
procope.data.networks | |
procope.data.purifications | |
procope.evaluation.complexquality.go | |
procope.examples | |
procope.methods.scores |
Uses of ProteinSet in procope.data.complexes |
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Classes in procope.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 procope.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 procope.data.networks |
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Classes in procope.data.networks that implement ProteinSet | |
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class |
ProteinNetwork
Represents a network of binary protein interactions. |
Methods in procope.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 procope.data.purifications |
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Classes in procope.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 procope.evaluation.complexquality.go |
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Classes in procope.evaluation.complexquality.go that implement ProteinSet | |
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class |
FunctionalSimilarities
This class is extended by classes which calculate a semantic similarity score of two given proteins based on GO information. |
class |
FunctionalSimilaritiesSchlicker
Implements the calculation of functional similarites between proteins as described in |
class |
GOAnnotations
Represents a set of gene-product to GO-term annotations which are normally read from a file. |
Uses of ProteinSet in procope.examples |
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Classes in procope.examples that implement ProteinSet | |
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class |
DummyScores
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Uses of ProteinSet in procope.methods.scores |
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Classes in procope.methods.scores that implement ProteinSet | |
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class |
DiceCoefficients
Provides an efficient implementation of "Dice coefficients", a protein protein affinity measure derived from purification datasets according to |
class |
HartCalculator
Calculates protein-protein interaction scores from purification data according to |
class |
PECalculator
Calculates Purification Enrichment scores according to |
class |
ScoresCalculator
Extended by all classes which calculate interaction scores between proteins based on experimental or other data. |
class |
SocioAffinityCalculator
Calculates socio affinity scores according to |
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