A B C D E F G H I L M N P R S T U V W X

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saveProteinAnnotations(String) - Static method in class procope.tools.namemapping.ProteinManager

Saves protein annotations to a given file.

saveProteinAnnotations(File) - Static method in class procope.tools.namemapping.ProteinManager

Saves protein annotations to a given file.

saveProteinAnnotations(OutputStream) - Static method in class procope.tools.namemapping.ProteinManager

Saves protein annotations to a given output stream.

scalarMultiplication(float) - Method in class procope.data.networks.ProteinNetwork

Multiplies all existing edge weights of the network with a given value.

ScoresCalculator - Class in procope.methods.scores

Extended by all classes which calculate interaction scores between proteins based on experimental or other data.

ScoresCalculator() - Constructor for class procope.methods.scores.ScoresCalculator

SequenceAligner - Class in procope.tools

Calculates pairwise sequence alignments using the JAligner library.

SequenceAligner() - Constructor for class procope.tools.SequenceAligner

Creates a new sequence aligner with activated caching.

SequenceAligner(boolean) - Constructor for class procope.tools.SequenceAligner

Creates a new sequence aligner.

Sequences - Class in procope.methods.interologs

A set of sequences internally represented by a internal_id=>sequence mapping.

Sequences() - Constructor for class procope.methods.interologs.Sequences

Creates an empty sequences set.

Sequences(Map<Integer, String>) - Constructor for class procope.methods.interologs.Sequences

Creates a sequence object from a given map.

set(int, int, int) - Method in class procope.tools.SparseMatrixInt

Set a cell in the matrix to a given value.

setCaseSensitivity(boolean) - Static method in class procope.tools.namemapping.ProteinManager

Set if text identifiers should be case sensitive.

setEdge(int, int, float) - Method in class procope.data.networks.ProteinNetwork

Sets a weighted edge between two given proteins.

setEdge(int, int) - Method in class procope.data.networks.ProteinNetwork

Sets an edge between two given proteins to a standard weight of 1.0.

setEdgeAnnotation(int, int, String, Object) - Method in class procope.data.networks.ProteinNetwork

Labels an edge between two proteins with a given key/value pair.

setEdgeAnnotations(int, int, Map<String, Object>) - Method in class procope.data.networks.ProteinNetwork

Labels an edge in the network with a given set of annotations.

setFullEdge(NetworkEdge) - Method in class procope.data.networks.ProteinNetwork

Takes an existing NetworkEdge object and inserts the edge into this network.

setGapExtend(float) - Method in class procope.tools.SequenceAligner

Sets the gap extension penality.

setGapOpen(float) - Method in class procope.tools.SequenceAligner

Sets the gap open penality.

setInflation(float) - Method in class procope.methods.clustering.MCLParameters

Set the inflation coefficient

setIterateEdgesTwice(boolean) - Method in class procope.data.networks.ProteinNetwork

For undirected networks this function determines the iterator behaviour.

setMapping(ProteinNetwork) - Method in class procope.data.networks.CombinationRules

Sets a mapping, mapped nodes will be merged into single nodes in the resulting network.

setMatrix(String) - Method in class procope.tools.SequenceAligner

Sets the substitution matrix.

setMCLBinary(String) - Static method in class procope.methods.clustering.MarkovClusterer

Sets the path to the mcl binary to be used.

setNodeMergeSeparator(String) - Method in class procope.data.networks.CombinationRules

Defines how the labels of merged nodes are separated.

setP(float) - Method in class procope.methods.clustering.MCLParameters

Set the pruning number

setPct(float) - Method in class procope.methods.clustering.MCLParameters

Set mass percentage below which to apply recovery

setR(float) - Method in class procope.methods.clustering.MCLParameters

Set the recover number

setRegularExpression(String) - Static method in class procope.tools.namemapping.ProteinManager

Use given regular expression to parse the actual identifier from the next incoming text identifiers (see above).

setS(float) - Method in class procope.methods.clustering.MCLParameters

Set the selection number

setScheme(int) - Method in class procope.methods.clustering.MCLParameters

Sets a scheme for the parameters p,s,r and pct.

setSeed(long) - Method in class procope.tools.math.MTRandom

This method resets the state of this instance using the 64 bits of seed data provided.

setSeed(byte[]) - Method in class procope.tools.math.MTRandom

This method resets the state of this instance using the byte array of seed data provided.

setSeed(int[]) - Method in class procope.tools.math.MTRandom

This method resets the state of this instance using the integer array of seed data provided.

setSeparator(String) - Static method in class procope.data.networks.NetworkReader

Set the separator used to divide protein identifiers, scores and eventual annotations in each line of the network data.

setTimeout(int) - Method in class procope.methods.clustering.MCLParameters

Set the timeout (in seconds) after which the mcl call will be terminated.

setWeightMergePolicy(CombinationRules.WeightMergePolicy) - Method in class procope.data.networks.CombinationRules

Sets how the weights of identical edges are merged in the resulting network.

setWeightMergePolicy(CombinationRules.WeightMergePolicy, String, String) - Method in class procope.data.networks.CombinationRules

Sets how the weights of identical edges are merged in the resulting network.

similarity - Variable in class procope.methods.clustering.HierarchicalTreeNode

Similarity at which the children of this node were merged

size() - Method in class procope.data.complexes.Complex

Returns the size of the complex.

size() - Method in class procope.evaluation.comparison.ComplexMappings

Returns the number of mappings in this mapping set

SocioAffinityCalculator - Class in procope.methods.scores

Calculates socio affinity scores according to

SocioAffinityCalculator(PurificationData) - Constructor for class procope.methods.scores.SocioAffinityCalculator

Creates a new socio affinity scores calculator based on a given purification data set.

sortBySize(boolean) - Method in class procope.data.complexes.ComplexSet

Sorts the list of complexes by their size.

SparseMatrixInt - Class in procope.tools

Implementation of a matrix (2-dimensional array) of integers.

SparseMatrixInt(boolean) - Constructor for class procope.tools.SparseMatrixInt

Creates an empty matrix

SpearmanCoefficient - Class in procope.tools.math

Implements Spearman's rank correlation coefficient to calulate the correlation between two given rows of data points.

SpearmanCoefficient() - Constructor for class procope.tools.math.SpearmanCoefficient

Creates the Spearman rank coefficient object.

StringToIntMapper - Class in procope.data

Maps strings to integers.

StringToIntMapper() - Constructor for class procope.data.StringToIntMapper

Creates a new string to int mapper.

Synonyms - Class in procope.tools.namemapping

Manages synonyms for protein identifiers.

Synonyms() - Constructor for class procope.tools.namemapping.Synonyms

Creates a new empty set of synonyms