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

E

EMPTY_ANNOTATION_MAP - Static variable in class procope.tools.Tools

An empty, immutable map of annotations, i.e.

EMPTY_STRING_MAP - Static variable in class procope.tools.Tools

An empty, immutable String => String map

equals(Object) - Method in class procope.data.complexes.Complex

Returns true if and only if the specified object is also a Complex and both complexes have identical members.

equals(Object) - Method in class procope.data.complexes.ComplexSet

Checks if two complex sets are equal.

equals(Object) - Method in class procope.data.networks.ProteinNetwork

Returns true if and only if obj is also of type ProteinNetwork, both network have the same directedness and all edge weights and annotations of the networks are identical

equals(Object) - Method in class procope.data.purifications.PurificationExperiment

Checks if two purification experiments are equal.

equalScores(ProteinNetwork) - Method in class procope.data.networks.ProteinNetwork

Checks whether two networks are equal regardings their edge weights

evaluate(Map<String, Object>) - Method in class procope.tools.BooleanExpression

Evaluate a given set of variable name => value mappings using the expression.

EvalueInterologScorer - Class in procope.methods.interologs

Implements interolog scoring using the geometric mean of the two BLAST evalues involved in a transferred protein interaction (when transferred using bidirectional best hits from BLAST).

EvalueInterologScorer(BlastHits, BlastHits) - Constructor for class procope.methods.interologs.EvalueInterologScorer

Creates a new e-value interolog scorer from the given BLAST results.

extractBaseFilename(String) - Static method in class procope.tools.Tools

Extract the base file name (without extension) from a full path

extractClustering(float) - Method in class procope.methods.clustering.HierarchicalTreeNode

Extracts a clustering from this tree by cutting it a given similarity threshold value.

extractFilename(String) - Static method in class procope.tools.Tools

Extracts the file name from a full path

extractOptimalClusterings(ArrayList<BootstrapClusterings>, int) - Static method in class procope.methods.scores.bootstrap.Bootstrap

Extracts all clusterings at a given index of the clustering lists.