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

B

BlastBBHAlignmentLengthConstraint - Class in procope.methods.interologs.blast

Ensures that BBHs are only accepted if their BLAST alignment covers a minimum fraction of both aligned protein sequences.

BlastBBHAlignmentLengthConstraint(Sequences, float) - Constructor for class procope.methods.interologs.blast.BlastBBHAlignmentLengthConstraint

Create new alignment length object.

BlastBBHConstraints - Interface in procope.methods.interologs.blast

Interface which is implemented by classes which define constraints for the calculation of BBHs from BLAST hits.

BlastHit - Class in procope.methods.interologs.blast

A single BLAST hit.

BlastHit(int, int, float, int, int, int, int, int, int, int, double, float) - Constructor for class procope.methods.interologs.blast.BlastHit

Creates an new BLAST hit object.

BlastHitFileParser - Class in procope.methods.interologs.blast

Contains static methods to parse hits from a BLAST hit file.

BlastHits - Class in procope.methods.interologs.blast

Represents an immutable list of BLAST hits which are normally parsed from a BLAST result file.

BlastHits(Collection<BlastHit>) - Constructor for class procope.methods.interologs.blast.BlastHits

Creates a new BLAST hits object from a given list of hits.

BooleanExpression - Class in procope.tools

Used to evaluate boolean expressions.

BooleanExpression(String) - Constructor for class procope.tools.BooleanExpression

Create expression object from a given expression string.

Bootstrap - Class in procope.methods.scores.bootstrap

Contains helper methods for the calculation of protein interaction scores using the Bootstrap approach according to

BootstrapClustering - Class in procope.methods.scores.bootstrap

Represents a single clustering in the bootstrap scores calculation process.

BootstrapClustering(ComplexSet, String, float) - Constructor for class procope.methods.scores.bootstrap.BootstrapClustering

Create new bootstrap MCL clustering result.

BootstrapClusterings - Class in procope.methods.scores.bootstrap

Container for bootstrap MCL clustering lists.

BootstrapClusterings() - Constructor for class procope.methods.scores.bootstrap.BootstrapClusterings

Create empty clusterings list.

BootstrapClusterings(String) - Constructor for class procope.methods.scores.bootstrap.BootstrapClusterings

Reads a clustering collection from a given file.

BootstrapClusterings(String, boolean) - Constructor for class procope.methods.scores.bootstrap.BootstrapClusterings

Reads a clusterings collection from a given file.

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

Performs a breadth-first search one the network.

broheeComparison(ComplexSet, ComplexSet) - Static method in class procope.evaluation.comparison.ComplexSetComparison

Calculate complex set similarity after

BroheeSimilarity - Class in procope.evaluation.comparison

Contains similarity comparison results of two complex sets after

BroheeSimilarity(float, float) - Constructor for class procope.evaluation.comparison.BroheeSimilarity

Creates a new similarity object.