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B

backgroundProb - Variable in class nct.networkblast.NetworkBlast
 
backgroundProbDefault - Static variable in class nct.networkblast.NetworkBlast
 
BasicDistanceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.graph
An extension of BasicGraph that calculates the minimum distance between nodes.
BasicDistanceGraph() - Constructor for class nct.graph.BasicDistanceGraph
Constructor.
BasicDistanceGraph(String) - Constructor for class nct.graph.BasicDistanceGraph
Constructor.
BasicDistanceGraph(Graph<NodeType, WeightType>) - Constructor for class nct.graph.BasicDistanceGraph
Copy Constructor.
BasicEdge<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.graph
A generic implementation of the Edge interface.
BasicEdge(NodeType, NodeType, WeightType, String) - Constructor for class nct.graph.BasicEdge
 
BasicEdge(NodeType, NodeType, WeightType) - Constructor for class nct.graph.BasicEdge
 
BasicGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.graph
A generic implementation of the Graph interface.
BasicGraph() - Constructor for class nct.graph.BasicGraph
Constructor.
BasicGraph(String) - Constructor for class nct.graph.BasicGraph
Constructor.
BasicGraph(Graph<NodeType, WeightType>) - Constructor for class nct.graph.BasicGraph
Copy Constructor.
BasicKPartiteGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>,PartitionType extends java.lang.Comparable<? super PartitionType>> - Class in nct.graph
A generic implementation of the KPartiteGraph interface.
BasicKPartiteGraph() - Constructor for class nct.graph.BasicKPartiteGraph
Constructor that names the graph "none" and allows unlimited partitions.
BasicKPartiteGraph(String) - Constructor for class nct.graph.BasicKPartiteGraph
Constructor that names the graph as specified and allows unlimited partitions.
BasicKPartiteGraph(String, int) - Constructor for class nct.graph.BasicKPartiteGraph
Constructor that names the graph as specified and limits the number of partitions allowed in this graph.
BasicWeightedNode<IDType extends java.lang.Comparable<? super IDType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.graph
 
BasicWeightedNode(IDType, WeightType) - Constructor for class nct.graph.BasicWeightedNode
 
BiojavaLocalBlast - Class in nct.service.homology
A Blast implementation of the HomologyModel interface that runs Blast locally.
BiojavaLocalBlast(Properties, String, double) - Constructor for class nct.service.homology.BiojavaLocalBlast
Constructor.
BiojavaLocalBlast(Properties, SynonymMapper, String, double) - Constructor for class nct.service.homology.BiojavaLocalBlast
Constructor.
BLAST - Static variable in interface nct.graph.SequenceGraph
A Blast database.
BlastGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.graph
An extension of BasicDistanceGraph that implements SequenceGraph and contains a pointer to a Blast database.
BlastGraph(String, String) - Constructor for class nct.graph.BlastGraph
 
blastOutputFile - Variable in class nct.service.homology.BiojavaLocalBlast
The file that contains the blast output to be parsed.
blastOutputFile - Variable in class nct.service.homology.LocalBlast
The file that contains the blast output to be parsed.
BlastXMLFileFilterInputStream - Class in nct.service.homology
This class extends a FilterInputStream and is used to filter out the extra xml version and DOCTYPE tags that come in Blast "XML" files for multiple queries and wraps the entire document in blast_aggregate tags.
BlastXMLFileFilterInputStream(String, boolean) - Constructor for class nct.service.homology.BlastXMLFileFilterInputStream
Constructor.
BlastXMLFileFilterInputStream(InputStream, boolean) - Constructor for class nct.service.homology.BlastXMLFileFilterInputStream
Constructor.
bytes - Variable in class nct.output.ZIPSIFWriter
The bytes of the content to be written.

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