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F

FASTA - Static variable in interface nct.graph.SequenceGraph
A Fasta database, usually referring to a multiple fasta formatted file.
FastaGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Class in nct.graph
An extension of BasicDistanceGraph that implements the SequenceGraph interface and contains a (pointer to a) fasta database.
FastaGraph(String, String) - Constructor for class nct.graph.FastaGraph
 
FastaGraph(SequenceDB, String, String) - Constructor for class nct.graph.FastaGraph
 
FastaProteinParser - Class in nct.parsers
A simple class that provides a method to parse a multiple FASTA file.
FastaProteinParser() - Constructor for class nct.parsers.FastaProteinParser
 
fatalError(SAXParseException) - Method in class nct.xml.XMLSaxEventDistributor
 
fileLocation - Variable in class nct.graph.FastaGraph
The location of the multiple fasta file
fileName - Variable in class nct.graph.FastaGraph
The name of the multiple fasta file
FILEOUTPUT - Static variable in class nct.networkblast.NetworkBlast
 
filter(List<Graph<NodeType, WeightType>>) - Method in class nct.filter.DuplicateThresholdFilter
Given the solutions, this filter compares the nodes contained in each graph, calculates the percentage of identical nodes, and throws out any solutions that have a percent identity greater than or equal to the specified threshold.
Filter<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>> - Interface in nct.filter
This provides the interface for a Filter type.
filter(List<Graph<NodeType, WeightType>>) - Method in interface nct.filter.Filter
This provides the basic foundation for filtering.
filter(List<Graph<NodeType, WeightType>>) - Method in class nct.filter.SortFilter
Given a List of Graphs, it sorts the graphs based on the comparable implementation of the graph.
filter(List<Graph<String, Double>>) - Method in class nct.filter.UniqueCompatNodeFilter
 
filterDuplicateComplexNodes - Static variable in class nct.networkblast.NetworkBlast
 
filterDuplicatePathNodes - Static variable in class nct.networkblast.NetworkBlast
 

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