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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.basic
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.basic.
FastaGraph
FastaGraph(SequenceDB, String, String)
- Constructor for class nct.graph.basic.
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.basic.
FastaGraph
The location of the multiple fasta file
fileName
- Variable in class nct.graph.basic.
FastaGraph
The name of the multiple fasta file
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.networkblast.filter.
UniqueCompatNodeFilter
filterDuplicateComplexNodes
- Static variable in class nct.networkblast.
NetworkBlast
filterDuplicatePathNodes
- Static variable in class nct.networkblast.
NetworkBlast
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