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P

parse(String) - Static method in class nct.parsers.SIFParser
A simple method that parses a SIF formatted file.
parse(String) - Method in class nct.xml.XMLSaxEventDistributor
 
parseFile(String) - Static method in class nct.parsers.FastaProteinParser
A simple method that parses a multiple FASTA file and returns a BioJava SequenceIterator.
parseString(String) - Static method in class nct.parsers.FastaProteinParser
A simple method that parses a multiple FASTA file and returns a BioJava SequenceIterator.
partitionMap - Variable in class nct.graph.BasicKPartiteGraph
A mapping of nodes to partitions.
PathGraph<NodeType extends java.lang.Comparable<? super NodeType>> - Class in nct.networkblast
 
PathGraph(NodeType) - Constructor for class nct.networkblast.PathGraph
 
pathSize - Static variable in class nct.networkblast.NetworkBlast
 
processingInstruction(String, String) - Method in class nct.xml.XMLSaxEventDistributor
 
props - Variable in class nct.service.homology.BiojavaLocalBlast
A properties object that contains the installation specific details of where and how to run Blast.
props - Variable in class nct.service.homology.LocalBlast
A properties object that contains the installation specific details of where and how to run Blast.

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