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

F

FastaReader - Class in phylonet.sequence.io

This class provides a tool for reading content from FASTA formatted sequence files.

FastaReader(Reader) - Constructor for class phylonet.sequence.io.FastaReader

FastaReader(InputStream) - Constructor for class phylonet.sequence.io.FastaReader

FastaReader(String) - Constructor for class phylonet.sequence.io.FastaReader

FastaReader(File) - Constructor for class phylonet.sequence.io.FastaReader

FastaReader.FastaRecord - Class in phylonet.sequence.io

This class holds the data for a single FASTA sequence.

findBinaryNodes(Tree) - Static method in class phylonet.tree.util.Trees

This method locates binary nodes (nodes with a parent and one child) in the tree.

findChains(MutableTree, MutableTree, List<Chain>, List<Chain>) - Method in class phylonet.riatahgt.RiataHgt

Finds maximal identical chains in st and gt.

findMatching() - Method in class phylonet.algorithms.bipartitemaching.HungarianBipartiteMatcher

Compute the maximum weighted matching over the bipartite graph specified using addEdge.

findNode(String) - Method in class phylonet.network.model.bni.BniNetwork

Return the node in the network with name.

findNode(String) - Method in interface phylonet.network.model.Network

Return the node in the network with name.

findShortestPath(Node, Node) - Method in class phylonet.algorithms.shortestpath.Dijkstra

Find the shortest path between the two nodes specified.

fromString(String) - Static method in enum phylonet.network.characterization.NetworkCharacterizationMeasure