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

E

Edge - Interface in phylonet.graph.model

This represents an edge in a @link{Graph}.

edgeAdded(int, String) - Method in interface phylonet.graph.model.GraphListener

EdgeListReader - Class in phylonet.graph.io

This class provides a utility that reads in a graph from an edge-list formatted source.

EdgeListReader(Reader) - Constructor for class phylonet.graph.io.EdgeListReader

edgeRemoved(int, String) - Method in interface phylonet.graph.model.GraphListener

EMPTY_BV - Static variable in class phylonet.mct.GaneshkumarWarnowMCT

enableCollapse() - Method in class phylonet.riatahgt.RiataHgt

This function tells RiataHgt to collapse the trees before computing HGT events.

enableRefine() - Method in class phylonet.riatahgt.RiataHgt

This function tells RiataHgt to refine the trees before computing HGT events.

enumerateSolutions() - Method in class phylonet.riatahgt.RiataHgt

Enumerate all solutions computed by RiataHgt.

equals(Object) - Method in class phylonet.bits.BitVector

equals(Object) - Method in class phylonet.network.characterization.NetworkCluster

This method checks if two clusters are equal or not.

equals(Object) - Method in class phylonet.network.characterization.NetworkEdge

This function tests if the two edges are equal.

equals(Object) - Method in class phylonet.network.characterization.NetworkTree

This method checks if two trees generated by two different sets of network edges are equal.

equals(Object) - Method in class phylonet.network.characterization.NetworkTripartition

This function tests if two network tripartitions are equal or not.

equals(Object) - Method in class phylonet.riatahgt.HgtEvent

equals(Object) - Method in class phylonet.tree.model.sti.STITreeCluster

Check if another cluster is equal to this cluster.

equals(Object) - Method in class phylonet.tree.model.sti.STITreeClusterWD

error(String, Throwable) - Static method in class phylonet.app.util.PhyloLogger

Appends an error log and an associated Throwable to the current list of logs.

error(String) - Static method in class phylonet.app.util.PhyloLogger

Appends an error log to the current list of logs.

EventBootstrap - Class in phylonet.riatahgt

This class is to compute bootstrap of HGT events.

EventBootstrap(STITree<Double>, STITree<Double>, STITree<List<HgtScenario>>) - Constructor for class phylonet.riatahgt.EventBootstrap

ExMultipleMasts - Class in phylonet.riatahgt

This class tries to list all possible masts between two trees.

ExMultipleMasts() - Constructor for class phylonet.riatahgt.ExMultipleMasts

ExMultipleMastsTestCase - Class in phylonet.riatahgt

ExMultipleMastsTestCase() - Constructor for class phylonet.riatahgt.ExMultipleMastsTestCase

ExNewickException - Exception in phylonet.network.io

This class is used in parsing eNewick-format network input.

ExNewickException(String) - Constructor for exception phylonet.network.io.ExNewickException

Instantiates a new ExNewickException with the given message.

ExNewickReader<T> - Class in phylonet.network.io

Provides methods for reading a network in the extended Newick (eNewick) format.

ExNewickReader(Reader) - Constructor for class phylonet.network.io.ExNewickReader

Instantiates a new network reader with the given Reader for input.

ExNewickReaderTestCase - Class in phylonet.network.io

ExNewickReaderTestCase() - Constructor for class phylonet.network.io.ExNewickReaderTestCase

ExNewickWriter<T> - Class in phylonet.network.io

This class writes a network in the extended Newick format to an output stream.

ExNewickWriter(Writer) - Constructor for class phylonet.network.io.ExNewickWriter

expand(Collapse.CollapseDescriptor, MutableTree) - Static method in class phylonet.tree.util.Collapse

Expand any collapsed clades in tree using the results of the collapse operation that created cd.

exprnd(double) - Method in class phylonet.simulator.SimGTInNetwork

ExRiataMultipleHgtTestCase - Class in phylonet.riatahgt

ExRiataMultipleHgtTestCase() - Constructor for class phylonet.riatahgt.ExRiataMultipleHgtTestCase

ExtendableComboBoxList - Class in phylonet.app.tool.component

Represents a list of combo-boxes used for selecting data from the workspace.

ExtendableComboBoxList(JDialog, String, DataCriterion, PhyloNetAppModel) - Constructor for class phylonet.app.tool.component.ExtendableComboBoxList

Instantiates a new list of combo-boxes with the given criterion and textual elements.

ExtendableNodeSetsList - Class in phylonet.app.tool.component

Represents an extendable list of text fields which can be used to input a list of node sets (for the LCA tool, for example).

ExtendableNodeSetsList(JDialog) - Constructor for class phylonet.app.tool.component.ExtendableNodeSetsList

Instantiates a new list of node set text fields with the given textual elements.