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

P

pad(String, int) - Static method in class statalign.postprocess.utils.RNAFoldingTools

A helper method which pads or truncates a string to a specific length.

paintComponent(Graphics) - Method in class statalign.postprocess.gui.AlignmentGUI

This function updates the graphics

paintComponent(Graphics) - Method in class statalign.postprocess.gui.CNetworkView

It repaints the graphics by grabbing the new data from the network.

paintComponent(Graphics) - Method in class statalign.postprocess.gui.DistanceGUI

paintComponent(Graphics) - Method in class statalign.postprocess.gui.EntropyGUI

It updates the graphics of the panel

paintComponent(Graphics) - Method in class statalign.postprocess.gui.LogLikelihoodTraceGUI

It updates the graphics of the panel

paintComponent(Graphics) - Method in class statalign.postprocess.gui.StructAlignTraceGUI

It updates the graphics of the panel

paintComponent(Graphics) - Method in class statalign.postprocess.gui.StructureGUI

paintComponent(Graphics) - Method in class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView

It repaints the graphics

paintComponent(Graphics) - Method in class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView

It repaints the graphics

paintComponent(Graphics) - Method in class statalign.postprocess.gui.treeviews.NetworkTreeView

It repaints the graphics

paintComponent(Graphics) - Method in class statalign.postprocess.gui.treeviews.VerticalPhylogramTreeView

Pair<L,R> - Class in statalign.distance

A Pair container.

Pair(L, R) - Constructor for class statalign.distance.Pair

PairCompare - Class in statalign.distance

Makes it possible to compare two pairs.

PairCompare() - Constructor for class statalign.distance.PairCompare

pairedSites - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSites - Variable in class statalign.postprocess.plugins.RNAalifoldResult

pairedSitesCombined - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesEntropyExp - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesEntropyObs - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesMatrix - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesMPD - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesPPfoldProjected - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesProjectedRnaAlifoldSamples - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesProjectedSamples - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesRefSeq - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesRNAalifold - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesRNAalifoldMPDProjected - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesRNAalifoldRefProjected - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesWeighted - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairedSitesWeightedRefSeq - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyMPDPosteriorWeighted - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityEntropyObs - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityEntropyObsPosteriorWeighted - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityMPD - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityScoreCombined - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityScoreConsensusEvol - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityScoreRNAalifold - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityScoreSamplingAndAveraging - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityScoreSamplingAndAveragingPosteriorWeighted - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliabilityScoreSamplingAndAveragingWeighted - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

pairsOnlyReliablityScore - Variable in class statalign.postprocess.plugins.RNAalifoldResult

pan - Variable in class statalign.postprocess.plugins.ConsensusNetwork

pan - Variable in class statalign.postprocess.plugins.CurrentAlignment

ParameterInterface - Interface in statalign.mcmc

params - Variable in class statalign.base.hmm.Hmm

HMM model parameters.

params - Variable in class statalign.model.subst.SubstitutionModel

Model parameters.

parent - Variable in class statalign.base.AlignColumn

This reference points to the parent of this AlignColumn

parent - Variable in class statalign.base.State

Tree representation: parent of each node (first nl are leaves), -1 for none

parent - Variable in class statalign.base.Vertex

This reference points to the parent of the vertex

parent - Variable in class statalign.postprocess.plugins.TreeNode

The parent of this node.

parentList - Variable in class statalign.postprocess.plugins.contree.CTree

pars - Variable in class statalign.base.InputData

MCMC parameters such as the number of burn-in cycles, number of steps and sampling rate

parse() - Method in class statalign.postprocess.utils.NewickParser

parseAlignmentString(String, ArrayList<String>, ArrayList<String>) - Static method in class statalign.distance.AlignmentSample

parseAlignmentString(String, ArrayList<String>, ArrayList<String>) - Static method in class statalign.postprocess.plugins.benchmarks.AlignmentSample

Fills a vector of sequences and vector of sequence names from a specified fasta alignment string.

partition - Variable in class statalign.postprocess.plugins.contree.hash.HashEntry

The bi-partition relevant to this entry.

pathOfEdges - Variable in class statalign.postprocess.plugins.contree.CNetworkPath

pathOfNodes - Variable in class statalign.postprocess.plugins.contree.CNetworkPath

paths - Variable in class statalign.postprocess.plugins.contree.CNetworkNode

pausable() - Method in class statalign.base.thread.Stoppable

Should be called from methods of the descendant classes at points where execution is allowed to be suspended by an external thread (by calling the StoppableThread's suspendSoft() method) If the descendant object has not been created from within a StoppableThread, calling this method has no effect.

pauseNoWait() - Method in class statalign.base.thread.StoppableThread

Can be called by an external thread to request suspension of this thread.

pauseToggleSoft() - Method in class statalign.base.thread.StoppableThread

Calls suspendSoft() or resumeSoft(), depending on the current state of this thread.

PDBReader - Class in statalign.io.input.plugins

PDBReader() - Constructor for class statalign.io.input.plugins.PDBReader

PERCENT_CONST - Static variable in class statalign.base.AutomateParameters

percentGreaterOrEqualTo(double, ArrayList<Double>) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

percentile(ArrayList<Double>, double) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Returns the percentile of the specified value in the specified list of values.

performConsensusEvolutionPrediction() - Method in class statalign.postprocess.plugins.PPFold

performDistanceBenchmarks(Dataset) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

performDistanceBenchmarks() - Method in class statalign.postprocess.plugins.benchmarks.Benchmarks

performEntropy() - Method in class statalign.postprocess.plugins.benchmarks.Benchmarks

performPosteriorDecodingMultiThreaded(double[][], double[]) - Method in class statalign.postprocess.utils.RNAFoldingTools

Performs posterior-decoding using multi-threading.

performPosteriorDecodingMultiThreaded(double[][]) - Method in class statalign.postprocess.utils.RNAFoldingTools

Performs posterior-decoding using multi-threading.

perSequenceData() - Method in class statalign.base.Tree

perSequenceData() - Method in interface statalign.io.DataType

perSequenceData() - Method in class statalign.io.ProteinSkeletons

perSequenceData() - Method in class statalign.io.RawSequences

PhiMove - Class in statalign.base.mcmc

PhiMove(McmcModule, PriorDistribution<Double>, ProposalDistribution<Double>, String) - Constructor for class statalign.base.mcmc.PhiMove

plotSide() - Method in class statalign.model.ext.plugins.structalign.StructAlignMoveParams

plotSide - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters.PlottableParameter

plottableParameters - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters

pluginParameters - Variable in class statalign.CommandLine

PluginParameters - Class in statalign.postprocess

A class which for storing plugin parameters.

PluginParameters() - Constructor for class statalign.postprocess.PluginParameters

PluginParameters(ArrayList<String>) - Constructor for class statalign.postprocess.PluginParameters

An alternative way to initialise this class.

pluginParameters - Static variable in class statalign.postprocess.PostprocessManager

Static object holding parameters, which are visible to all plugins.

pop() - Method in class statalign.base.CircularArray

Retrieves the last element in the array (element with key endKey-1) and decreases endKey.

positions - Variable in class statalign.postprocess.gui.ColorGradient

posteriors - Variable in class statalign.postprocess.plugins.benchmarks.AlignmentSample

posteriors - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

posteriorsAverage - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

Postprocess - Class in statalign.postprocess

Common ancestor for post-processing plugin classes.

Postprocess() - Constructor for class statalign.postprocess.Postprocess

postprocessable - Variable in class statalign.postprocess.Postprocess

True if this class can generate a postprocess file

PostprocessManager - Class in statalign.postprocess

This class manages the postprocesses.

PostprocessManager(MainManager) - Constructor for class statalign.postprocess.PostprocessManager

This constructor recognizes the plugins

postprocessWrite - Variable in class statalign.postprocess.Postprocess

True if it writes a postprocess file

postProcMan - Variable in class statalign.base.MainManager

This is the postprocess-manager of our program, which handles the postprocesses applied on the MCMC run.

postprocMan - Variable in class statalign.base.Mcmc

PostprocessManager that handles the postprocessing modules.

PPFold - Class in statalign.model.ext.plugins

PPFold() - Constructor for class statalign.model.ext.plugins.PPFold

PPFold - Class in statalign.postprocess.plugins

PPFold() - Constructor for class statalign.postprocess.plugins.PPFold

ppfold - Variable in class statalign.postprocess.plugins.Structure

PPFoldGUI - Class in statalign.postprocess.gui

PPFoldGUI(String, JScrollPane, PPFold) - Constructor for class statalign.postprocess.gui.PPFoldGUI

ppfoldReliabilityEntropyObs - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

ppfoldReliabilityMPD - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

ppfoldReliabilityScoreCombined - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

ppfoldReliabilityScoreConsensusEvol - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

ppfoldReliabilityScoreRNAalifold - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

ppfoldReliabilityScoreSamplingAndAveraging - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

ppfoldReliabilityScoreSamplingAndAveragingWeighted - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

preCalcRedTransMatrix(double[][], double[][]) - Method in class statalign.base.hmm.HmmNonParam

Returns the transition matrix.

preCalcRedTransMatrix(double[][], double[][]) - Method in class statalign.base.hmm.HmmSilent

Silent state elimination.

preCalcTransMatrix(double[][], double) - Method in class statalign.base.hmm.Hmm2

Calculates the transition matrix given an edge length t.

preCalcTransMatrix(double[][], double, double[]) - Method in class statalign.base.hmm.Hmm2

preCalcTransMatrix(double[][], double, double) - Method in class statalign.base.hmm.HmmNonParam

Returns the transition matrix.

preCalcTransMatrix(double[][], double, double) - Method in class statalign.base.hmm.HmmSilent

Calculates the transition matrix given edge lengths t1 and t2 of a cherry-motif.

preCalcTransMatrix(double[][], double) - Method in class statalign.base.hmm.HmmTkf92

Calculates a transition matrix given an edge length.

preCalcTransMatrix(double[][], double, double[]) - Method in class statalign.base.hmm.HmmTkf92

prefix - Static variable in class statalign.postprocess.plugins.contree.test.CorrectnessTester

prev - Variable in class statalign.base.AlignColumn

This reference points to the previous AlignColumn in the alignment

previousFullAlign - Variable in class statalign.base.Tree

print(StringBuffer) - Method in class statalign.base.Vertex

print(StringBuffer, boolean) - Method in class statalign.base.Vertex

print(int) - Method in class statalign.base.Vertex

print() - Method in class statalign.model.subst.plugins.AminoAcidModel

Dummy function with the possibility of further developments.

print() - Method in class statalign.model.subst.plugins.Felsenstein81

Prints the current state of model.

print() - Method in class statalign.model.subst.plugins.Felsenstein84

Prints the parameters of the model

print() - Method in class statalign.model.subst.plugins.HKY85

Prints the parameters of the model

print() - Method in class statalign.model.subst.plugins.Kimura3

Prints the parameters of the model

print() - Method in class statalign.model.subst.plugins.NucleotideModel

returns the description of the current parameters of the model

print() - Method in class statalign.model.subst.plugins.ReversibleNucleotide

Prints the parameters of the model

print() - Method in class statalign.model.subst.plugins.Tamura92

Prints the parameters of the model

print() - Method in class statalign.model.subst.plugins.TamuraNei

Prints the parameters of the model

print() - Method in class statalign.model.subst.SubstitutionModel

Represents model state as a String (usually parameter values concatenated)

print() - Method in class statalign.postprocess.PluginParameters

printChildren(Vertex) - Static method in class statalign.base.Vertex

printConfig() - Method in class statalign.postprocess.plugins.contree.CTMain

Print some configuration information

printDetails(CTree, CNetwork) - Method in class statalign.postprocess.plugins.contree.CTMain

FOR TESTING ONLY Print details from the network - call after it has been constructed!

printedAlignment(boolean) - Method in class statalign.base.Vertex

printedAlignment() - Method in class statalign.base.Vertex

printEdges(Vertex) - Static method in class statalign.base.Vertex

printedTree() - Method in class statalign.base.Tree

Generates a String contaning the description of the tree in Newick format.

printedTreeWithNumbers() - Method in class statalign.base.Tree

printExtraInfo - Variable in class statalign.mcmc.McmcModule

println(int, String) - Static method in class statalign.MPIUtils

printMatrix(double[][]) - Static method in class statalign.postprocess.plugins.structalign.RmsdTrace

printMatrix(double[][]) - Static method in class statalign.postprocess.plugins.structalign.StructTrace

printMatrix(double[][]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

A helper method which prints double matrices.

PrintOut(int, int, TaxaMap) - Method in class statalign.postprocess.plugins.contree.CNetwork

Prints out the network in Nexus format.

printPairs(int[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

printPointers() - Method in class statalign.base.Vertex

printToScreenAlignment(int, int) - Method in class statalign.base.Vertex

printToScreenAlignment(int, int, boolean) - Method in class statalign.base.Vertex

printTree(Vertex, String) - Method in class statalign.model.ext.plugins.StructAlign

printValues(int[], int[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

printWithNumbers(StringBuffer) - Method in class statalign.base.Vertex

PriorDistribution<T> - Interface in statalign.mcmc

probability(double, double) - Method in class statalign.utils.NormalDistribution

probMatrix - Variable in class statalign.postprocess.plugins.PPFold

probMatrix - Static variable in class statalign.postprocess.plugins.Structure

probMode - Variable in class statalign.postprocess.gui.StructureGUI

projectarray(String, float[], char) - Static method in class statalign.postprocess.utils.Mapping

projectArray2(String, float[], char) - Static method in class statalign.postprocess.utils.Mapping

projectMatrix(String, float[][], char) - Static method in class statalign.postprocess.utils.Mapping

projectMatrix(String, double[][], char) - Static method in class statalign.postprocess.utils.Mapping

projectMatrix2(String, float[][], char) - Static method in class statalign.postprocess.utils.Mapping

Given an aligned sequence of length n from an alignment of length n and a n*n matrix corresponding to the alignment.

projectPairedSites(String, int[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Takes an integer array of paired sites and deletes nucleotide positions corresponding to gaps in the aligned sequence.

projectPairedSites(String, int[]) - Static method in class statalign.postprocess.utils.Mapping

projectPairedSitesOnCumulativeMatrix - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

projectSequence(String, String, char) - Static method in class statalign.postprocess.utils.Mapping

projectSequence2(String, String, char) - Static method in class statalign.postprocess.utils.Mapping

properties - Variable in class statalign.postprocess.plugins.TreeNode

Properties associated with this node.

proposal(Object) - Method in class statalign.base.mcmc.AlignmentMove

proposal(Object) - Method in class statalign.base.mcmc.AllEdgeMove

proposal(Object) - Method in class statalign.base.mcmc.EdgeMove

proposal(Object) - Method in class statalign.base.mcmc.LOCALTopologyMove

proposal(Object) - Method in class statalign.base.mcmc.SilentIndelMove

proposal(Object) - Method in class statalign.base.mcmc.SubstMove

proposal(Object) - Method in class statalign.base.mcmc.TopologyMove

proposal(Object) - Method in class statalign.mcmc.ContinuousPositiveParameterMove

proposal(Object) - Method in class statalign.mcmc.McmcCombinationMove

proposal(Object) - Method in class statalign.mcmc.McmcMove

proposal(Object) - Method in class statalign.model.ext.plugins.structalign.AlignmentMove

proposal(Object) - Method in class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

proposal(Object) - Method in class statalign.model.ext.plugins.structalign.HierarchicalContinuousPositiveStructAlignMove

proposal(Object) - Method in class statalign.model.ext.plugins.structalign.LibraryMove

proposal(Object) - Method in class statalign.model.ext.plugins.structalign.RotationMove

proposal(Object) - Method in class statalign.model.ext.plugins.structalign.RotationOrTranslationMove

proposal(Object) - Method in class statalign.model.ext.plugins.structalign.TranslationMove

proposalCount - Variable in class statalign.mcmc.McmcMove

proposalCount - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters.PlottableParameter

ProposalDistribution<T> - Class in statalign.mcmc

ProposalDistribution() - Constructor for class statalign.mcmc.ProposalDistribution

proposalWidthControlVariable - Variable in class statalign.mcmc.McmcMove

propose(int) - Method in class statalign.model.ext.plugins.structalign.RotationProposal

propose from a library mixture distribution

proposedLogLike - Variable in class statalign.base.McmcStep

loglikelihood of proposed step

proposeParamChange(Tree) - Method in class statalign.base.mcmc.CoreMcmcModule

proposeParamChange(Tree) - Method in class statalign.mcmc.McmcModule

proposeParamChange(Tree) - Method in class statalign.model.ext.ModelExtManager

ProteinSkeletons - Class in statalign.io

Represents simplified tertiary structures of a set of sequences (primarily proteins), only one 3d-coordinate per character (amino acid) is stored.

ProteinSkeletons() - Constructor for class statalign.io.ProteinSkeletons

push(E) - Method in class statalign.base.CircularArray

Adds new element at the end of the array (key endKey is assigned), growing the array if full, then endKey is increased.

put(int, E) - Method in class statalign.base.CircularArray

Puts a new (key,element) pair into the CircularArray, growing the array if the new key range doesn't fit into the array.

put(BitSet, double, int, int, double, LinkedList<HashEntry>) - Method in class statalign.postprocess.plugins.contree.hash.HashTable

Puts a bi-partition into the hash table.

put(String, Integer) - Method in class statalign.postprocess.plugins.contree.TaxaMap

putInArray - Variable in class statalign.postprocess.gui.CNetworkView

putInArray - Variable in class statalign.postprocess.gui.treeviews.NetworkTreeView