Serialized Form

Package statalign.base.thread

Class statalign.base.thread.StoppedException extends java.lang.Exception implements Serializable

serialVersionUID: 1L

Package statalign.io.input

Class statalign.io.input.IllegalFormatException extends java.io.IOException implements Serializable

serialVersionUID: 1L

Package statalign.io.input.plugins

Class statalign.io.input.plugins.NewickReader.FormatException extends java.io.IOException implements Serializable

serialVersionUID: 1L

Serialized Fields

type

NewickReader.FormatExceptType type

expected

java.lang.String expected

Package statalign.model.subst

Class statalign.model.subst.RecognitionError extends java.lang.Error implements Serializable

serialVersionUID: 1L

Serialized Fields

message

java.lang.String message

The message of the error

Package statalign.postprocess.gui

Class statalign.postprocess.gui.AlignmentGUI extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

subst

SubstitutionModel subst

owner

Postprocess owner

alignment

java.lang.String[] alignment

The alignment that is written onto the screen is stored in this array

sequenceNames

java.lang.String[] sequenceNames

title

java.lang.String title

The title of the current analysis

decoding

double[] decoding

These are the posterior decoding values

aligNum

int aligNum

aligLen

int aligLen

Class statalign.postprocess.gui.CNetworkView extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

leaflabel

java.util.ArrayList<E> leaflabel

lines

java.util.ArrayList<E> lines

minX

int minX

minY

int minY

maxX

int maxX

maxY

int maxY

visX

int visX

visY

int visY

zoomFactor

int zoomFactor

g

java.awt.Graphics2D g

putInArray

boolean putInArray

height

int height

width

int width

scroll

javax.swing.JScrollPane scroll

zoomDivisor

int zoomDivisor

network

CNetwork network

Class statalign.postprocess.gui.DistanceGUI extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

title

java.lang.String title

owner

VisualDistance owner

distance

int distance

Class statalign.postprocess.gui.EntropyGUI extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

title

java.lang.String title

owner

Entropy owner

oe

javax.swing.JLabel oe

se

javax.swing.JLabel se

border

int border

Class statalign.postprocess.gui.InputGUI extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

pan

javax.swing.JPanel pan

owner

Input owner

text

java.awt.TextArea text

manager

MainManager manager

seqPan

javax.swing.JPanel seqPan

sequences

javax.swing.JList sequences

dlmSequences

javax.swing.DefaultListModel dlmSequences

jbDelete

javax.swing.JButton jbDelete

jbDeleteAll

javax.swing.JButton jbDeleteAll

sequencesAreRemovable

boolean sequencesAreRemovable

showWelcome

boolean showWelcome

spSeq

javax.swing.JScrollPane spSeq

Class statalign.postprocess.gui.LogLikelihoodTraceGUI extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

owner

LogLikelihoodTrace owner

Class statalign.postprocess.gui.PPFoldGUI extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

title

java.lang.String title

owner

PPFold owner

dimension

int dimension

x

int x

y

int y

gr2

java.awt.Graphics2D gr2

scroll

javax.swing.JScrollPane scroll

count

int count

cg

ColorGradient cg

probs

float[][] probs

Class statalign.postprocess.gui.StructAlignTraceGUI extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

owner

StructTrace owner

burninLength

int burninLength

Class statalign.postprocess.gui.StructureDetails extends fr.orsay.lri.varna.VARNAPanel implements Serializable

serialVersionUID: 1L

Class statalign.postprocess.gui.StructureGUI extends fr.orsay.lri.varna.VARNAPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

g2

java.awt.Graphics2D g2

cg

ColorGradient cg

_RNA

fr.orsay.lri.varna.models.rna.RNA _RNA

title

java.lang.String title

probMode

boolean probMode

_scaleFactor

double _scaleFactor

probs

float[][] probs

_conf

fr.orsay.lri.varna.models.VARNAConfig _conf

_manager

javax.swing.undo.UndoManager _manager

_blink

fr.orsay.lri.varna.controlers.ControleurBlinkingThread _blink

_translation

java.awt.Point _translation

_horsCadre

boolean _horsCadre

_premierAffichage

boolean _premierAffichage

_interpolator

fr.orsay.lri.varna.controlers.ControleurInterpolator _interpolator

_UI

fr.orsay.lri.varna.views.VueUI _UI

Package statalign.postprocess.gui.treeviews

Class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView extends TreeView implements Serializable

serialVersionUID: 1L

Serialized Fields

noOfSamples

int noOfSamples

Class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView extends TreeView implements Serializable

Serialized Fields

noOfSamples

int noOfSamples

Class statalign.postprocess.gui.treeviews.NetworkTreeView extends TreeView implements Serializable

serialVersionUID: 1L

Serialized Fields

leaflabel

java.util.ArrayList<E> leaflabel

lines

java.util.ArrayList<E> lines

minX

int minX

minY

int minY

maxX

int maxX

maxY

int maxY

visX

int visX

visY

int visY

zoomFactor

int zoomFactor

g

java.awt.Graphics2D g

putInArray

boolean putInArray

height

int height

width

int width

scroll

javax.swing.JScrollPane scroll

zoomDivisor

int zoomDivisor

Class statalign.postprocess.gui.treeviews.TreeView extends javax.swing.JPanel implements Serializable

Serialized Fields

root

TreeNode root

noOfTaxa

int noOfTaxa

identifier

java.lang.String identifier

parent

javax.swing.JComponent parent

Class statalign.postprocess.gui.treeviews.VerticalPhylogramTreeView extends TreeView implements Serializable

serialVersionUID: 1L

Package statalign.postprocess.plugins

Class statalign.postprocess.plugins.RNAalifoldResult extends java.lang.Object implements Serializable

serialVersionUID: 957877165963191430L

Serialized Fields

matrix

double[][] matrix

pairedSites

int[] pairedSites

reliablityScore

double reliablityScore

pairsOnlyReliablityScore

double pairsOnlyReliablityScore

Package statalign.postprocess.plugins.benchmarks

Class statalign.postprocess.plugins.benchmarks.AlignmentSample extends java.lang.Object implements Serializable

serialVersionUID: 8798582281020900675L

Serialized Fields

reference

statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment reference

mpd

statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment mpd

posteriors

java.util.ArrayList<E> posteriors

samples

java.util.ArrayList<E> samples

Class statalign.postprocess.plugins.benchmarks.Dataset extends java.lang.Object implements Serializable

serialVersionUID: -3205713573185024480L

Serialized Fields

title

java.lang.String title

randomSeed

long randomSeed

burnIn

int burnIn

mcmcSteps

int mcmcSteps

samplingRate

int samplingRate

fastaFile

java.io.File fastaFile

inputAlignment

com.ppfold.algo.AlignmentData inputAlignment

mpdAlignment

com.ppfold.algo.AlignmentData mpdAlignment

posteriors

java.util.ArrayList<E> posteriors

posteriorsAverage

double posteriorsAverage

mpdVsInputSim

double mpdVsInputSim

sampledAlignments

java.util.ArrayList<E> sampledAlignments

logLikelihoods

java.util.ArrayList<E> logLikelihoods

sampledStructures

java.util.ArrayList<E> sampledStructures

pairedSitesProjectedSamples

java.util.ArrayList<E> pairedSitesProjectedSamples

projectPairedSitesOnCumulativeMatrix

java.util.ArrayList<E> projectPairedSitesOnCumulativeMatrix

cumulativeFuzzyAlignment

java.util.ArrayList<E> cumulativeFuzzyAlignment

cumulativeFuzzyExpResults

java.util.ArrayList<E> cumulativeFuzzyExpResults

cumulativeFuzzyObsResults

java.util.ArrayList<E> cumulativeFuzzyObsResults

resultBundleReference

com.ppfold.algo.ResultBundle resultBundleReference

resultBundleMPD

com.ppfold.algo.ResultBundle resultBundleMPD

resultBundleEntropyExp

com.ppfold.algo.ResultBundle resultBundleEntropyExp

resultBundleEntropyObs

com.ppfold.algo.ResultBundle resultBundleEntropyObs

resultBundlePPfold

com.ppfold.algo.ResultBundle resultBundlePPfold

fuzzyAlignmentObsEntropyVal

double fuzzyAlignmentObsEntropyVal

fuzzyAlignmentObsEntropyPerc

double fuzzyAlignmentObsEntropyPerc

fuzzyAlignmentObsEntropyMax

double fuzzyAlignmentObsEntropyMax

ppfoldReliabilityEntropyObs

double ppfoldReliabilityEntropyObs

pairsOnlyReliabilityEntropyObs

double pairsOnlyReliabilityEntropyObs

pairsOnlyReliabilityEntropyObsPosteriorWeighted

double pairsOnlyReliabilityEntropyObsPosteriorWeighted

ppfoldReliabilityScoreSamplingAndAveraging

double ppfoldReliabilityScoreSamplingAndAveraging

ppfoldReliabilityScoreSamplingAndAveragingWeighted

double ppfoldReliabilityScoreSamplingAndAveragingWeighted

pairsOnlyReliabilityScoreSamplingAndAveragingPosteriorWeighted

double pairsOnlyReliabilityScoreSamplingAndAveragingPosteriorWeighted

ppfoldReliabilityMPD

double ppfoldReliabilityMPD

pairsOnlyReliabilityScoreSamplingAndAveraging

double pairsOnlyReliabilityScoreSamplingAndAveraging

pairsOnlyReliabilityScoreSamplingAndAveragingWeighted

double pairsOnlyReliabilityScoreSamplingAndAveragingWeighted

pairsOnlyReliabilityMPD

double pairsOnlyReliabilityMPD

pairsOnlyMPDPosteriorWeighted

double pairsOnlyMPDPosteriorWeighted

pairedSites

int[] pairedSites

pairedSitesWeighted

int[] pairedSitesWeighted

pairedSitesMPD

int[] pairedSitesMPD

pairedSitesPPfoldProjected

int[] pairedSitesPPfoldProjected

pairedSitesRefSeq

java.lang.String pairedSitesRefSeq

pairedSitesWeightedRefSeq

java.lang.String pairedSitesWeightedRefSeq

pairedSitesEntropyExp

int[] pairedSitesEntropyExp

pairedSitesEntropyObs

int[] pairedSitesEntropyObs

pairedSitesProjectedRnaAlifoldSamples

java.util.ArrayList<E> pairedSitesProjectedRnaAlifoldSamples

pairedSitesRNAalifold

int[] pairedSitesRNAalifold

ppfoldReliabilityScoreRNAalifold

double ppfoldReliabilityScoreRNAalifold

pairsOnlyReliabilityScoreRNAalifold

double pairsOnlyReliabilityScoreRNAalifold

rnaAlifoldMPD

RNAalifoldResult rnaAlifoldMPD

rnaAlifoldRef

RNAalifoldResult rnaAlifoldRef

pairedSitesRNAalifoldMPDProjected

int[] pairedSitesRNAalifoldMPDProjected

pairedSitesRNAalifoldRefProjected

int[] pairedSitesRNAalifoldRefProjected

pairedSitesCombined

int[] pairedSitesCombined

ppfoldReliabilityScoreCombined

double ppfoldReliabilityScoreCombined

pairsOnlyReliabilityScoreCombined

double pairsOnlyReliabilityScoreCombined

matrixFolds

java.util.ArrayList<E> matrixFolds

pairedSitesMatrix

int[] pairedSitesMatrix

ppfoldReliabilityScoreConsensusEvol

double ppfoldReliabilityScoreConsensusEvol

pairsOnlyReliabilityScoreConsensusEvol

double pairsOnlyReliabilityScoreConsensusEvol

Package statalign.postprocess.plugins.contree

Class statalign.postprocess.plugins.contree.Cluster extends java.util.ArrayList<TreeNode> implements Serializable

Serialized Fields

noOfOccurrences

int noOfOccurrences

edgeLength

double edgeLength

aboveSplit

java.util.BitSet aboveSplit

nodeRefA

int nodeRefA

nodeRefB

int nodeRefB

added

boolean added

isMajority

boolean isMajority

Class statalign.postprocess.plugins.contree.TaxaMap extends java.util.HashMap<java.lang.String,java.lang.Integer> implements Serializable

Serialized Fields

taxaNames

java.util.ArrayList<E> taxaNames

Package statalign.postprocess.utils

Class statalign.postprocess.utils.NewickParserException extends java.lang.RuntimeException implements Serializable

Package statalign.ui

Class statalign.ui.AboutDlg extends javax.swing.JDialog implements Serializable

Serialized Fields

owner

javax.swing.JFrame owner

scroll

javax.swing.JScrollPane scroll

pane

javax.swing.JEditorPane pane

Class statalign.ui.ErrorMessage extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

cp

java.awt.Container cp

btOK

javax.swing.JButton btOK

Class statalign.ui.HelpWindow extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

WIDTH

int WIDTH

HEIGHT

int HEIGHT

editorpane

javax.swing.JEditorPane editorpane

homeURL

java.net.URL homeURL

visitedPages

java.util.ArrayList<E> visitedPages

visitedIndex

int visitedIndex

btnback

javax.swing.JButton btnback

btnforward

javax.swing.JButton btnforward

Class statalign.ui.MainFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

tab

javax.swing.JTabbedPane tab

pluginTabs

java.util.List<E> pluginTabs

input

Input input

toolBar

javax.swing.JToolBar toolBar

openButton

javax.swing.JButton openButton

runButton

javax.swing.JButton runButton

pauseButton

javax.swing.JButton pauseButton

resumeButton

javax.swing.JButton resumeButton

stopButton

javax.swing.JButton stopButton

rnaButton

javax.swing.JToggleButton rnaButton

openItem

javax.swing.JMenuItem openItem

runItem

javax.swing.JMenuItem runItem

pauseItem

javax.swing.JMenuItem pauseItem

resumeItem

javax.swing.JMenuItem resumeItem

stopItem

javax.swing.JMenuItem stopItem

modelButtons

javax.swing.JMenuItem[] modelButtons

statusText

javax.swing.JLabel statusText

tabPluginMap

java.util.HashMap<K,V> tabPluginMap

lastSelectedTabIndex

int lastSelectedTabIndex

manager

MainManager manager

The main manager that handles the MCMC run.

mcmcSettingsDlg

McmcSettingsDlg mcmcSettingsDlg

inFile

java.io.File inFile

substModels

java.lang.Class<T>[] substModels

op

OutputPreferences op

dlg

RNASettingsDlg dlg

Class statalign.ui.McmcSettingsDlg extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

pars

MCMCPars pars

burnIn

javax.swing.JTextField burnIn

cycles

javax.swing.JTextField cycles

sampRate

javax.swing.JTextField sampRate

seed

javax.swing.JTextField seed

randomisationPeriod

javax.swing.JTextField randomisationPeriod

automateStepRate

javax.swing.JCheckBox automateStepRate

automateNumberOfSamples

javax.swing.JCheckBox automateNumberOfSamples

automateBurnIn

javax.swing.JCheckBox automateBurnIn

owner

MainFrame owner

Class statalign.ui.OutputPreferences extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

owner

MainFrame owner

Class statalign.ui.RNASettingsDlg extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

rnaalifoldOptions

javax.swing.JPanel rnaalifoldOptions

useSamplingAndAveragingButton

javax.swing.JCheckBox useSamplingAndAveragingButton

useSamplingAndAveragingRNAalifoldButton

javax.swing.JCheckBox useSamplingAndAveragingRNAalifoldButton

fuzzyNucleotidePredictionAndEntropy

javax.swing.JCheckBox fuzzyNucleotidePredictionAndEntropy

consensusEvolutionPrediction

javax.swing.JCheckBox consensusEvolutionPrediction

fileChooser

javax.swing.JFileChooser fileChooser

executableField

javax.swing.JTextField executableField

executableButton

javax.swing.JButton executableButton

temperatureModel

javax.swing.SpinnerNumberModel temperatureModel

temperatureSpinner

javax.swing.JSpinner temperatureSpinner

linearButton

javax.swing.JRadioButton linearButton

circularButton

javax.swing.JRadioButton circularButton

covarianceModel

javax.swing.SpinnerNumberModel covarianceModel

covarianceSpinner

javax.swing.JSpinner covarianceSpinner

nonCompatibleModel

javax.swing.SpinnerNumberModel nonCompatibleModel

nonCompatibleSpinner

javax.swing.JSpinner nonCompatibleSpinner

owner

javax.swing.JFrame owner

prefs

java.util.prefs.Preferences prefs

wasCancelled

boolean wasCancelled

Class statalign.ui.TextDlg extends javax.swing.JDialog implements Serializable

Serialized Fields

scroll

javax.swing.JScrollPane scroll

Package statalign.utils

Class statalign.utils.BetaDistribution extends org.apache.commons.math3.distribution.AbstractRealDistribution implements Serializable

serialVersionUID: -1221965979403477668L

Serialized Fields

alpha

double alpha

First shape parameter.

beta

double beta

Second shape parameter.

z

double z

Normalizing factor used in density computations. updated whenever alpha or beta are changed.

solverAbsoluteAccuracy

double solverAbsoluteAccuracy

Inverse cumulative probability accuracy.

Class statalign.utils.GammaDistribution extends org.apache.commons.math3.distribution.AbstractRealDistribution implements Serializable

serialVersionUID: 20120524L

Serialized Fields

shape

double shape

The shape parameter.

scale

double scale

The scale parameter.

shiftedShape

double shiftedShape

The constant value of shape + g + 0.5, where g is the Lanczos constant Gamma.LANCZOS_G.

densityPrefactor1

double densityPrefactor1

The constant value of shape / scale * sqrt(e / (2 * pi * (shape + g + 0.5))) / L(shape), where L(shape) is the Lanczos approximation returned by Gamma.lanczos(double). This prefactor is used in GammaDistribution.density(double), when no overflow occurs with the natural calculation.

densityPrefactor2

double densityPrefactor2

The constant value of shape * sqrt(e / (2 * pi * (shape + g + 0.5))) / L(shape), where L(shape) is the Lanczos approximation returned by Gamma.lanczos(double). This prefactor is used in GammaDistribution.density(double), when overflow occurs with the natural calculation.

minY

double minY

Lower bound on y = x / scale for the selection of the computation method in GammaDistribution.density(double). For y <= minY, the natural calculation overflows.

maxLogY

double maxLogY

Upper bound on log(y) (y = x / scale) for the selection of the computation method in GammaDistribution.density(double). For log(y) >= maxLogY, the natural calculation overflows.

solverAbsoluteAccuracy

double solverAbsoluteAccuracy

Inverse cumulative probability accuracy.

Class statalign.utils.NormalDistribution extends org.apache.commons.math3.distribution.AbstractRealDistribution implements Serializable

serialVersionUID: 8589540077390120676L

Serialized Fields

mean

double mean

Mean of this distribution.

standardDeviation

double standardDeviation

Standard deviation of this distribution.

solverAbsoluteAccuracy

double solverAbsoluteAccuracy

Inverse cumulative probability accuracy.