Home
Java
JSTL
Struts
Spring
Hibernate
Webservice
Eclipse
API
Guest Post
Menu
Explorer
statalign-master
src
com
ppfold
algo
AlignmentData.java
AsynchronousJobExecutor.java
AsynchronousJobExecutorBlocking.java
AsynchronousJobExecutorThreadPool.java
CYKJob.java
ExpectationMatrixCalc.java
ExportTools.java
FoldingProject.java
FuzzyAlignment.java
FuzzyNucleotide.java
Inside.java
JobListener.java
JobResults.java
Master.java
MatrixTools.java
MaximumLikelihoodTree.java
NeighbourJoining.java
Node.java
NullProgress.java
Outside.java
Parameters.java
PhyloCalc.java
PhyloCalcFuzzy.java
PhyloJob.java
PhyloJobFuzzy.java
PointRes.java
Progress.java
ResMatrix.java
ResultBundle.java
Sector.java
SectorGenerator.java
Tree.java
extradata
BinaryStringData.java
BinaryStringDataDiffBp.java
ExtraData.java
ExtraDataBars.java
ExtraDataProbMapping.java
ForcedConstraints.java
SHAPEData.java
SHAPEDataFctDiffBp.java
main
Alignment.java
AlignmentReader.java
ArgumentParser.java
AutoScrollingTextArea.java
CheckAllData.java
CompIntensityGroup.java
CustomTextDialog.java
DataButtonGroup.java
DataChooserDialog.java
DataInfo.java
ExportsGroup.java
MainButtonPanel.java
NewickReader.java
PPfold.java
PPfoldButtonGroup.java
PPfoldGUIMainWindow.java
PPfoldMain.java
PPfoldProgressBar.java
SequenceExportsGroup.java
TextAreaOutputStream.java
Updatable.java
fr
orsay
lri
varna
VARNAPanel.java
applications
AlignmentDemo.java
FileNameExtensionFilter.java
NussinovDemo.java
SuperpositionDemo.java
VARNAConsoleDemo.java
VARNAEditor.java
VARNAGUI.java
VARNAOnlineDemo.java
VARNAPrinter.java
VARNAcmd.java
templateEditor
Connection.java
Couple.java
GraphicalTemplateElement.java
Helix.java
MouseControler.java
TemplateEditor.java
TemplateEditorPanelUI.java
TemplateEdits.java
TemplatePanel.java
UnpairedRegion.java
components
ActionEditor.java
ActionRenderer.java
AnnotationTableModel.java
BaseSpecialColorEditor.java
BaseTableModel.java
ColorRenderer.java
GradientEditorPanel.java
ReorderableJList.java
VARNAConsole.java
controlers
ControleurBPHeightIncrement.java
ControleurBaseSpecialColorEditor.java
ControleurBlinkingThread.java
ControleurBorder.java
ControleurClicMovement.java
ControleurDemoTextField.java
ControleurDraggedMolette.java
ControleurGlobalRotation.java
ControleurInterpolator.java
ControleurJCheckBoxMenuItem.java
ControleurMenu.java
ControleurMolette.java
ControleurNumPeriod.java
ControleurScriptParser.java
ControleurSelectionHighlight.java
ControleurSliderLabel.java
ControleurSpaceBetweenBases.java
ControleurTableAnnotations.java
ControleurVARNAPanelKeys.java
ControleurVueAnnotation.java
ControleurZoom.java
exceptions
ExceptionDrawingAlgorithm.java
ExceptionEdgeEndpointAlreadyConnected.java
ExceptionExportFailed.java
ExceptionFileFormatOrSyntax.java
ExceptionInvalidRNATemplate.java
ExceptionJPEGEncoding.java
ExceptionLoadingFailed.java
ExceptionModeleStyleBaseSyntaxError.java
ExceptionNAViewAlgorithm.java
ExceptionNonEqualLength.java
ExceptionParameterError.java
ExceptionPermissionDenied.java
ExceptionUnmatchedClosingParentheses.java
ExceptionWritingForbidden.java
ExceptionXMLGeneration.java
ExceptionXmlLoading.java
MappingException.java
factories
RNAFactory.java
interfaces
InterfaceParameterLoader.java
InterfaceVARNAListener.java
InterfaceVARNAObservable.java
InterfaceVARNARNAListener.java
InterfaceVARNASelectionListener.java
models
BaseList.java
CubicBezierCurve.java
FullBackup.java
VARNAConfig.java
VARNAConfigLoader.java
VARNAEdits.java
annotations
ChemProbAnnotation.java
HighlightRegionAnnotation.java
TextAnnotation.java
export
ArcCommand.java
CircleCommand.java
ColorCommand.java
FillCircleCommand.java
FillPolygonCommand.java
FontCommand.java
GraphicElement.java
LineCommand.java
PSExport.java
PolygonCommand.java
RectangleCommand.java
SVGExport.java
SecStrDrawingProducer.java
SecStrProducerGraphics.java
SwingGraphics.java
TextCommand.java
VueVARNAGraphics.java
XFIGExport.java
naView
Base.java
Connection.java
Loop.java
NAView.java
Radloop.java
Region.java
rna
ExtendedMB.java
Mapping.java
ModeleBP.java
ModeleBPStyle.java
ModeleBase.java
ModeleBaseNucleotide.java
ModeleBasesComparison.java
ModeleColorMap.java
ModeleStrand.java
ModeleStyleBase.java
Motif.java
RNA.java
RNAMLParser.java
StructureTemp.java
VARNAPoint.java
VARNASecDraw.java
templates
RNANodeValue2TemplateDistance.java
RNANodeValueTemplate.java
RNANodeValueTemplateBasePair.java
RNANodeValueTemplateBrokenBasePair.java
RNANodeValueTemplateSequence.java
RNATemplate.java
RNATemplateAlign.java
RNATemplateDrawingAlgorithmException.java
RNATemplateMapping.java
RNATemplateMappingException.java
treealign
AlignedNode.java
ExampleDistance2.java
ExampleDistance3.java
GraphvizDrawableNodeValue.java
RNANodeValue.java
RNANodeValue2.java
RNANodeValue2WrongTypeException.java
RNATree.java
RNATree2.java
RNATree2Exception.java
Tree.java
TreeAlign.java
TreeAlignException.java
TreeAlignLabelDistanceAsymmetric.java
TreeAlignLabelDistanceSymmetric.java
TreeAlignResult.java
TreeGraphviz.java
views
Imprimer.java
PrintTest.java
VueAboutPanel.java
VueAnnotation.java
VueBPHeightIncrement.java
VueBPList.java
VueBPThickness.java
VueBPType.java
VueBaseValues.java
VueBases.java
VueBorder.java
VueChemProbAnnotation.java
VueColorMapStyle.java
VueFont.java
VueGlobalRotation.java
VueHighlightRegionEdit.java
VueJPEG.java
VueListeAnnotations.java
VueLoadColorMapValues.java
VueManualInput.java
VueMenu.java
VueNumPeriod.java
VueSpaceBetweenBases.java
VueStyleBP.java
VueUI.java
VueZoom.java
statalign
CommandLine.java
MPIUtils.java
StatAlign.java
StatAlignParallel.java
base
AlignColumn.java
AutomateParameters.java
CircularArray.java
Input.java
InputData.java
MCMCPars.java
MainManager.java
Mcmc.java
McmcStep.java
State.java
Tree.java
TreeAlgo.java
Utils.java
Vertex.java
hmm
Hmm.java
Hmm2.java
HmmNonParam.java
HmmSilent.java
HmmTkf92.java
mcmc
AlignmentMove.java
AllEdgeMove.java
CoreMcmcModule.java
EdgeMove.java
IndelMove.java
LOCALTopologyMove.java
LambdaMove.java
MuMove.java
PhiMove.java
RMove.java
RhoMove.java
SilentIndelMove.java
StatAlignMcmc.java
StatAlignParallelMcmc.java
SubstMove.java
ThetaMove.java
TopologyMove.java
thread
MainThread.java
Stoppable.java
StoppableThread.java
StoppedException.java
distance
AlignmentSample.java
ComplexPair.java
Distance.java
Pair.java
PairCompare.java
io
DataManager.java
DataType.java
ProteinSkeletons.java
RawSequences.java
input
ConfReader.java
DataReader.java
FileTokenReader.java
IllegalFormatException.java
InputReader.java
plugins
CoorReader.java
FastaReader.java
NewickReader.java
PDBReader.java
mcmc
BetaPrior.java
ContinuousPositiveParameterMove.java
GammaPrior.java
GammaProposal.java
GaussianProposal.java
HyperbolicPrior.java
InverseGammaPrior.java
LinearPrior.java
LogNormalPrior.java
LogisticProposal.java
McmcCombinationMove.java
McmcModule.java
McmcMove.java
MultiplicativeProposal.java
ParameterInterface.java
PriorDistribution.java
ProposalDistribution.java
UniformPrior.java
UniformProposal.java
model
ext
ModelExtManager.java
ModelExtension.java
plugins
PPFold.java
RNAAliFold.java
StructAlign.java
structalign
AlignmentMove.java
ContinuousPositiveStructAlignMove.java
Funcs.java
HierarchicalContinuousPositiveStructAlignMove.java
LibraryMove.java
LinearLink.java
MultiNormCholesky.java
QuadraticLink.java
RotationMove.java
RotationOrTranslationMove.java
RotationProposal.java
StructAlignMoveParams.java
StructAlignParameterInterface.java
Subtree.java
Transformation.java
TranslationMove.java
vonMises.java
vonMisesFisher.java
score
SubstitutionScore.java
plugins
Blosum62.java
DNAScore.java
subst
RecognitionError.java
SubstitutionModel.java
plugins
AminoAcidModel.java
Blosum.java
CpRev.java
Dayhoff.java
Felsenstein81.java
Felsenstein84.java
HKY85.java
Jones.java
JukesCantor.java
Kimura3.java
MtMam.java
MtREV.java
NucleotideModel.java
NucleotideModelUtils.java
ReversibleNucleotide.java
RtREV.java
Tamura92.java
TamuraNei.java
Vt.java
Wag.java
postprocess
PluginParameters.java
Postprocess.java
PostprocessManager.java
Track.java
TreeVisualizer.java
gui
AlignmentGUI.java
CNetworkView.java
ColorGradient.java
DistanceGUI.java
EntropyGUI.java
InputGUI.java
LogLikelihoodTraceGUI.java
PPFoldGUI.java
StructAlignTraceGUI.java
StructureDetails.java
StructureGUI.java
treeviews
HorizontalCladogramTreeView.java
HorizontalPhylogramTreeView.java
NetworkTreeView.java
TreeView.java
VerticalPhylogramTreeView.java
plugins
ConsensusNetwork.java
ConsensusTreeVisualizer.java
CurrentAlignment.java
CurrentTreeVisualizer.java
Entropy.java
LogLikelihoodTrace.java
MpdAlignment.java
PPFold.java
RNAalifoldResult.java
Structure.java
TreeNode.java
VisualDistance.java
benchmarks
AlignmentSample.java
Benchmarks.java
Dataset.java
ExperimentalData.java
StatAlignResult.java
contree
CNetwork.java
CNetworkEdge.java
CNetworkNode.java
CNetworkPath.java
CNetworkSplit.java
CTMain.java
CTree.java
Cluster.java
TaxaMap.java
Utils.java
hash
HashEntry.java
HashTable.java
HashUtils.java
test
ConsensusNetworkTester.java
CorrectnessTester.java
EdgeLengthTester.java
TestNetwork.java
structalign
RmsdTrace.java
StructAlignTraceParameters.java
StructTrace.java
StructTreeVisualizer.java
utils
DisplayString.java
EntropyContainer.java
LogLikelihoodTraceContainer.java
Mapping.java
NewickParser.java
NewickParserException.java
RNAFoldingTools.java
RNAalifold.java
tests
McmcTest.java
ui
AboutDlg.java
ErrorMessage.java
HelpWindow.java
MainFrame.java
McmcSettingsDlg.java
OutputPreferences.java
RNASettingsDlg.java
ScrollAdapter.java
TextDlg.java
utils
BetaDistribution.java
GammaDistribution.java
Libraries.java
LinkFunction.java
NormalDistribution.java
Reversed.java
SimpleStats.java
package statalign.utils; public interface LinkFunction<T> { public abstract T f(T t); }