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

A

aboutMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
ActionEditor - Class in fr.orsay.lri.varna.components
 
ActionEditor(ActionListener) - Constructor for class fr.orsay.lri.varna.components.ActionEditor
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.components.VARNAConsole
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.views.VueBPList
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.views.VueBPType
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.views.VueColorMapStyle
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.views.VueLoadColorMapValues
 
actionPerformed(ActionEvent) - Method in class fr.orsay.lri.varna.views.VueStyleBP
 
ActionRenderer - Class in fr.orsay.lri.varna.components
 
ActionRenderer() - Constructor for class fr.orsay.lri.varna.components.ActionRenderer
 
adaptColorMapToValues(ModeleColorMap) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addAnnotationMenu(JMenu) - Method in class fr.orsay.lri.varna.views.VueMenu
 
addAnnotationMenu(JMenu, boolean) - Method in class fr.orsay.lri.varna.views.VueMenu
 
addBase(ModeleBase) - Method in class fr.orsay.lri.varna.models.BaseList
 
addBase(ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
addBase(int, ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
addBases(Collection<? extends ModeleBase>) - Method in class fr.orsay.lri.varna.models.BaseList
 
addBP(int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addBP(int, int, ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addBPAux(int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addBPAux(int, int, ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addBPToStructure(int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addBPToStructure(int, int, ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addBPToStructureUsingNumbers(int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
Adds a base pair to this RNA's structure.
addBPToStructureUsingNumbers(int, int, ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.RNA
Adds a base pair to this RNA's structure.
addChemProbAnnotation(ChemProbAnnotation) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addColor(double, Color) - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
addColorOptions(JMenu) - Method in class fr.orsay.lri.varna.views.VueMenu
add default color options to a menu
addConnection(int, Connection) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
addConnectionIfNecessary(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToXml
 
addCouple(int, int) - Method in class fr.orsay.lri.varna.models.rna.Mapping
 
addCouple(int, RNATemplate.RNATemplateElement) - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
Tell this mapping object that this base index and this element are mapped with each other.
addEdgeIfNecessary(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.MakeEdgeList
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.AddBPEdit
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.BasesShiftEdit
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixFlipEdit
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixRotateEdit
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.RemoveBPEdit
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.RotateRNAEdit
 
addEdit(UndoableEdit) - Method in class fr.orsay.lri.varna.models.VARNAEdits.SingleBaseMoveEdit
 
addHelixEmbedding(VARNASecDraw.HelixEmbedding, int) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
addHighlightRegion(HighlightRegionAnnotation) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addHighlightRegion(int, int, Color, Color, double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addHighlightRegion(int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addHighlightRegion(HighlightRegionAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addHighlightRegion(int, int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addHighlightRegion(int, int, Color, Color, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addPortion(VARNASecDraw.Portion) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.RNATree
 
addRNA(String, String) - Method in class fr.orsay.lri.varna.views.VueAboutPanel.AboutAnimator
 
addRNAListener(InterfaceVARNARNAListener) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addSelectionListener(InterfaceVARNASelectionListener) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addSelectionMenu(JMenuItem) - Method in class fr.orsay.lri.varna.views.VueMenu
 
addStrand(ModeleStrand) - Method in class fr.orsay.lri.varna.models.rna.StructureTemp
 
addTitle(String, boolean) - Method in class fr.orsay.lri.varna.views.VueMenu
 
addToSelection(Collection<? extends Integer>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addToSelection(int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addUndoableEditListener(UndoManager) - Method in class fr.orsay.lri.varna.views.VueUI
 
addVARNAListener(InterfaceVARNAListener) - Method in class fr.orsay.lri.varna.interfaces.InterfaceVARNAObservable
 
addVARNAListener(InterfaceVARNAListener) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
addVARNAListener(InterfaceVARNAListener) - Method in class fr.orsay.lri.varna.VARNAPanel
 
ajusteSpecificStrand(int) - Method in class fr.orsay.lri.varna.models.rna.Motif
 
ajusteStrand() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
algoOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ALGORITHM_CIRCULAR - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ALGORITHM_LINE - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ALGORITHM_MOTIF_VIEW - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ALGORITHM_NAVIEW - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ALGORITHM_RADIATE - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ALGORITHM_VARNA_VIEW - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
align(Tree<ValueType1>, Tree<ValueType2>) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign
Align T1 with T2, computing both the distance and the alignment.
align() - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
AlignedNode<OriginalNodeValueType1,OriginalNodeValueType2> - Class in fr.orsay.lri.varna.models.treealign
The type of node values in an alignment.
AlignedNode() - Constructor for class fr.orsay.lri.varna.models.treealign.AlignedNode
 
alignment - Variable in class fr.orsay.lri.varna.models.treealign.ExampleDistance3.SequenceAlignResult
 
alignment - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlignResult
 
alignRNAWithTemplate(RNA, RNATemplate) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
Align the given RNA with the given RNA template.
alignSequenceNodes(RNANodeValue2, RNANodeValue2) - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3
Align two sequences contained in nodes.
alignSequences(char[], char[]) - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3
Align sequences using the Needleman-Wunsch algorithm.
ALL_MODE - Static variable in class fr.orsay.lri.varna.views.VueBases
for all bases
allMode() - Method in class fr.orsay.lri.varna.views.VueBases
 
alterColor(Color, int) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
angle - Variable in class fr.orsay.lri.varna.models.naView.Connection
 
angle(Point2D.Double, Point2D.Double, Point2D.Double) - Static method in class fr.orsay.lri.varna.models.rna.RNA
 
angleFromVector(Point2D.Double) - Static method in class fr.orsay.lri.varna.models.rna.RNA
Compute the angle made by a vector.
angleFromVector(double, double) - Static method in class fr.orsay.lri.varna.models.rna.RNA
 
angleinc - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
annotationMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
annotationsOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
AnnotationTableModel - Class in fr.orsay.lri.varna.components
 
AnnotationTableModel(ArrayList<Object>) - Constructor for class fr.orsay.lri.varna.components.AnnotationTableModel
 
ANUM - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
applyAnnotations(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
Format: string:[type=[H|B|L|P]|x=double|y=double|anchor=int|size=int|color=Color];
applyAuxBPs(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyBasesCustomStyles(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyBasesStyle(String) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyBasesStyleOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyBPs(ArrayList<ModeleBP>) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
applyBPsCustomStyles(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyChemProbs(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyColorMapStyle(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyColorMapValues(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyFont() - Method in class fr.orsay.lri.varna.views.VueAnnotation
 
applyHighlightRegion(VARNAPanel) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
applyStruct(int[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
applyStyle(String) - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
applyStyleOnBases(ArrayList<Integer>, ModeleStyleBase) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
applyValues(String) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ArcCommand - Class in fr.orsay.lri.varna.models.export
 
ArcCommand(Point2D.Double, double, double, double, double) - Constructor for class fr.orsay.lri.varna.models.export.ArcCommand
 
assignParameters(String) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
assignParameters(String) - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
attributes - Variable in class fr.orsay.lri.varna.views.PrintTestFrame
 
autoAnnotateHelices() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
autoAnnotateInteriorLoops() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
autoAnnotateStrandEnds() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
autoAnnotateTerminalLoops() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
autoHelicesOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
autoInteriorLoopsOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
autoTerminalLoopsOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
auxBPsOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 

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