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 _

V

value - Variable in class fr.orsay.lri.varna.models.treealign.Tree
 
VALUE_CIS - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
VALUE_HOOGSTEEN - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
VALUE_SUGAR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
VALUE_TRANS - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
VALUE_WATSON_CRICK - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide.STATE_SPECIAL_CHARS_STATES
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.rna.ModeleBP.Edge
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.rna.ModeleBP.Stericity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.rna.ModeleColorMap.NamedColorMapTypes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.templates.RNATemplate.In1Is
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.treealign.RNANodeValue.Origin
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.orsay.lri.varna.views.VueBPList.Actions
Returns the enum constant of this type with the specified name.
values() - Static method in enum fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide.STATE_SPECIAL_CHARS_STATES
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.models.rna.ModeleBP.Edge
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.models.rna.ModeleBP.Stericity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.models.rna.ModeleColorMap.NamedColorMapTypes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.models.templates.RNATemplate.In1Is
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.models.treealign.RNANodeValue.Origin
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.TreeData
Values of nodes.
values() - Static method in enum fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.orsay.lri.varna.views.VueBPList.Actions
Returns an array containing the constants of this enum type, in the order they are declared.
VARNA_SESSION_EXTENSION - Static variable in class fr.orsay.lri.varna.VARNAPanel
 
VARNAConfig - Class in fr.orsay.lri.varna.models
 
VARNAConfig() - Constructor for class fr.orsay.lri.varna.models.VARNAConfig
 
VARNAConfig.BP_STYLE - Enum in fr.orsay.lri.varna.models
Enum types and internal classes
VARNAConfig.BP_STYLE() - Constructor for enum fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE
 
VARNAConfigLoader - Class in fr.orsay.lri.varna.models
An RNA 2d Panel demo applet
VARNAConfigLoader(InterfaceParameterLoader) - Constructor for class fr.orsay.lri.varna.models.VARNAConfigLoader
 
VARNAConsole - Class in fr.orsay.lri.varna.components
 
VARNAConsole(VARNAPanel) - Constructor for class fr.orsay.lri.varna.components.VARNAConsole
 
VARNAEdits - Class in fr.orsay.lri.varna.models
 
VARNAEdits() - Constructor for class fr.orsay.lri.varna.models.VARNAEdits
 
VARNAEdits.AddBPEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.AddBPEdit(int, int, ModeleBP, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.AddBPEdit
 
VARNAEdits.BasesShiftEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.BasesShiftEdit(ArrayList<Integer>, double, double, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.BasesShiftEdit
 
VARNAEdits.HelixFlipEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.HelixFlipEdit(Point, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.HelixFlipEdit
 
VARNAEdits.HelixRotateEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.HelixRotateEdit(double, double, double, double, Point, Point, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.HelixRotateEdit
 
VARNAEdits.RedrawEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.RedrawEdit(VARNAPanel, boolean) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
VARNAEdits.RedrawEdit(int, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
VARNAEdits.RedrawEdit(int, VARNAPanel, boolean) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
VARNAEdits.RemoveBPEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.RemoveBPEdit(int, int, ModeleBP, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.RemoveBPEdit
 
VARNAEdits.RotateRNAEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.RotateRNAEdit(double, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.RotateRNAEdit
 
VARNAEdits.SingleBaseMoveEdit - Class in fr.orsay.lri.varna.models
 
VARNAEdits.SingleBaseMoveEdit(int, double, double, VARNAPanel) - Constructor for class fr.orsay.lri.varna.models.VARNAEdits.SingleBaseMoveEdit
 
VARNAPanel - Class in fr.orsay.lri.varna
The RNA 2D Panel is a lightweight component that allows for an automatic basic drawing of an RNA secondary structures.
VARNAPanel() - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates an RNA 2D panel with initially displays the empty structure.
VARNAPanel(String, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates an RNA 2D panel, and creates and displays an RNA coupled with its secondary structure formatted as a well-balanced parenthesis with dots word (DBN format).
VARNAPanel(String, String, int) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates a VARNAPanel instance, and creates and displays an RNA coupled with its secondary structure formatted as a well-balanced parenthesis with dots word (DBN format).
VARNAPanel(Reader) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 
VARNAPanel(Reader, int) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 
VARNAPanel(Reader, int, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 
VARNAPanel(RNA) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates a VARNAPanel instance, and displays an RNA.
VARNAPanel(String, String, int, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates a VARNAPanel instance, and creates and displays an RNA coupled with its secondary structure formatted as a well-balanced parenthesis with dots word (DBN format).
VARNAPanel(String, String, String, String, int, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 
VARNAPoint - Class in fr.orsay.lri.varna.models.rna
 
VARNAPoint() - Constructor for class fr.orsay.lri.varna.models.rna.VARNAPoint
 
VARNAPoint(double, double) - Constructor for class fr.orsay.lri.varna.models.rna.VARNAPoint
 
VARNAPoint(Point2D.Double) - Constructor for class fr.orsay.lri.varna.models.rna.VARNAPoint
 
VARNASecDraw - Class in fr.orsay.lri.varna.models.rna
 
VARNASecDraw() - Constructor for class fr.orsay.lri.varna.models.rna.VARNASecDraw
 
VARNASecDraw.HelixEmbedding - Class in fr.orsay.lri.varna.models.rna
 
VARNASecDraw.HelixEmbedding(Point2D.Double, VARNASecDraw.PairedPortion, RNA, VARNASecDraw.HelixEmbedding) - Constructor for class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
VARNASecDraw.PairedPortion - Class in fr.orsay.lri.varna.models.rna
 
VARNASecDraw.PairedPortion(int, int, int, VARNASecDraw.RNATree) - Constructor for class fr.orsay.lri.varna.models.rna.VARNASecDraw.PairedPortion
 
VARNASecDraw.Portion - Class in fr.orsay.lri.varna.models.rna
 
VARNASecDraw.Portion() - Constructor for class fr.orsay.lri.varna.models.rna.VARNASecDraw.Portion
 
VARNASecDraw.RNATree - Class in fr.orsay.lri.varna.models.rna
 
VARNASecDraw.RNATree() - Constructor for class fr.orsay.lri.varna.models.rna.VARNASecDraw.RNATree
 
VARNASecDraw.UnpairedPortion - Class in fr.orsay.lri.varna.models.rna
 
VARNASecDraw.UnpairedPortion(int, int) - Constructor for class fr.orsay.lri.varna.models.rna.VARNASecDraw.UnpairedPortion
 
vectorAngleFromXml(Element) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.LoadFromXml
 
vectorLengthFromXml(Element) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.LoadFromXml
 
vertex3 - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
Position of the end (at the "out" endpoint) of the line.
vertex5 - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
Position of the begginning (at the "in" endpoint) of the line.
vertexIterator() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Iterates over the elements edge endpoints of the template, in the sequence order.
viewMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
VIRTUAL_LOOP_RADIUS - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
VueAboutPanel - Class in fr.orsay.lri.varna.views
 
VueAboutPanel() - Constructor for class fr.orsay.lri.varna.views.VueAboutPanel
 
VueAboutPanel.AboutAnimator - Class in fr.orsay.lri.varna.views
 
VueAboutPanel.AboutAnimator(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueAboutPanel.AboutAnimator
 
VueAnnotation - Class in fr.orsay.lri.varna.views
annoted text view for edition
VueAnnotation(VARNAPanel, boolean) - Constructor for class fr.orsay.lri.varna.views.VueAnnotation
creates a view for a new annoted text
VueAnnotation(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueAnnotation
creates a view for a new annoted text, without limited option
VueAnnotation(VARNAPanel, int, int) - Constructor for class fr.orsay.lri.varna.views.VueAnnotation
creates a view for a new annoted text at a given position, without limited option
VueAnnotation(VARNAPanel, int, int, boolean) - Constructor for class fr.orsay.lri.varna.views.VueAnnotation
creates a view for a new annoted text at a given position, without limited option
VueAnnotation(VARNAPanel, TextAnnotation, boolean) - Constructor for class fr.orsay.lri.varna.views.VueAnnotation
creates a view for an annoted text, without limited option
VueAnnotation(VARNAPanel, TextAnnotation, boolean, boolean) - Constructor for class fr.orsay.lri.varna.views.VueAnnotation
creates a view for an annoted text
VueBases - Class in fr.orsay.lri.varna.views
 
VueBases(VARNAPanel, int) - Constructor for class fr.orsay.lri.varna.views.VueBases
 
VueBaseValues - Class in fr.orsay.lri.varna.views
 
VueBaseValues(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueBaseValues
 
VueBaseValues.ValueTableModel - Class in fr.orsay.lri.varna.views
 
VueBaseValues.ValueTableModel() - Constructor for class fr.orsay.lri.varna.views.VueBaseValues.ValueTableModel
 
VueBorder - Class in fr.orsay.lri.varna.views
 
VueBorder(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueBorder
 
VueBPHeightIncrement - Class in fr.orsay.lri.varna.views
 
VueBPHeightIncrement(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueBPHeightIncrement
 
VueBPList - Class in fr.orsay.lri.varna.views
 
VueBPList(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueBPList
 
VueBPList.Actions - Enum in fr.orsay.lri.varna.views
 
VueBPList.Actions() - Constructor for enum fr.orsay.lri.varna.views.VueBPList.Actions
 
VueBPList.BPTableModel - Class in fr.orsay.lri.varna.views
 
VueBPList.BPTableModel() - Constructor for class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
VueBPThickness - Class in fr.orsay.lri.varna.views
 
VueBPThickness(VARNAPanel, ArrayList<ModeleBP>) - Constructor for class fr.orsay.lri.varna.views.VueBPThickness
 
VueBPType - Class in fr.orsay.lri.varna.views
 
VueBPType(VARNAPanel, ModeleBP) - Constructor for class fr.orsay.lri.varna.views.VueBPType
 
VueChemProbAnnotation - Class in fr.orsay.lri.varna.views
 
VueChemProbAnnotation(VARNAPanel, ChemProbAnnotation) - Constructor for class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
VueColorMapStyle - Class in fr.orsay.lri.varna.views
 
VueColorMapStyle(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueColorMapStyle
 
vueFont - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
VueFont - Class in fr.orsay.lri.varna.views
 
VueFont(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueFont
 
VueFont(Font) - Constructor for class fr.orsay.lri.varna.views.VueFont
 
VueGlobalRotation - Class in fr.orsay.lri.varna.views
 
VueGlobalRotation(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueGlobalRotation
 
VueHighlightRegionEdit - Class in fr.orsay.lri.varna.views
 
VueHighlightRegionEdit(VARNAPanel, HighlightRegionAnnotation) - Constructor for class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
VueJPEG - Class in fr.orsay.lri.varna.views
 
VueJPEG(boolean, boolean) - Constructor for class fr.orsay.lri.varna.views.VueJPEG
 
VueListeAnnotations - Class in fr.orsay.lri.varna.views
a view for all annoted texts on the VARNAPanel
VueListeAnnotations(VARNAPanel, int) - Constructor for class fr.orsay.lri.varna.views.VueListeAnnotations
creates the view
VueLoadColorMapValues - Class in fr.orsay.lri.varna.views
 
VueLoadColorMapValues(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueLoadColorMapValues
 
VueManualInput - Class in fr.orsay.lri.varna.views
 
VueManualInput(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueManualInput
 
VueMenu - Class in fr.orsay.lri.varna.views
 
VueMenu(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueMenu
 
VueNumPeriod - Class in fr.orsay.lri.varna.views
 
VueNumPeriod(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueNumPeriod
 
VueSpaceBetweenBases - Class in fr.orsay.lri.varna.views
 
VueSpaceBetweenBases(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueSpaceBetweenBases
 
VueStyleBP - Class in fr.orsay.lri.varna.views
 
VueStyleBP(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueStyleBP
 
VueUI - Class in fr.orsay.lri.varna.views
 
VueUI(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueUI
 
VueVARNAGraphics - Interface in fr.orsay.lri.varna.models.export
 
VueZoom - Class in fr.orsay.lri.varna.views
 
VueZoom(VARNAPanel) - Constructor for class fr.orsay.lri.varna.views.VueZoom
 

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 _