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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
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
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All Classes
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C
D
E
F
G
H
I
K
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M
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