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I
i
- Variable in class fr.orsay.lri.varna.models.treealign.
RNATree.ConvertToTree
importSession(String)
- Static method in class fr.orsay.lri.varna.
VARNAPanel
importSession(InputStream, String)
- Static method in class fr.orsay.lri.varna.
VARNAPanel
imprimer()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Imprimer
- Class in
fr.orsay.lri.varna.views
Imprimer(String)
- Constructor for class fr.orsay.lri.varna.views.
Imprimer
in
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateUnpairedSequence
The helixes connected on both sides.
in1
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateHelix
If we go through all bases of the RNA from first to last, we will pass twice through this helix.
in1Is
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateHelix
For an helix, tells us whether IN1/OUT1 is the 5' strand (the first strand we meet if we follow the RNA sequence) or the 3' strand (the second we meet if we follow the RNA sequence).
in2
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateHelix
If we go through all bases of the RNA from first to last, we will pass twice through this helix.
infoBasesExtracted()
- Method in class fr.orsay.lri.varna.models.naView.
NAView
infoBasesMate()
- Method in class fr.orsay.lri.varna.models.naView.
NAView
infoRegions()
- Method in class fr.orsay.lri.varna.models.naView.
NAView
infoRoot()
- Method in class fr.orsay.lri.varna.models.naView.
NAView
infoStructure(ArrayList<Integer>)
- Method in class fr.orsay.lri.varna.models.naView.
NAView
init()
- Method in class fr.orsay.lri.varna.components.
VARNAConsole
init()
- Method in class fr.orsay.lri.varna.models.rna.
RNA
init()
- Method in class fr.orsay.lri.varna.
VARNAPanel
init()
- Method in class fr.orsay.lri.varna.views.
VueAboutPanel
init()
- Method in class fr.orsay.lri.varna.views.
VueBaseValues
init()
- Method in class fr.orsay.lri.varna.views.
VueBPList
init()
- Method in class fr.orsay.lri.varna.views.
VueColorMapStyle
init()
- Method in class fr.orsay.lri.varna.views.
VueFont
init()
- Method in class fr.orsay.lri.varna.views.
VueLoadColorMapValues
initArrays()
- Method in class fr.orsay.lri.varna.models.templates.
RNATemplate.RemovePseudoKnots
initChecker(ModeleStrand)
- Method in class fr.orsay.lri.varna.models.rna.
Motif
initCheckerAll()
- Method in class fr.orsay.lri.varna.models.rna.
Motif
initInterv()
- Method in class fr.orsay.lri.varna.models.rna.
Motif
initStrand()
- Method in class fr.orsay.lri.varna.models.rna.
Motif
initValues()
- Method in class fr.orsay.lri.varna.models.
VARNAConfigLoader
innerColor
- Variable in class fr.orsay.lri.varna.components.
BaseTableModel
input
- Variable in class fr.orsay.lri.varna.views.
VueLoadColorMapValues
insert(RNANodeValueTemplate)
- Method in class fr.orsay.lri.varna.models.templates.
RNANodeValue2TemplateDistance
inTangentVectorAngle
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateUnpairedSequence
The sequence is drawn along a cubic Bezier curve.
inTangentVectorLength
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateUnpairedSequence
The sequence is drawn along a cubic Bezier curve.
intArrayFromList(List<Integer>)
- Static method in class fr.orsay.lri.varna.models.templates.
RNATemplateAlign
Convert a list of integers into an array of integers.
intensity
- Variable in class fr.orsay.lri.varna.views.
VueChemProbAnnotation
InterfaceParameterLoader
- Interface in
fr.orsay.lri.varna.interfaces
InterfaceVARNAListener
- Interface in
fr.orsay.lri.varna.interfaces
Observable design pattern
InterfaceVARNAObservable
- Class in
fr.orsay.lri.varna.interfaces
Observable design pattern
InterfaceVARNAObservable()
- Constructor for class fr.orsay.lri.varna.interfaces.
InterfaceVARNAObservable
InterfaceVARNARNAListener
- Interface in
fr.orsay.lri.varna.interfaces
InterfaceVARNASelectionListener
- Interface in
fr.orsay.lri.varna.interfaces
intervDroite
- Variable in class fr.orsay.lri.varna.models.rna.
ExtendedMB
intervDroite
- Variable in class fr.orsay.lri.varna.models.rna.
ModeleBase
intervGauche
- Variable in class fr.orsay.lri.varna.models.rna.
ExtendedMB
intervGauche
- Variable in class fr.orsay.lri.varna.models.rna.
ModeleBase
invmap
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplateMapping
isAutoCentered()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Returns the current state of auto centering mode.
isBent()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBPStyle
isBordered
- Variable in class fr.orsay.lri.varna.components.
ColorRenderer
isBroken()
- Method in class fr.orsay.lri.varna.models.naView.
Connection
isCanonical()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBP
isCanonicalAU()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBP
isCanonicalGC()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBP
isCellEditable(EventObject)
- Method in class fr.orsay.lri.varna.components.
ActionEditor
isCellEditable(int, int)
- Method in class fr.orsay.lri.varna.components.
AnnotationTableModel
isCellEditable(int, int)
- Method in class fr.orsay.lri.varna.components.
BaseTableModel
isCellEditable(int, int)
- Method in class fr.orsay.lri.varna.views.
VueBaseValues.ValueTableModel
isCellEditable(int, int)
- Method in class fr.orsay.lri.varna.views.
VueBPList.BPTableModel
isChooseColor(int, int)
- Method in class fr.orsay.lri.varna.components.
GradientEditorPanel
isCIS()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBP
isComparisonMode()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Checks if the current mode is the "comparison" mode
isConnected()
- Method in class fr.orsay.lri.varna.models.templates.
RNATemplate
Tells whether the template elements are all connected, ie.
isConnected()
- Method in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateElement.EdgeEndPoint
Tells whether this endpoint is connected with an edge to an other endpoint.
isCustomColored()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBPStyle
isDataFlavorSupported(DataFlavor)
- Method in class fr.orsay.lri.varna.components.
ReorderableJList.RJLTransferable
isEmpty()
- Method in class fr.orsay.lri.varna.models.rna.
StructureTemp
isEmpty()
- Method in class fr.orsay.lri.varna.models.templates.
RNATemplate
Tells whether the template contains elements.
isErrorsOn()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Checks whether errors are to be displayed
isExtracted()
- Method in class fr.orsay.lri.varna.models.naView.
Base
isExtruded()
- Method in class fr.orsay.lri.varna.models.naView.
Connection
isFlipped()
- Method in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateHelix
isInSelection(int)
- Method in class fr.orsay.lri.varna.
VARNAPanel
isInterpolationInProgress()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Checks whether an interpolated transition bewteen two RNAs is occurring.
isLastItem
- Variable in class fr.orsay.lri.varna.components.
ReorderableJList.ReorderableListCellRenderer
isLimited()
- Method in class fr.orsay.lri.varna.views.
VueAnnotation
isMark()
- Method in class fr.orsay.lri.varna.models.naView.
Loop
isModifiable()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Returns current modification status
isNewAnnotation()
- Method in class fr.orsay.lri.varna.views.
VueAnnotation
isNull()
- Method in class fr.orsay.lri.varna.models.naView.
Connection
isNumberDrawn(ModeleBase, int)
- Method in class fr.orsay.lri.varna.models.rna.
RNA
isOut()
- Method in class fr.orsay.lri.varna.models.annotations.
ChemProbAnnotation
isOutOfFrame()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Checks whether the drawn RNA is too large to be displayed, allowing for shifting mouse interactions.
isRemove(int, int)
- Method in class fr.orsay.lri.varna.components.
GradientEditorPanel
isSelfCrossing(int[])
- Static method in class fr.orsay.lri.varna.models.rna.
RNAMLParser
isSelfCrossing()
- Method in class fr.orsay.lri.varna.models.templates.
RNATemplate.RemovePseudoKnots
Tells whether there is a pseudoknot.
isSingleNode()
- Method in class fr.orsay.lri.varna.models.treealign.
RNANodeValue2
isTargetCell
- Variable in class fr.orsay.lri.varna.components.
ReorderableJList.ReorderableListCellRenderer
isTRANS()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBP
isWobbleUG()
- Method in class fr.orsay.lri.varna.models.rna.
ModeleBP
itemStateChanged(ItemEvent)
- Method in class fr.orsay.lri.varna.views.
VueChemProbAnnotation
itemStateChanged(ItemEvent)
- Method in class fr.orsay.lri.varna.views.
VueColorMapStyle
iter
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.ConvertToTree
iter
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNAIterator
iterator()
- Method in class fr.orsay.lri.varna.models.treealign.
Tree
Overview
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