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 _

P

P0 - Variable in class fr.orsay.lri.varna.models.CubicBezierCurve
The four points defining the curve.
P1 - Variable in class fr.orsay.lri.varna.models.CubicBezierCurve
The four points defining the curve.
P2 - Variable in class fr.orsay.lri.varna.models.CubicBezierCurve
The four points defining the curve.
P3 - Variable in class fr.orsay.lri.varna.models.CubicBezierCurve
The four points defining the curve.
paginateStructure() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
paintComponent(Graphics) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
paintComponent(Graphics) - Method in class fr.orsay.lri.varna.components.ReorderableJList.ReorderableListCellRenderer
 
paintComponent(Graphics) - Method in class fr.orsay.lri.varna.VARNAPanel
 
paintComponent(Graphics, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
paintComponent(Graphics) - Method in class fr.orsay.lri.varna.views.PrintPanel
 
PALETTE_HEIGHT - Static variable in class fr.orsay.lri.varna.components.GradientEditorPanel
 
panel - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
panel - Variable in class fr.orsay.lri.varna.views.VueBorder
 
panel - Variable in class fr.orsay.lri.varna.views.VueBPHeightIncrement
 
panel - Variable in class fr.orsay.lri.varna.views.VueBPThickness
 
panel - Variable in class fr.orsay.lri.varna.views.VueBPType
 
panel - Variable in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
panel - Variable in class fr.orsay.lri.varna.views.VueFont
 
panel - Variable in class fr.orsay.lri.varna.views.VueGlobalRotation
 
panel - Variable in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
panel - Variable in class fr.orsay.lri.varna.views.VueJPEG
 
panel - Variable in class fr.orsay.lri.varna.views.VueManualInput
 
panel - Variable in class fr.orsay.lri.varna.views.VueNumPeriod
 
panel - Variable in class fr.orsay.lri.varna.views.VueSpaceBetweenBases
 
panel - Variable in class fr.orsay.lri.varna.views.VueStyleBP
 
panel - Variable in class fr.orsay.lri.varna.views.VueZoom
 
panelToLogicPoint(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
PARAM_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
PARAM_EDGE3 - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
PARAM_EDGE5 - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
PARAM_INNER_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
PARAM_NUMBER_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
PARAM_OUTLINE_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
PARAM_STERICITY - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
PARAM_TEXT_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
PARAM_THICKNESS - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
parseColorMap(String) - Static method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
parseDimension(String) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
parseHighlightRegionAnnotation(String, VARNAPanel) - Static method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
parseStruct(String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
periodNumOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
phrase - Variable in class fr.orsay.lri.varna.views.Imprimer
 
placeTerminalLoop(ArrayList<ModeleBase>, RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
planarize(int[]) - Static method in class fr.orsay.lri.varna.models.rna.RNAMLParser
Computes and returns a maximal planar subset of the current structure.
planarize(ArrayList<ModeleBP>, ArrayList<ModeleBP>, ArrayList<ModeleBP>, int) - Static method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
pointFromXml(Element) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.LoadFromXml
 
points - Variable in class fr.orsay.lri.varna.models.CubicBezierCurve
The n+1 points between the n lines.
PolygonCommand - Class in fr.orsay.lri.varna.models.export
 
PolygonCommand(Point2D.Double[], double) - Constructor for class fr.orsay.lri.varna.models.export.PolygonCommand
 
pos3 - Variable in class fr.orsay.lri.varna.models.rna.RNAMLParser.BPTemp
 
pos3 - Variable in class fr.orsay.lri.varna.models.rna.RNAMLParser.HelixTemp
 
pos5 - Variable in class fr.orsay.lri.varna.models.rna.RNAMLParser.BPTemp
 
pos5 - Variable in class fr.orsay.lri.varna.models.rna.RNAMLParser.HelixTemp
 
POSITION - Static variable in class fr.orsay.lri.varna.models.annotations.TextAnnotation
if the annoted text is located by a static position
position - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
positionInHelix - Variable in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair
The position (in the 5' to 3' order) of this base pair in the original helix.
positionInHelix - Variable in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBrokenBasePair
The position (in the 5' to 3' order) of this base in the original helix.
positionneSpecificStrand(int, double) - Method in class fr.orsay.lri.varna.models.rna.Motif
Set the coordinates of all bases for one strand in particular
positionneStrand() - Method in class fr.orsay.lri.varna.models.rna.Motif
Set the coordinates of all bases for all strands in the list of strands
postProcess() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
predrawTree(double, double, VARNASecDraw.RNATree, double, RNA, VARNASecDraw.HelixEmbedding, ArrayList<VARNASecDraw.HelixEmbedding>) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw
 
prev - Variable in class fr.orsay.lri.varna.models.naView.Radloop
 
print(Graphics, PageFormat, int) - Method in class fr.orsay.lri.varna.views.Imprimer
 
print(Graphics, PageFormat, int) - Method in class fr.orsay.lri.varna.views.PrintPanel
 
printIntArray(int[]) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
Print an integer array.
printIntArrayList(ArrayList<Integer>) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
Print an integer ArrayList.
printMapping(RNATemplateMapping, RNATemplate, String) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
 
PrintPanel - Class in fr.orsay.lri.varna.views
This panel generates a 2D graphics image for screen display and printing.
PrintPanel() - Constructor for class fr.orsay.lri.varna.views.PrintPanel
 
printShortMatrix(short[][]) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
Print an matrix of shorts.
PrintTest - Class in fr.orsay.lri.varna.views
This program demonstrates how to print 2D graphics
PrintTest() - Constructor for class fr.orsay.lri.varna.views.PrintTest
 
PrintTestFrame - Class in fr.orsay.lri.varna.views
This frame shows a panel with 2D graphics and buttons to print the graphics and to set up the page format.
PrintTestFrame() - Constructor for class fr.orsay.lri.varna.views.PrintTestFrame
 
project(Point2D.Double, Point2D.Double, Point2D.Double) - Method in class fr.orsay.lri.varna.views.VueUI
 
propertyChange(PropertyChangeEvent) - Method in class fr.orsay.lri.varna.views.VueColorMapStyle
 
PSArc(double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSArc(double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSBBox(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSClosePath() - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSExport - Class in fr.orsay.lri.varna.models.export
 
PSExport() - Constructor for class fr.orsay.lri.varna.models.export.PSExport
 
PSFill() - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSLineTo(double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSMacros() - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSMoveTo(double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSNewPath() - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSRLineTo(double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSSetColor(Color) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSSetFont(int, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSSetLineWidth(double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSShow() - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSStroke() - Method in class fr.orsay.lri.varna.models.export.PSExport
 
PSText(String) - Method in class fr.orsay.lri.varna.models.export.PSExport
 

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 _