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C

calculLoop() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
calculLoopHelix() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
callFireEditingStopped() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
canBePartOfABrokenHelix(RNANodeValue2) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
 
canBePartOfAnHelix(RNANodeValue2) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
 
canBePartOfASequence(RNANodeValue2) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
 
cancelChanges() - Method in class fr.orsay.lri.varna.views.VueBaseValues
 
cancelChanges() - Method in class fr.orsay.lri.varna.views.VueBPList
 
cancelChanges() - Method in class fr.orsay.lri.varna.views.VueColorMapStyle
 
cancelMove(int) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.AddBPEdit
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.BasesShiftEdit
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixFlipEdit
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixRotateEdit
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RemoveBPEdit
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RotateRNAEdit
 
canRedo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.SingleBaseMoveEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.AddBPEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.BasesShiftEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixFlipEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixRotateEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RemoveBPEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RotateRNAEdit
 
canUndo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.SingleBaseMoveEdit
 
canvas - Variable in class fr.orsay.lri.varna.views.PrintTestFrame
 
caption - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
A string displayed on the helix.
characters(char[], int, int) - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
checkIsValidTemplate() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Checks whether this template is a valid RNA template, ie.
checkTranslation() - Method in class fr.orsay.lri.varna.VARNAPanel
Checks if the current translation doesn't "kick" the whole RNA out of the panel, and corrects the situation if necessary.
CHEM_PROB_ARROW_HEIGHT - Variable in class fr.orsay.lri.varna.models.rna.RNA
 
CHEM_PROB_ARROW_THICKNESS - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
CHEM_PROB_ARROW_WIDTH - Variable in class fr.orsay.lri.varna.models.rna.RNA
 
CHEM_PROB_BASE_LENGTH - Variable in class fr.orsay.lri.varna.models.rna.RNA
 
CHEM_PROB_DIST - Variable in class fr.orsay.lri.varna.models.rna.RNA
 
CHEM_PROB_DOT_RADIUS - Variable in class fr.orsay.lri.varna.models.rna.RNA
 
CHEM_PROB_PIN_SEMIDIAG - Variable in class fr.orsay.lri.varna.models.rna.RNA
 
CHEM_PROB_TRIANGLE_WIDTH - Variable in class fr.orsay.lri.varna.models.rna.RNA
 
ChemProbAnnotation - Class in fr.orsay.lri.varna.models.annotations
 
ChemProbAnnotation(ModeleBase, ModeleBase, String) - Constructor for class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
ChemProbAnnotation(ModeleBase, ModeleBase) - Constructor for class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
ChemProbAnnotation(ModeleBase, ModeleBase, double) - Constructor for class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
ChemProbAnnotation(ModeleBase, ModeleBase, ChemProbAnnotation.ChemProbAnnotationType) - Constructor for class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
ChemProbAnnotation(ModeleBase, ModeleBase, ChemProbAnnotation.ChemProbAnnotationType, double) - Constructor for class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
ChemProbAnnotation.ChemProbAnnotationType - Enum in fr.orsay.lri.varna.models.annotations
 
ChemProbAnnotation.ChemProbAnnotationType() - Constructor for enum fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType
 
chemProbOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
children - Variable in class fr.orsay.lri.varna.models.treealign.Tree
 
children - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.TreeData
children[i] is the array of children (as indexes in nodes) of i (an index in nodes)
chooseNextMove() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
CircleCommand - Class in fr.orsay.lri.varna.models.export
 
CircleCommand(Point2D.Double, double, double) - Constructor for class fr.orsay.lri.varna.models.export.CircleCommand
 
classicIterator() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Iterates over all elements (each endpoint is given only once) in an arbitrary order.
clear() - Method in class fr.orsay.lri.varna.models.BaseList
 
clearAnnotations() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
clearListStrands() - Method in class fr.orsay.lri.varna.models.rna.StructureTemp
 
clearSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
Stops highlighting bases
clone() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
clone() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
clone() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
clone a TextAnnotation
clone() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
clone() - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
clone() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
clone() - Method in class fr.orsay.lri.varna.models.VARNAConfig
 
color - Variable in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
colorButton - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
colorChooser - Variable in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
colorClassesMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
ColorCommand - Class in fr.orsay.lri.varna.models.export
 
ColorCommand(Color) - Constructor for class fr.orsay.lri.varna.models.export.ColorCommand
 
colorMapCaptionOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
colorMapDefOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
colorMapOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
ColorRenderer - Class in fr.orsay.lri.varna.components
 
ColorRenderer(boolean) - Constructor for class fr.orsay.lri.varna.components.ColorRenderer
 
columnNames - Variable in class fr.orsay.lri.varna.components.AnnotationTableModel
 
columnNames - Variable in class fr.orsay.lri.varna.components.BaseTableModel
 
columns - Variable in class fr.orsay.lri.varna.views.VueBaseValues
 
columns - Variable in class fr.orsay.lri.varna.views.VueBPList
 
compareTo(ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
compareTo(ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
comparisonModeOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
computeAlignment(double[][], int[][], char[], char[]) - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3
 
computeAlignment() - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
computeAlignmentP1(int, int, int, int, int, int, int) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
computeAngle(Point2D.Double, Point2D.Double) - Static method in class fr.orsay.lri.varna.views.VueUI
 
computeArcCenter(double, double) - Static method in class fr.orsay.lri.varna.models.rna.RNA.ComputeArcCenter
Given an arc length (l) and segment length (delta) of the arc, find where to put the center, returned as a position of the perpendicular bisector of the segment.
computeBezierTangentVectorTarget(RNATemplate.RNATemplateElement.EdgeEndPoint, Point2D.Double, Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
A cubic Bezier curve can be defined by 4 points, see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves For each of the curve end points, there is the last/first point of the curve and a point which gives the direction and length of the tangent vector on that side.
computeData() - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
 
computeDegree() - Method in class fr.orsay.lri.varna.models.treealign.Tree
Compute the tree degree, ie.
computeExcentricUnitVector(int, Point2D.Double[], Point2D.Double[]) - Method in class fr.orsay.lri.varna.VARNAPanel
 
computeForestAlignment(int, int, int, int, int, int) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
Align F1[i_s,i_p] with F2[j_t,j_q].
computeHelixEndPointDirections(RNATemplate.RNATemplateElement.EdgeEndPoint, Point2D.Double, Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
IN: Argument helixEndPoint is an IN argument (will be read), and must contain an helix edge endpoint.
computeHelixRealLength(int[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
Compute helix actual length (as drawHelixLikeTemplateHelix() would draw it).
computeHelixTemplateLength(RNATemplate.RNATemplateHelix) - Method in class fr.orsay.lri.varna.models.rna.RNA
Get helix length in template.
computeHelixTranslations(Tree<RNANodeValueTemplate>, Map<RNATemplate.RNATemplateHelix, Point2D.Double>, RNATemplateMapping, Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
computeHelixTranslations(Tree<RNANodeValueTemplate>, RNATemplateMapping) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
computeIn1Is() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
For each helix, compute the in1Is field.
computeLengthIncreaseDelta(int[], RNATemplate.RNATemplateHelix) - Method in class fr.orsay.lri.varna.models.rna.RNA
Compute (actual helix vector - helix vector in template).
computeLengthIncreaseFactor(int[], RNATemplate.RNATemplateHelix) - Method in class fr.orsay.lri.varna.models.rna.RNA
Compute (actual helix length / helix length in template).
computeSequence() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
In case of multiple nodes, return the sequence of nucleotides.
computeTemplateHelixVectors(RNATemplate.RNATemplateHelix, Point2D.Double, Point2D.Double, Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
Compute helix interesting vectors from template helix.
computeTreeAlignment(int, int) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
config - Variable in class fr.orsay.lri.varna.models.FullBackup
 
configMenuItem(JMenuItem, String, String, Container) - Method in class fr.orsay.lri.varna.views.VueMenu
 
configMenuItem(JMenuItem, String, String, Container, boolean) - Method in class fr.orsay.lri.varna.views.VueMenu
 
connect(RNATemplate.RNATemplateElement.EdgeEndPoint, RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.LoadFromXml
 
connected_connection(Connection, Connection) - Method in class fr.orsay.lri.varna.models.naView.NAView
Determines if the connections cp and cpnext are connected
connectedComponentIsCyclic(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Tells whether the connected component to which endPoint belongs to is cyclic.
connectErrMsg(RNATemplate.RNATemplateElement.EdgeEndPoint, RNATemplate.RNATemplateElement.EdgeEndPoint, String) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.LoadFromXml
 
Connection - Class in fr.orsay.lri.varna.models.naView
 
Connection() - Constructor for class fr.orsay.lri.varna.models.naView.Connection
 
connections - Variable in class fr.orsay.lri.varna.models.naView.Loop
 
connectionsXmlElement - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToXml
 
connectTo(RNATemplate.EdgeEndPointPosition, RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Connect the endpoint at position positionHere of this endpoint to the otherEndPoint.
connectTo(RNATemplate.EdgeEndPointPosition, RNATemplate.RNATemplateElement, RNATemplate.EdgeEndPointPosition) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Connect the endpoint at position positionHere of this endpoint to the endpoint of otherElement at position positionOnOtherElement.
connectTo(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Create an edge between two edge endpoints.
construct_circle_segment(int, int) - Method in class fr.orsay.lri.varna.models.naView.NAView
Draws the segment of residue between the bases numbered start through end, where start and end are presumed to be part of a base pairing region.
construct_extruded_segment(Connection, Connection) - Method in class fr.orsay.lri.varna.models.naView.NAView
Constructs the segment between cp and cpnext as a circle if possible.
construct_loop(int) - Method in class fr.orsay.lri.varna.models.naView.NAView
Starting at residue ibase, recursively constructs the loop containing said base and all deeper bases.
contains(ModeleBase) - Method in class fr.orsay.lri.varna.models.BaseList
 
CONTROL_HEIGHT - Static variable in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
CONTROL_HEIGHT - Static variable in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
CONTROL_WIDTH - Static variable in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
CONTROL_WIDTH - Static variable in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
convert() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToTree
 
convert(Tree<AlignedNode<RNANodeValue, RNANodeValue>>) - Method in class fr.orsay.lri.varna.models.treealign.RNATree.ConvertToMapping
 
convert(Tree<AlignedNode<RNANodeValue2, RNANodeValue2>>) - Method in class fr.orsay.lri.varna.models.treealign.RNATree2.ConvertToMapping
 
convert() - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.ConvertTreeToArray
Reads: treeData.tree Computes: treeData.nodes, treeData.degree, treeData.degrees treeData.fathers, treeData.children, treeData.size, treeData.values Converts a tree to an array of nodes, in postorder.
convertSubTree(Tree<AlignedNode<RNANodeValue, RNANodeValue>>) - Method in class fr.orsay.lri.varna.models.treealign.RNATree.ConvertToMapping
 
convertSubTree(Tree<AlignedNode<RNANodeValue2, RNANodeValue2>>) - Method in class fr.orsay.lri.varna.models.treealign.RNATree2.ConvertToMapping
 
convertTreeToArrayAux(Tree<ValueType>, int[], int) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign.ConvertTreeToArray
 
copy(TextAnnotation) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
copy a textAnnotation
correctReciprocity(int[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
countNodes() - Method in class fr.orsay.lri.varna.models.treealign.Tree
Count the nodes in the tree.
COUPLE_MODE - Static variable in class fr.orsay.lri.varna.views.VueBases
for base pairs by king
coupleMode() - Method in class fr.orsay.lri.varna.views.VueBases
 
createBPStyle(ModeleBase, ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser.BPTemp
 
createMenuItem(String, String, String, Container, boolean) - Method in class fr.orsay.lri.varna.views.VueMenu
 
createMenuItem(String, String, String, Container) - Method in class fr.orsay.lri.varna.views.VueMenu
 
createSourceFromURL(String) - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
createVARNAPanels() - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
createView() - Method in class fr.orsay.lri.varna.views.VueBases
 
createView() - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
CubicBezierCurve - Class in fr.orsay.lri.varna.models
This class implements a cubic Bezier curve with a constant speed parametrization.
CubicBezierCurve(Point2D.Double, Point2D.Double, Point2D.Double, Point2D.Double, int) - Constructor for class fr.orsay.lri.varna.models.CubicBezierCurve
A Bezier curve can be defined by four points, see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves Here we give this four points and a integer to say in how many line segments we want to cut the Bezier curve (if n is bigger the computation takes longer but the precision is better).
currentColor - Variable in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
customBasesOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
customBPsOpt - 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 _