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M

m - Variable in class fr.orsay.lri.varna.models.treealign.RNATree.ConvertToMapping
 
m - Variable in class fr.orsay.lri.varna.models.treealign.RNATree2.ConvertToMapping
 
main(String[]) - Static method in class fr.orsay.lri.varna.views.Imprimer
 
main(String[]) - Static method in class fr.orsay.lri.varna.views.PrintTest
 
MAJOR_VERSION - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
make() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.MakeEdgeList
 
makeChildren(Tree<RNANodeValueTemplate>) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToTree
 
makeEdgeList() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Return over all edges in an arbitrary order.
makeSet() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RemovePseudoKnots
 
makeTemplateMapping(TreeAlignResult<RNANodeValue2, RNANodeValueTemplate>, RNA) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
This method takes an alignment between a tree of RNANodeValue2 of RNANodeValue and a tree of RNANodeValue2 of RNANodeValueTemplate, and the original RNA object that was used to create the first tree in the alignment.
map - Variable in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
 
Mapping - Class in fr.orsay.lri.varna.models.rna
 
Mapping() - Constructor for class fr.orsay.lri.varna.models.rna.Mapping
 
mappingFromAlignment(Tree<AlignedNode<RNANodeValue, RNANodeValue>>) - Static method in class fr.orsay.lri.varna.models.treealign.RNATree
Convert an RNA tree alignment into a Mapping.
mappingFromAlignment(Tree<AlignedNode<RNANodeValue2, RNANodeValue2>>) - Static method in class fr.orsay.lri.varna.models.treealign.RNATree2
Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.
mapRNAWithTemplate(RNA, RNATemplate) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplateAlign
Map an RNA with an RNATemplate using tree alignment.
mark - Variable in class fr.orsay.lri.varna.models.naView.Loop
 
mate - Variable in class fr.orsay.lri.varna.models.naView.Base
 
MAX_AMOUNT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
MAX_DISTANCE - Static variable in class fr.orsay.lri.varna.models.VARNAEdits
 
MAX_NUM_DIR - Static variable in class fr.orsay.lri.varna.models.rna.VARNASecDraw
 
MAX_ZOOM - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
Default values for config options
maxf2(double, double) - Method in class fr.orsay.lri.varna.models.naView.NAView
 
MAXITER - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
MAXSCALINGFACTOR - Static variable in class fr.orsay.lri.varna.models.rna.RNA.DrawRNATemplateMethod
 
MAXSTYLE - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
maybeNodeToGraphvizNodeName(Tree<? extends GraphvizDrawableNodeValue>) - Method in class fr.orsay.lri.varna.models.treealign.AlignedNode
 
MIN_AMOUNT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
MIN_ZOOM - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
minf2(double, double) - Method in class fr.orsay.lri.varna.models.naView.NAView
 
MINOR_VERSION - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
ModeleBase - Class in fr.orsay.lri.varna.models.rna
The abstract rna base model
ModeleBase() - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBase
 
ModeleBaseNucleotide - Class in fr.orsay.lri.varna.models.rna
The rna base model with the first character of the nitrogenous base and it display
ModeleBaseNucleotide(int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
Creates a new rna base with the default display style and a space as nitrogenous base
ModeleBaseNucleotide(String, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
Creates a new rna base with the nitrogenous base
ModeleBaseNucleotide(String, int, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
Creates a new rna base with the nitrogenous base
ModeleBaseNucleotide(String, ModeleStyleBase, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
Creates a new rna base with the nitrogenous base and the display style
ModeleBaseNucleotide(ModeleStyleBase, int, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
Creates a new rna base with a display style
ModeleBaseNucleotide(Point2D.Double, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
Creates a new rna base with a space as the nitrogenous base and the display style
ModeleBaseNucleotide(ModeleBaseNucleotide, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
Creates a new rna base from another one with the same attributes
ModeleBaseNucleotide(Point2D.Double, Point2D.Double, boolean, String, ModeleStyleBase, int, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
ModeleBaseNucleotide.STATE_SPECIAL_CHARS_STATES - Enum in fr.orsay.lri.varna.models.rna
 
ModeleBaseNucleotide.STATE_SPECIAL_CHARS_STATES() - Constructor for enum fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide.STATE_SPECIAL_CHARS_STATES
 
ModeleBasesComparison - Class in fr.orsay.lri.varna.models.rna
The RNA base comparison model.
ModeleBasesComparison(int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Creates a new comparison base with the default display style and no nitrogenous bases.
ModeleBasesComparison(Point2D, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Creates a new comparison base at the specified coordinates, with the default display style and no nitrogenous bases.
ModeleBasesComparison(char, char, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Creates a new comparison base with the specified nitrogenous bases.
ModeleBasesComparison(char, char, Point2D, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Creates a new comparison base with the specified nitrogenous bases, at the specified coordinates.
ModeleBasesComparison(char, char, int, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Creates a new comparison base with the specified nitrogenous bases.
ModeleBasesComparison(Point2D, char, char, boolean, ModeleStyleBase, int, int) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Creates a new comparison base with the specified nitrogenous bases.
ModeleBP - Class in fr.orsay.lri.varna.models.rna
 
ModeleBP(ModeleBase, ModeleBase) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBP
 
ModeleBP(ModeleBase, ModeleBase, ModeleBP.Edge, ModeleBP.Edge, ModeleBP.Stericity) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBP
 
ModeleBP(String) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBP
 
ModeleBP.Edge - Enum in fr.orsay.lri.varna.models.rna
 
ModeleBP.Edge() - Constructor for enum fr.orsay.lri.varna.models.rna.ModeleBP.Edge
 
ModeleBP.Stericity - Enum in fr.orsay.lri.varna.models.rna
 
ModeleBP.Stericity() - Constructor for enum fr.orsay.lri.varna.models.rna.ModeleBP.Stericity
 
ModeleBPStyle - Class in fr.orsay.lri.varna.models.rna
 
ModeleBPStyle() - Constructor for class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
ModeleColorMap - Class in fr.orsay.lri.varna.models.rna
 
ModeleColorMap() - Constructor for class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
ModeleColorMap(Vector<Color>, Vector<Double>) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
ModeleColorMap.NamedColorMapTypes - Enum in fr.orsay.lri.varna.models.rna
 
ModeleColorMap.NamedColorMapTypes(String, ModeleColorMap) - Constructor for enum fr.orsay.lri.varna.models.rna.ModeleColorMap.NamedColorMapTypes
 
ModeleStrand - Class in fr.orsay.lri.varna.models.rna
 
ModeleStrand() - Constructor for class fr.orsay.lri.varna.models.rna.ModeleStrand
 
ModeleStyleBase - Class in fr.orsay.lri.varna.models.rna
The display Style of a rna base with the base name font, the ouline, innerline, number and name color
ModeleStyleBase() - Constructor for class fr.orsay.lri.varna.models.rna.ModeleStyleBase
Creates a new base style with default colors and font
ModeleStyleBase(Color, Color, Color, Color, Font) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleStyleBase
Creates a new base style with custom colors and custom font
ModeleStyleBase(String) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
ModeleStyleBase(ModeleStyleBase) - Constructor for class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
modifiableOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
Motif - Class in fr.orsay.lri.varna.models.rna
 
Motif(RNA, ArrayList<ModeleBase>) - Constructor for class fr.orsay.lri.varna.models.rna.Motif
 
mouseClicked(MouseEvent) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
mouseDragged(MouseEvent) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
mouseEntered(MouseEvent) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
mouseExited(MouseEvent) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
mouseMoved(MouseEvent) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
mousePressed(MouseEvent) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
mouseReleased(MouseEvent) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
MULTILOOP_DISTANCE - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 

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