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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
Overview
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