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edge3
- Variable in class fr.orsay.lri.varna.models.rna.
RNAMLParser.BPTemp
edge5
- Variable in class fr.orsay.lri.varna.models.rna.
RNAMLParser.BPTemp
EDGES
- Variable in class fr.orsay.lri.varna.components.
GradientEditorPanel
EDIT
- Static variable in class fr.orsay.lri.varna.components.
BaseSpecialColorEditor
EDIT
- Static variable in class fr.orsay.lri.varna.views.
VueListeAnnotations
if this view is for editing annoted texts
editStructMenu()
- Method in class fr.orsay.lri.varna.views.
VueMenu
element
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateElement
This variable is just there so that "this" can be accessed by a name from the internal class EdgeEndPoint.
elementNames
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.ConvertToXml
elementNames
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.LoadFromXml
elements
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate
The list of template elements.
emitWarning(String)
- Method in class fr.orsay.lri.varna.
VARNAPanel
Displays a warning message through a modal dialog if warnings are set to be displayed.
end
- Variable in class fr.orsay.lri.varna.models.naView.
Connection
endAngle
- Variable in class fr.orsay.lri.varna.models.export.
ArcCommand
endDocument()
- Method in class fr.orsay.lri.varna.models.rna.
RNAMLParser
endElement(String, String, String)
- Method in class fr.orsay.lri.varna.models.rna.
RNAMLParser
endpoint
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.VertexIterator
endPointFromXml(Element)
- Method in class fr.orsay.lri.varna.models.templates.
RNATemplate.LoadFromXml
Takes an element of the form:
and returns the corresponding EdgeEndPoint object.
endPosition
- Variable in class fr.orsay.lri.varna.models.templates.
RNATemplate.RNATemplateHelix
Position of the helix end point, ie.
energyColorMap()
- Static method in class fr.orsay.lri.varna.models.rna.
ModeleColorMap
ensureColorDefinition(Color)
- Method in class fr.orsay.lri.varna.models.export.
XFIGExport
EPSFooter()
- Method in class fr.orsay.lri.varna.models.export.
PSExport
EPSHeader(double, double, double, double)
- Method in class fr.orsay.lri.varna.models.export.
PSExport
equals(ModeleColorMap)
- Method in class fr.orsay.lri.varna.models.rna.
ModeleColorMap
eraseSequence()
- Method in class fr.orsay.lri.varna.models.rna.
RNA
eraseSequence()
- Method in class fr.orsay.lri.varna.
VARNAPanel
errorDialog(Exception)
- Method in class fr.orsay.lri.varna.
VARNAPanel
Pops up an error Dialog displaying an exception in an human-readable way.
errorDialog(Exception, Component)
- Method in class fr.orsay.lri.varna.
VARNAPanel
Pops up an error Dialog displaying an exception in an human-readable way if errors are set to be displayed.
errorDialogStatic(Exception, Component)
- Static method in class fr.orsay.lri.varna.
VARNAPanel
Pops up an error Dialog displaying an exception in an human-readable way.
errorOpt
- Static variable in class fr.orsay.lri.varna.models.
VARNAConfigLoader
estimateBulgeArcLength(int, int)
- Method in class fr.orsay.lri.varna.models.rna.
RNA
Estimate bulge arc length.
estimateBulgeWidth(int, int)
- Method in class fr.orsay.lri.varna.models.rna.
RNA
Estimate bulge width, the given first and last bases must be those in the helix.
estimateBulgeWidthOLD(int, int)
- Method in class fr.orsay.lri.varna.models.rna.
RNA
Estimate bulge width, the given first and last bases must be those in the helix.
ExampleDistance2
- Class in
fr.orsay.lri.varna.models.treealign
This distance is such that a substitution costs nothing.
ExampleDistance2()
- Constructor for class fr.orsay.lri.varna.models.treealign.
ExampleDistance2
ExampleDistance3
- Class in
fr.orsay.lri.varna.models.treealign
ExampleDistance3()
- Constructor for class fr.orsay.lri.varna.models.treealign.
ExampleDistance3
ExampleDistance3.SequenceAlignResult
- Class in
fr.orsay.lri.varna.models.treealign
ExampleDistance3.SequenceAlignResult()
- Constructor for class fr.orsay.lri.varna.models.treealign.
ExampleDistance3.SequenceAlignResult
existInStrand(int)
- Method in class fr.orsay.lri.varna.models.rna.
ModeleStrand
explodeSequence(String)
- Static method in class fr.orsay.lri.varna.models.rna.
RNA
export()
- Method in class fr.orsay.lri.varna.models.export.
SecStrDrawingProducer
exportMenu()
- Method in class fr.orsay.lri.varna.views.
VueMenu
ExtendedMB
- Class in
fr.orsay.lri.varna.models.rna
ExtendedMB()
- Constructor for class fr.orsay.lri.varna.models.rna.
ExtendedMB
extracted
- Variable in class fr.orsay.lri.varna.models.naView.
Base
extractedArrayListModeleBaseFromAncrage()
- Method in class fr.orsay.lri.varna.models.annotations.
TextAnnotation
extractMaxContiguousPortion(ArrayList<ModeleBase>)
- Method in class fr.orsay.lri.varna.views.
VueUI
extruded
- Variable in class fr.orsay.lri.varna.models.naView.
Connection
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