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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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