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Packages that use RNATemplate.RNATemplateHelix | |
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fr.orsay.lri.varna.models.rna | |
fr.orsay.lri.varna.models.templates |
Uses of RNATemplate.RNATemplateHelix in fr.orsay.lri.varna.models.rna |
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Methods in fr.orsay.lri.varna.models.rna that return types with arguments of type RNATemplate.RNATemplateHelix | |
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private Map<RNATemplate.RNATemplateHelix,Point2D.Double> |
RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree,
RNATemplateMapping mapping)
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Methods in fr.orsay.lri.varna.models.rna with parameters of type RNATemplate.RNATemplateHelix | |
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private double |
RNA.computeHelixTemplateLength(RNATemplate.RNATemplateHelix helix)
Get helix length in template. |
private Point2D.Double |
RNA.computeLengthIncreaseDelta(int[] basesInHelixArray,
RNATemplate.RNATemplateHelix helix)
Compute (actual helix vector - helix vector in template). |
private double |
RNA.computeLengthIncreaseFactor(int[] basesInHelixArray,
RNATemplate.RNATemplateHelix helix)
Compute (actual helix length / helix length in template). |
private void |
RNA.computeTemplateHelixVectors(RNATemplate.RNATemplateHelix helix,
Point2D.Double o,
Point2D.Double i,
Point2D.Double j)
Compute helix interesting vectors from template helix. |
private double |
RNA.drawHelixLikeTemplateHelix(int[] basesInHelixArray,
RNATemplate.RNATemplateHelix helix,
Point2D.Double[] coords,
Point2D.Double[] centers,
double scaleHelixOrigin,
Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors)
Draw the given helix (given as a *SORTED* array of indexes) like defined in the given template helix. |
private void |
RNA.drawHelixLikeTemplateHelixOLD(int[] basesInHelixArray,
RNATemplate.RNATemplateHelix helix,
Point2D.Double[] coords,
Point2D.Double[] centers,
double scaleHelixOrigin,
Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors)
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Method parameters in fr.orsay.lri.varna.models.rna with type arguments of type RNATemplate.RNATemplateHelix | |
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private void |
RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree,
Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors,
RNATemplateMapping mapping,
Point2D.Double parentDeltaVector)
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private double |
RNA.drawHelixLikeTemplateHelix(int[] basesInHelixArray,
RNATemplate.RNATemplateHelix helix,
Point2D.Double[] coords,
Point2D.Double[] centers,
double scaleHelixOrigin,
Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors)
Draw the given helix (given as a *SORTED* array of indexes) like defined in the given template helix. |
private void |
RNA.drawHelixLikeTemplateHelixOLD(int[] basesInHelixArray,
RNATemplate.RNATemplateHelix helix,
Point2D.Double[] coords,
Point2D.Double[] centers,
double scaleHelixOrigin,
Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors)
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Uses of RNATemplate.RNATemplateHelix in fr.orsay.lri.varna.models.templates |
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Fields in fr.orsay.lri.varna.models.templates declared as RNATemplate.RNATemplateHelix | |
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private RNATemplate.RNATemplateHelix |
RNANodeValueTemplateBrokenBasePair.helix
The original template element this node came from. |
private RNATemplate.RNATemplateHelix |
RNANodeValueTemplateBasePair.helix
The original template element this node came from. |
Fields in fr.orsay.lri.varna.models.templates with type parameters of type RNATemplate.RNATemplateHelix | |
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private ArrayList<RNATemplate.RNATemplateHelix> |
RNATemplate.RemovePseudoKnots.helixesSeq
The elements of the template as an array, in the order of the RNA sequence. |
private Set<RNATemplate.RNATemplateHelix> |
RNATemplate.ConvertToTree.knownHelixes
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private Set<RNATemplate.RNATemplateHelix> |
RNATemplate.ConvertToTree.removedHelixes
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Methods in fr.orsay.lri.varna.models.templates that return RNATemplate.RNATemplateHelix | |
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RNATemplate.RNATemplateHelix |
RNANodeValueTemplateBrokenBasePair.getHelix()
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RNATemplate.RNATemplateHelix |
RNANodeValueTemplateBasePair.getHelix()
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Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNATemplate.RNATemplateHelix | |
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private Set<RNATemplate.RNATemplateHelix> |
RNATemplate.RemovePseudoKnots.makeSet()
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Set<RNATemplate.RNATemplateHelix> |
RNATemplate.RemovePseudoKnots.removePseudoKnots()
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Methods in fr.orsay.lri.varna.models.templates with parameters of type RNATemplate.RNATemplateHelix | |
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void |
RNANodeValueTemplateBrokenBasePair.setHelix(RNATemplate.RNATemplateHelix helix)
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void |
RNANodeValueTemplateBasePair.setHelix(RNATemplate.RNATemplateHelix helix)
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Constructor parameters in fr.orsay.lri.varna.models.templates with type arguments of type RNATemplate.RNATemplateHelix | |
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RNATemplate.ConvertToTree(Set<RNATemplate.RNATemplateHelix> removedHelixes)
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