Uses of Class
fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix

Packages that use RNATemplate.RNATemplateHelix
fr.orsay.lri.varna.models.rna   
fr.orsay.lri.varna.models.templates   
 

Uses of RNATemplate.RNATemplateHelix in fr.orsay.lri.varna.models.rna
 

Methods in fr.orsay.lri.varna.models.rna that return types with arguments of type RNATemplate.RNATemplateHelix
private  Map<RNATemplate.RNATemplateHelix,Point2D.Double> RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree, RNATemplateMapping mapping)
           
 

Methods in fr.orsay.lri.varna.models.rna with parameters of type RNATemplate.RNATemplateHelix
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)
           
 

Method parameters in fr.orsay.lri.varna.models.rna with type arguments of type RNATemplate.RNATemplateHelix
private  void RNA.computeHelixTranslations(Tree<RNANodeValueTemplate> tree, Map<RNATemplate.RNATemplateHelix,Point2D.Double> translateVectors, RNATemplateMapping mapping, Point2D.Double parentDeltaVector)
           
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)
           
 

Uses of RNATemplate.RNATemplateHelix in fr.orsay.lri.varna.models.templates
 

Fields in fr.orsay.lri.varna.models.templates declared as RNATemplate.RNATemplateHelix
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
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
           
private  Set<RNATemplate.RNATemplateHelix> RNATemplate.ConvertToTree.removedHelixes
           
 

Methods in fr.orsay.lri.varna.models.templates that return RNATemplate.RNATemplateHelix
 RNATemplate.RNATemplateHelix RNANodeValueTemplateBrokenBasePair.getHelix()
           
 RNATemplate.RNATemplateHelix RNANodeValueTemplateBasePair.getHelix()
           
 

Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNATemplate.RNATemplateHelix
private  Set<RNATemplate.RNATemplateHelix> RNATemplate.RemovePseudoKnots.makeSet()
           
 Set<RNATemplate.RNATemplateHelix> RNATemplate.RemovePseudoKnots.removePseudoKnots()
           
 

Methods in fr.orsay.lri.varna.models.templates with parameters of type RNATemplate.RNATemplateHelix
 void RNANodeValueTemplateBrokenBasePair.setHelix(RNATemplate.RNATemplateHelix helix)
           
 void RNANodeValueTemplateBasePair.setHelix(RNATemplate.RNATemplateHelix helix)
           
 

Constructor parameters in fr.orsay.lri.varna.models.templates with type arguments of type RNATemplate.RNATemplateHelix
RNATemplate.ConvertToTree(Set<RNATemplate.RNATemplateHelix> removedHelixes)