Uses of Class
fr.orsay.lri.varna.models.templates.RNANodeValueTemplate

Packages that use RNANodeValueTemplate
fr.orsay.lri.varna.models.rna   
fr.orsay.lri.varna.models.templates   
 

Uses of RNANodeValueTemplate in fr.orsay.lri.varna.models.rna
 

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

Uses of RNANodeValueTemplate in fr.orsay.lri.varna.models.templates
 

Subclasses of RNANodeValueTemplate in fr.orsay.lri.varna.models.templates
 class RNANodeValueTemplateBasePair
          See RNANodeValueTemplate.
 class RNANodeValueTemplateBrokenBasePair
          See RNANodeValueTemplate.
 class RNANodeValueTemplateSequence
          See RNANodeValueTemplate.
 

Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNANodeValueTemplate
static TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> RNATemplateAlign.alignRNAWithTemplate(RNA rna, RNATemplate template)
          Align the given RNA with the given RNA template.
 Tree<RNANodeValueTemplate> RNATemplate.ConvertToTree.convert()
           
 Tree<RNANodeValueTemplate> RNATemplate.toTree()
          Make a tree of the template.
 

Methods in fr.orsay.lri.varna.models.templates with parameters of type RNANodeValueTemplate
 double RNANodeValue2TemplateDistance.f(RNANodeValue2 v1, RNANodeValueTemplate v2)
           
 double RNANodeValue2TemplateDistance.insert(RNANodeValueTemplate v)
           
 

Method parameters in fr.orsay.lri.varna.models.templates with type arguments of type RNANodeValueTemplate
private  void RNATemplate.ConvertToTree.makeChildren(Tree<RNANodeValueTemplate> father)
           
static RNATemplateMapping RNATemplateAlign.makeTemplateMapping(TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> alignResult, RNA rna)
          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.