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

Packages that use RNATemplate.RNATemplateElement
fr.orsay.lri.varna.models.templates   
 

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

Subclasses of RNATemplate.RNATemplateElement in fr.orsay.lri.varna.models.templates
 class RNATemplate.RNATemplateHelix
          An helix in an RNA template.
 class RNATemplate.RNATemplateUnpairedSequence
          A sequence of non-paired bases in an RNA template.
 

Fields in fr.orsay.lri.varna.models.templates declared as RNATemplate.RNATemplateElement
private  RNATemplate.RNATemplateElement RNATemplate.RNATemplateElement.element
          This variable is just there so that "this" can be accessed by a name from the internal class EdgeEndPoint.
 

Fields in fr.orsay.lri.varna.models.templates with type parameters of type RNATemplate.RNATemplateElement
private  Map<RNATemplate.RNATemplateElement,String> RNATemplate.ConvertToXml.elementNames
           
private  Map<String,RNATemplate.RNATemplateElement> RNATemplate.LoadFromXml.elementNames
           
private  Collection<RNATemplate.RNATemplateElement> RNATemplate.elements
          The list of template elements.
private  Map<RNATemplate.RNATemplateElement,ArrayList<Integer>> RNATemplateMapping.invmap
           
private  Iterator<RNATemplate.RNATemplateElement> RNATemplate.ConvertToTree.iter
           
private  Map<Integer,RNATemplate.RNATemplateElement> RNATemplateMapping.map
           
 

Methods in fr.orsay.lri.varna.models.templates that return RNATemplate.RNATemplateElement
 RNATemplate.RNATemplateElement RNATemplate.getAny()
          Return an arbitrary element of the template, null if empty.
 RNATemplate.RNATemplateElement RNATemplate.RNATemplateElement.EdgeEndPoint.getElement()
          Returns the endpoint on which this edge endpoint is.
 RNATemplate.RNATemplateElement RNATemplate.getFirst()
          The first endpoint (in sequence order) of the template.
 RNATemplate.RNATemplateElement RNATemplate.RNATemplateElement.EdgeEndPoint.getOtherElement()
          Returns the endpoint at the other endpoint of the edge.
 RNATemplate.RNATemplateElement RNATemplateMapping.getPartner(int baseIndex)
          If the given base index is in the mapping, return the corresponding template element, otherwise return null.
 RNATemplate.RNATemplateElement RNATemplate.RNAIterator.next()
           
 

Methods in fr.orsay.lri.varna.models.templates that return types with arguments of type RNATemplate.RNATemplateElement
 Iterator<RNATemplate.RNATemplateElement> RNATemplate.classicIterator()
          Iterates over all elements (each endpoint is given only once) in an arbitrary order.
 Set<RNATemplate.RNATemplateElement> RNATemplateMapping.getTargetElemsAsSet()
          Return a set containing all the template elements in the mapping.
 Iterator<RNATemplate.RNATemplateElement> RNATemplate.rnaIterator()
          Iterates over the elements of the template, in the sequence order.
 

Methods in fr.orsay.lri.varna.models.templates with parameters of type RNATemplate.RNATemplateElement
 void RNATemplateMapping.addCouple(int baseIndex, RNATemplate.RNATemplateElement templateElement)
          Tell this mapping object that this base index and this element are mapped with each other.
 void RNATemplate.RNATemplateElement.connectTo(RNATemplate.EdgeEndPointPosition positionHere, RNATemplate.RNATemplateElement otherElement, RNATemplate.EdgeEndPointPosition positionOnOtherElement)
          Connect the endpoint at position positionHere of this endpoint to the endpoint of otherElement at position positionOnOtherElement.
 ArrayList<Integer> RNATemplateMapping.getAncestor(RNATemplate.RNATemplateElement templateElement)
          If the given template element is in the mapping, return an ArrayList containing the corresponding base indexes, otherwise return null.
 boolean RNATemplate.removeElement(RNATemplate.RNATemplateElement element)
          Remove the element from the template.