Uses of Class
fr.orsay.lri.varna.models.treealign.RNANodeValue

Packages that use RNANodeValue
fr.orsay.lri.varna.models.treealign   
 

Uses of RNANodeValue in fr.orsay.lri.varna.models.treealign
 

Fields in fr.orsay.lri.varna.models.treealign declared as RNANodeValue
private  RNANodeValue RNANodeValue2.node
          Defined if singleNode is true.
 

Fields in fr.orsay.lri.varna.models.treealign with type parameters of type RNANodeValue
private  List<RNANodeValue> RNANodeValue2.nodes
          Defined if singleNode is false;
 

Methods in fr.orsay.lri.varna.models.treealign that return RNANodeValue
 RNANodeValue RNANodeValue2.getNode()
          In case of a single node, return it.
 

Methods in fr.orsay.lri.varna.models.treealign that return types with arguments of type RNANodeValue
 List<RNANodeValue> RNANodeValue2.getNodes()
          In case of multiple nodes, return them.
static Tree<RNANodeValue> RNATree.RNATreeFromRNA(RNA rna)
          Convert an RNA object into a RNA tree.
 Tree<RNANodeValue> RNATree.ConvertToTree.toTreeAux(int depth)
          Starts at the current position i in the sequence and converts the sequence to a tree.
 

Methods in fr.orsay.lri.varna.models.treealign with parameters of type RNANodeValue
 void RNANodeValue2.setNode(RNANodeValue node)
           
 

Method parameters in fr.orsay.lri.varna.models.treealign with type arguments of type RNANodeValue
 Mapping RNATree.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
           
 Mapping RNATree.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
           
private  void RNATree.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
           
private  void RNATree.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree)
           
static Mapping RNATree.mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment)
          Convert an RNA tree alignment into a Mapping.
static Mapping RNATree.mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment)
          Convert an RNA tree alignment into a Mapping.
private static List<Tree<RNANodeValue2>> RNATree2.RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
           
private static void RNATree2.RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest, List<RNANodeValue> consecutiveNonPairedBases)
           
static Tree<RNANodeValue2> RNATree2.RNATree2FromRNATree(Tree<RNANodeValue> originalTree)
          Convert from RNANodeValue model to RNANodeValue2 model, ie.
 void RNANodeValue2.setNodes(List<RNANodeValue> nodes)