Uses of Class
fr.orsay.lri.varna.models.treealign.RNANodeValue2

Packages that use RNANodeValue2
fr.orsay.lri.varna.models.templates   
fr.orsay.lri.varna.models.treealign   
 

Uses of RNANodeValue2 in fr.orsay.lri.varna.models.templates
 

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

Methods in fr.orsay.lri.varna.models.templates with parameters of type RNANodeValue2
private static boolean RNATemplateAlign.canBePartOfABrokenHelix(RNANodeValue2 leftNodeValue)
           
private static boolean RNATemplateAlign.canBePartOfAnHelix(RNANodeValue2 leftNodeValue)
           
private static boolean RNATemplateAlign.canBePartOfASequence(RNANodeValue2 leftNodeValue)
           
 double RNANodeValue2TemplateDistance.delete(RNANodeValue2 v)
           
 double RNANodeValue2TemplateDistance.f(RNANodeValue2 v1, RNANodeValueTemplate v2)
           
 

Method parameters in fr.orsay.lri.varna.models.templates with type arguments of type RNANodeValue2
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.
 

Uses of RNANodeValue2 in fr.orsay.lri.varna.models.treealign
 

Methods in fr.orsay.lri.varna.models.treealign that return types with arguments of type RNANodeValue2
private static List<Tree<RNANodeValue2>> RNATree2.RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
           
static Tree<RNANodeValue2> RNATree2.RNATree2FromRNA(RNA rna)
          Convert an RNA object into a RNA tree with RNANodeValue2.
static Tree<RNANodeValue2> RNATree2.RNATree2FromRNATree(Tree<RNANodeValue> originalTree)
          Convert from RNANodeValue model to RNANodeValue2 model, ie.
 

Methods in fr.orsay.lri.varna.models.treealign with parameters of type RNANodeValue2
 ExampleDistance3.SequenceAlignResult ExampleDistance3.alignSequenceNodes(RNANodeValue2 v1, RNANodeValue2 v2)
          Align two sequences contained in nodes.
 double ExampleDistance3.f(RNANodeValue2 v1, RNANodeValue2 v2)
           
 double ExampleDistance2.f(RNANodeValue2 v1, RNANodeValue2 v2)
           
 

Method parameters in fr.orsay.lri.varna.models.treealign with type arguments of type RNANodeValue2
 Mapping RNATree2.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
           
 Mapping RNATree2.ConvertToMapping.convert(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
           
private  void RNATree2.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
           
private  void RNATree2.ConvertToMapping.convertSubTree(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree)
           
static Mapping RNATree2.mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment)
          Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.
static Mapping RNATree2.mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment)
          Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.
private static void RNATree2.RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest, List<RNANodeValue> consecutiveNonPairedBases)