fr.orsay.lri.varna.models.treealign
Class RNATree2

java.lang.Object
  extended by fr.orsay.lri.varna.models.treealign.RNATree2

public class RNATree2
extends Object

This class contains all functions that are specific to trees (class Tree) of RNA, with RNANodeValue2.

Author:
Raphael Champeimont

Nested Class Summary
private static class RNATree2.ConvertToMapping
           
 
Constructor Summary
RNATree2()
           
 
Method Summary
static Mapping mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment)
          Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.
private static List<Tree<RNANodeValue2>> RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
           
private static void RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest, List<RNANodeValue> consecutiveNonPairedBases)
           
static Tree<RNANodeValue2> RNATree2FromRNA(RNA rna)
          Convert an RNA object into a RNA tree with RNANodeValue2.
static Tree<RNANodeValue2> RNATree2FromRNATree(Tree<RNANodeValue> originalTree)
          Convert from RNANodeValue model to RNANodeValue2 model, ie.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RNATree2

public RNATree2()
Method Detail

RNATree2FromRNA

public static Tree<RNANodeValue2> RNATree2FromRNA(RNA rna)
                                           throws RNATree2Exception
Convert an RNA object into a RNA tree with RNANodeValue2.

Throws:
RNATree2Exception

RNATree2FromRNATree

public static Tree<RNANodeValue2> RNATree2FromRNATree(Tree<RNANodeValue> originalTree)
                                               throws RNATree2Exception
Convert from RNANodeValue model to RNANodeValue2 model, ie. compact consecutive non-paired bases.

Throws:
RNATree2Exception

RNAForest2FromRNAForestCommitNonPaired

private static void RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest,
                                                           List<RNANodeValue> consecutiveNonPairedBases)

RNAForest2FromRNAForest

private static List<Tree<RNANodeValue2>> RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest)
                                                          throws RNATree2Exception
Throws:
RNATree2Exception

mappingFromAlignment

public static Mapping mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment)
                                    throws fr.orsay.lri.varna.exceptions.MappingException
Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.

Throws:
fr.orsay.lri.varna.exceptions.MappingException