fr.orsay.lri.varna.models.treealign
Class RNATree2
java.lang.Object
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
RNATree2
public RNATree2()
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