+++ /dev/null
-package fr.orsay.lri.varna.models.treealign;
-import java.util.ArrayList;
-import java.util.LinkedList;
-import java.util.List;
-
-import fr.orsay.lri.varna.exceptions.MappingException;
-import fr.orsay.lri.varna.models.rna.Mapping;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-
-/**
- * This class contains all functions that are specific to trees
- * (class Tree) of RNA, with RNANodeValue2.
- *
- * @author Raphael Champeimont
- *
- */
-public class RNATree2 {
- /**
- * Convert an RNA object into a RNA tree with RNANodeValue2.
- * @throws RNATree2Exception
- */
- public static Tree<RNANodeValue2> RNATree2FromRNA(RNA rna) throws RNATree2Exception {
- Tree<RNANodeValue> fullTree = RNATree.RNATreeFromRNA(rna);
- return RNATree2FromRNATree(fullTree);
- }
-
- /**
- * Convert from RNANodeValue model to RNANodeValue2 model,
- * ie. compact consecutive non-paired bases.
- */
- public static Tree<RNANodeValue2> RNATree2FromRNATree(Tree<RNANodeValue> originalTree) throws RNATree2Exception {
- Tree<RNANodeValue2> newTree = new Tree<RNANodeValue2>();
- // Root in original tree is fake, so make a fake root
- newTree.setValue(null);
- newTree.replaceChildrenListBy(RNAForest2FromRNAForest(originalTree.getChildren()));
- return newTree;
- }
-
- private static void RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>> forest, List<RNANodeValue> consecutiveNonPairedBases) {
- // add the group of non-paired bases if there is one
- if (consecutiveNonPairedBases.size() > 0) {
- RNANodeValue2 groupOfConsecutiveBases = new RNANodeValue2(false);
- groupOfConsecutiveBases.getNodes().addAll(consecutiveNonPairedBases);
- Tree<RNANodeValue2> groupOfConsecutiveBasesNode = new Tree<RNANodeValue2>();
- groupOfConsecutiveBasesNode.setValue(groupOfConsecutiveBases);
- forest.add(groupOfConsecutiveBasesNode);
- consecutiveNonPairedBases.clear();
- }
- }
-
- private static List<Tree<RNANodeValue2>> RNAForest2FromRNAForest(List<Tree<RNANodeValue>> originalForest) throws RNATree2Exception {
- List<Tree<RNANodeValue2>> forest = new ArrayList<Tree<RNANodeValue2>>();
- List<RNANodeValue> consecutiveNonPairedBases = new LinkedList<RNANodeValue>();
- for (Tree<RNANodeValue> originalTree: originalForest) {
- if (originalTree.getValue().getRightBasePosition() == -1) {
- // non-paired base
- if (originalTree.getChildren().size() > 0) {
- throw (new RNATree2Exception("Non-paired base cannot have children."));
- }
-
- switch (originalTree.getValue().getOrigin()) {
- case BASE_FROM_HELIX_STRAND5:
- case BASE_FROM_HELIX_STRAND3:
- // This base is part of a broken base pair
-
- // if we have gathered some non-paired bases, add a node with
- // the group of them
- RNAForest2FromRNAForestCommitNonPaired(forest, consecutiveNonPairedBases);
-
- // now add the node
- RNANodeValue2 pairedBase = new RNANodeValue2(true);
- pairedBase.setNode(originalTree.getValue());
- Tree<RNANodeValue2> pairedBaseNode = new Tree<RNANodeValue2>();
- pairedBaseNode.setValue(pairedBase);
- forest.add(pairedBaseNode);
- break;
- case BASE_FROM_UNPAIRED_REGION:
- consecutiveNonPairedBases.add(originalTree.getValue());
- break;
- case BASE_PAIR_FROM_HELIX:
- throw (new RNATree2Exception("Origin is BASE_PAIR_FROM_HELIX but this is not a pair."));
- }
- } else {
- // paired bases
-
- // if we have gathered some non-paired bases, add a node with
- // the group of them
- RNAForest2FromRNAForestCommitNonPaired(forest, consecutiveNonPairedBases);
-
- // now add the node
- RNANodeValue2 pairedBase = new RNANodeValue2(true);
- pairedBase.setNode(originalTree.getValue());
- Tree<RNANodeValue2> pairedBaseNode = new Tree<RNANodeValue2>();
- pairedBaseNode.setValue(pairedBase);
- pairedBaseNode.replaceChildrenListBy(RNAForest2FromRNAForest(originalTree.getChildren()));
- forest.add(pairedBaseNode);
- }
- }
-
- // if there we have some non-paired bases, add them grouped
- RNAForest2FromRNAForestCommitNonPaired(forest, consecutiveNonPairedBases);
-
- return forest;
- }
-
-
- /**
- * Convert an RNA tree (with RNANodeValue2) alignment into a Mapping.
- */
- public static Mapping mappingFromAlignment(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> alignment) throws MappingException {
- ConvertToMapping converter = new ConvertToMapping();
- return converter.convert(alignment);
- }
-
- private static class ConvertToMapping {
- private Mapping m;
- ExampleDistance3 sequenceAligner = new ExampleDistance3();
-
- public Mapping convert(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree) throws MappingException {
- m = new Mapping();
- convertSubTree(tree);
- return m;
- }
-
- private void convertSubTree(Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> tree) throws MappingException {
- AlignedNode<RNANodeValue2,RNANodeValue2> alignedNode = tree.getValue();
- Tree<RNANodeValue2> leftNode = alignedNode.getLeftNode();
- Tree<RNANodeValue2> rightNode = alignedNode.getRightNode();
- if (leftNode != null && rightNode != null) {
- RNANodeValue2 v1 = leftNode.getValue();
- RNANodeValue2 v2 = rightNode.getValue();
- if (v1.isSingleNode() && v2.isSingleNode()) {
- // we have aligned (x,y) with (x',y')
- // so we map x with x' and y with y'
- RNANodeValue vsn1 = v1.getNode();
- RNANodeValue vsn2 = v2.getNode();
- int l1 = vsn1.getLeftBasePosition();
- int r1 = vsn1.getRightBasePosition();
- int l2 = vsn2.getLeftBasePosition();
- int r2 = vsn2.getRightBasePosition();
- if (l1 >= 0 && l2 >= 0) {
- m.addCouple(l1, l2);
- }
- if (r1 >= 0 && r2 >= 0) {
- m.addCouple(r1, r2);
- }
- } else if (!v1.isSingleNode() && !v2.isSingleNode()) {
- // We have aligned x1 x2 ... xn with y1 y2 ... ym.
- // So we will now (re-)compute this sequence alignment.
- int[][] sequenceAlignment = sequenceAligner.alignSequenceNodes(v1, v2).getAlignment();
- int l = sequenceAlignment[0].length;
- for (int i=0; i<l; i++) {
- // b1 and b2 are indexes in the aligned sequences
- int b1 = sequenceAlignment[0][i];
- int b2 = sequenceAlignment[1][i];
- if (b1 != -1 && b2 != -1) {
- int l1 = v1.getNodes().get(b1).getLeftBasePosition();
- int l2 = v2.getNodes().get(b2).getLeftBasePosition();
- m.addCouple(l1, l2);
- }
- }
-
- }
- }
-
- for (Tree<AlignedNode<RNANodeValue2,RNANodeValue2>> child: tree.getChildren()) {
- convertSubTree(child);
- }
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff