+++ /dev/null
-package fr.orsay.lri.varna.models.treealign;
-
-import java.util.ArrayList;
-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.ModeleBase;
-import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
-import fr.orsay.lri.varna.models.rna.ModeleBP;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-
-
-/**
- * This class contains all functions that are specific to trees
- * (class Tree) of RNA.
- *
- * @author Raphael Champeimont
- *
- */
-public class RNATree {
- /**
- * Convert an RNA object into a RNA tree.
- * The root node will have a null value because it is a fake
- * node added to have a tree (otherwise we would have a forest).
- */
- public static Tree<RNANodeValue> RNATreeFromRNA(RNA rna) {
- ConvertToTree converter = new ConvertToTree(rna);
- return converter.toTreeAux(0);
- }
-
- private static class ConvertToTree {
- private RNA rna;
-
- private int i = 0;
-
- /** Starts at the current position i in the sequence and converts the sequence
- * to a tree.
- * @return the created tree
- */
- public Tree<RNANodeValue> toTreeAux(int depth) {
- Tree<RNANodeValue> tree = new Tree<RNANodeValue>();
- List<Tree<RNANodeValue>> children = tree.getChildren();
- // No value because it is a fake root
- tree.setValue(null);
-
- int length = rna.getSize();
- while (i < length) {
- ModeleBase base = rna.getBaseAt(i);
- int indexOfAssociatedBase = base.getElementStructure();
- if (indexOfAssociatedBase >= 0) {
- if (indexOfAssociatedBase > i) {
- // left parenthesis, we must analyze the children
- RNANodeValue childValue = new RNANodeValue();
- childValue.setLeftBasePosition(i);
- childValue.setRightBasePosition(indexOfAssociatedBase);
- childValue.setOrigin(RNANodeValue.Origin.BASE_PAIR_FROM_HELIX);
-
- if (base instanceof ModeleBaseNucleotide) {
- childValue.setLeftNucleotide(((ModeleBaseNucleotide) base).getBase());
- childValue.setRightNucleotide(((ModeleBaseNucleotide) rna.getBaseAt(indexOfAssociatedBase)).getBase());
- }
- i++;
- Tree<RNANodeValue> child = toTreeAux(depth+1);
- child.setValue(childValue);
- children.add(child);
- } else {
- // right parenthesis, we have finished analyzing the children
- i++;
- break;
- }
- } else {
- // we have a non-paired base
- Tree<RNANodeValue> child = new Tree<RNANodeValue>();
- RNANodeValue childValue = new RNANodeValue();
- childValue.setLeftBasePosition(i);
- if (base instanceof ModeleBaseNucleotide) {
- childValue.setLeftNucleotide(((ModeleBaseNucleotide) base).getBase());
- }
-
- // Even in this case (getElementStructure() < 0)
- // this base may still come from an helix which may have
- // been broken to remove a pseudoknot.
- childValue.setOrigin(RNANodeValue.Origin.BASE_FROM_UNPAIRED_REGION);
- ArrayList<ModeleBP> auxBasePairs = rna.getAuxBPs(i);
- for (ModeleBP auxBasePair: auxBasePairs) {
- if (auxBasePair.isCanonical()) {
- int partner5 = ((ModeleBaseNucleotide) auxBasePair.getPartner5()).getIndex();
- int partner3 = ((ModeleBaseNucleotide) auxBasePair.getPartner3()).getIndex();
- if (i == partner5) {
- childValue.setOrigin(RNANodeValue.Origin.BASE_FROM_HELIX_STRAND5);
- } else if (i == partner3) {
- childValue.setOrigin(RNANodeValue.Origin.BASE_FROM_HELIX_STRAND3);
- } else {
- System.err.println("Warning: Base index is " + i + " but neither endpoint matches it (edge endpoints are " + partner5 + " and " + partner3 + ").");
- }
-
- }
- }
-
- child.setValue(childValue);
- children.add(child);
- i++;
- }
- }
-
- return tree;
- }
-
- public ConvertToTree(RNA rna) {
- this.rna = rna;
- }
- }
-
-
- /**
- * Convert an RNA tree alignment into a Mapping.
- */
- public static Mapping mappingFromAlignment(Tree<AlignedNode<RNANodeValue,RNANodeValue>> alignment) throws MappingException {
- ConvertToMapping converter = new ConvertToMapping();
- return converter.convert(alignment);
- }
-
- private static class ConvertToMapping {
- private Mapping m;
-
- public Mapping convert(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree) throws MappingException {
- m = new Mapping();
- convertSubTree(tree);
- return m;
- }
-
- private void convertSubTree(Tree<AlignedNode<RNANodeValue,RNANodeValue>> tree) throws MappingException {
- AlignedNode<RNANodeValue,RNANodeValue> alignedNode = tree.getValue();
- Tree<RNANodeValue> leftNode = alignedNode.getLeftNode();
- Tree<RNANodeValue> rightNode = alignedNode.getRightNode();
- if (leftNode != null && rightNode != null) {
- RNANodeValue v1 = leftNode.getValue();
- RNANodeValue v2 = rightNode.getValue();
- int l1 = v1.getLeftBasePosition();
- int r1 = v1.getRightBasePosition();
- int l2 = v2.getLeftBasePosition();
- int r2 = v2.getRightBasePosition();
- if (l1 >= 0 && l2 >= 0) {
- m.addCouple(l1, l2);
- }
- if (r1 >= 0 && r2 >= 0) {
- m.addCouple(r1, r2);
- }
- }
- for (Tree<AlignedNode<RNANodeValue,RNANodeValue>> child: tree.getChildren()) {
- convertSubTree(child);
- }
- }
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff