--- /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