--- /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