X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FRNATree2.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FRNATree2.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=753819b85c4e2954a82aa284843b22a699be9787;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/models/treealign/RNATree2.java b/srcjar/fr/orsay/lri/varna/models/treealign/RNATree2.java
deleted file mode 100644
index 753819b..0000000
--- a/srcjar/fr/orsay/lri/varna/models/treealign/RNATree2.java
+++ /dev/null
@@ -1,172 +0,0 @@
-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);
-			}
-		}
-	}
-}