X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FSecStrConsensus.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FSecStrConsensus.java;h=0000000000000000000000000000000000000000;hb=a1225b9392dc7657d5cef12907385b07527d6122;hp=5fce12bf4d5eb275dcde03730325b65b2a07b028;hpb=b513684c725997c77341f30ce4e584cf9f7cdfed;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/applications/SecStrConsensus.java b/src2/fr/orsay/lri/varna/applications/SecStrConsensus.java
deleted file mode 100644
index 5fce12b..0000000
--- a/src2/fr/orsay/lri/varna/applications/SecStrConsensus.java
+++ /dev/null
@@ -1,189 +0,0 @@
-package fr.orsay.lri.varna.applications;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-import fr.orsay.lri.varna.models.rna.ModeleBP;
-
-public class SecStrConsensus {
-	
-	
-	/**
-	 * Internal class to represent a simple base-pair.
-	 * @author Yawn
-	 *
-	 */
-	static class SimpleBP{
-		int bp5;
-		int bp3;
-		
-		public SimpleBP(int i5, int i3)
-		{
-			bp5=i5;
-			bp3=i3;
-		}
-	}
-	
-	public static int[] extractConsensus(ArrayList<ArrayList<SimpleBP>> bps)
-	{
-		// We do not currently know the length of the alignment
-		// => Estimate it as the biggest index of a base-pair plus one. 
-		int maxlength = 0;
-		for (ArrayList<SimpleBP> strs : bps)
-		{
-			for (SimpleBP bp : strs)
-			{
-				maxlength = Math.max(1+Math.max(bp.bp5, bp.bp3), maxlength);
-			}
-		}
-		// Now we have a good estimate for length, allocate and initialize data
-		// to be fed to the dynamic programming procedure.
-		ArrayList<Hashtable<Integer,Double>> seq = new ArrayList<Hashtable<Integer,Double>>();
-		for (int i=0;i<seq.size();i++)
-		{ seq.add(new Hashtable<Integer,Double>()); }
-		for (ArrayList<SimpleBP> strs : bps)
-		{
-			for (SimpleBP bp : strs)
-			{
-				int i = bp.bp5;
-				int j = bp.bp3;
-				Hashtable<Integer,Double> h = seq.get(i);
-				if (!h.containsKey(j))
-				{
-					h.put(j, 0.0);
-				}
-				h.put(j, h.get(i)+1.);
-			}
-		}
-		// At this point, seq contains, at each position i, a hashtable which associates,
-		// to each possible end j, the number of time a base-pair (i,j) occurs in the alignment
-		
-		// We can now run the dynamic programming procedure on this data
-		double[][] mat = fillMatrix(seq); 
-		ArrayList<SimpleBP> res = backtrack(mat,seq);
-		
-		// Convert it to an array, ie finalres[i] = j >= 0 iff a base-pair (i,j) is present 
-		// in the consensus, or -1 otherwise
-		int[] finalres = new int[seq.size()];
-		for (int i=0;i<seq.size();i++)
-		{ finalres[i] = -1; }
-		for (SimpleBP bp : res)
-		{
-			finalres[bp.bp5] = bp.bp3;
-			finalres[bp.bp3] = bp.bp5;
-		}
-		
-		return finalres;
-	}
-	
-	private static boolean canBasePair(ArrayList<Hashtable<Integer,Double>> seq, int i, int k)
-	{
-		return seq.get(i).containsKey(k);
-	}
-	
-	// Returns the score of a potential base-pair, ie the number of structures in which it is found.
-	private static double basePairScore(ArrayList<Hashtable<Integer,Double>> seq, int i, int k)
-	{
-		return seq.get(i).get(k);	
-	}
-	
-	
- 	private static double[][] fillMatrix(ArrayList<Hashtable<Integer,Double>> seq)
- 	{
-		int n = seq.size();
-		double[][] tab = new double[n][n];
-		for(int m=1;m<=n;m++)
-		{
-			for(int i=0;i<n-m+1;i++)
-			{
-				int j = i+m-1;
-				tab[i][j] = 0;
-				if (i<j)
-				{ 
-					tab[i][j] = Math.max(tab[i][j], tab[i+1][j]); 
-					for (int k=i+1;k<=j;k++)
-					{
-						if (canBasePair(seq,i,k))
-						{
-							double fact1 = 0;
-							if (k>i+1)
-							{
-								fact1 = tab[i+1][k-1];
-							}
-							double fact2 = 0;
-							if (k<j)
-							{
-								fact2 = tab[k+1][j];
-							}
-							tab[i][j] = Math.max(tab[i][j],basePairScore(seq,i,k)+fact1+fact2);
-						} 
-					}
-				}
-			}			
-		}
- 		return tab;
- 	}	
-	
- 	private static  ArrayList<SimpleBP> backtrack(double[][] tab,ArrayList<Hashtable<Integer,Double>> seq)
- 	{
- 		return backtrack(tab,seq,0,seq.size()-1);
- 	}
-	
- 	private static ArrayList<SimpleBP> backtrack(double[][] tab,ArrayList<Hashtable<Integer,Double>> seq, int i, int j)
- 	{
- 		ArrayList<SimpleBP> result = new ArrayList<SimpleBP>();
- 		if (i<j)
-		{ 
- 			ArrayList<Integer> indices = new ArrayList<Integer>();
- 			indices.add(-1);
-			for (int k=i+1;k<=j;k++)
-			{
-				indices.add(k);
-			}
-			for (int k : indices)
- 			{
- 				if (k==-1)
- 				{
- 					if (tab[i][j] == tab[i+1][j])
- 					{
- 						result = backtrack(tab, seq, i+1,j);
- 					}
- 				}
- 				else
- 				{
- 					if (canBasePair(seq,i,k))
- 					{
- 						double fact1 = 0;
- 						if (k>i+1)
- 						{
- 							fact1 = tab[i+1][k-1];
- 						}
- 						double fact2 = 0;
- 						if (k<j)
- 						{
- 							fact2 = tab[k+1][j];
- 						}
- 						if (tab[i][j]==basePairScore(seq,i,k)+fact1+fact2)
- 						{ 
- 							result = backtrack(tab, seq, i+1,k-1);
- 							result.addAll(backtrack(tab, seq, k+1,j));
- 							result.add(new SimpleBP(i,k));
- 						}
- 					}  					
- 				} 				
-			}
-		}
-		else if  (i==j)
-		{
-			
-		}
-		else 
-		{
-			
-		}
- 		return result;
- 	}
-	
-
-
-}