X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FVARNASecDraw.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FVARNASecDraw.java;h=0000000000000000000000000000000000000000;hb=d27359893c99db0e749a59d8a7ab73ea751da09e;hp=8a9e06e932c8b515c465eb97acd54dd991e44a08;hpb=9f55415c9f8005e9dcd8243453883ff853fd5b76;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/models/rna/VARNASecDraw.java b/src2/fr/orsay/lri/varna/models/rna/VARNASecDraw.java
deleted file mode 100644
index 8a9e06e..0000000
--- a/src2/fr/orsay/lri/varna/models/rna/VARNASecDraw.java
+++ /dev/null
@@ -1,896 +0,0 @@
-package fr.orsay.lri.varna.models.rna;
-
-import java.awt.Rectangle;
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Area;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.lang.reflect.Array;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedList;
-import java.util.Random;
-import java.util.Stack;
-import java.util.Vector;
-
-import fr.orsay.lri.varna.VARNAPanel;
-
-public class VARNASecDraw {
-	public static VARNAPanel _vp = null;
-
-	
-	public abstract class Portion
-	{
-		public abstract ArrayList<Integer> getBaseList();
-		public abstract int getNumBases();
-		public abstract GeneralPath getOutline(RNA r);
-		
-	};
-	
-	public class UnpairedPortion extends Portion
-	{
-		int _pos;
-		int _len;
-		public UnpairedPortion(int pos, int len)
-		{
-			_len = len;
-			_pos = pos;
-		}
-		@Override
-		public ArrayList<Integer> getBaseList() {
-			// TODO Auto-generated method stub
-			return null;
-		}		
-		public String toString()
-		{
-			return "U["+_pos+","+(_pos+_len-1)+"]";
-		}
-
-		public int getNumBases() {
-			return _len;
-		}
-
-		
-		public GeneralPath getOutline(RNA r) {
-			
-			GeneralPath gp = new GeneralPath();
-			ArrayList<ModeleBase> l = r.get_listeBases();
-			Point2D.Double p0 = l.get(_pos).getCoords();
-			gp.moveTo((float)p0.x, (float)p0.y);
-			for (int i=1;i<_len;i++)
-			{
-				Point2D.Double p = l.get(_pos+i).getCoords();
-				gp.lineTo((float)p.x, (float)p.y);
-			}
-			return gp;
-		}
-	};
-	
-	public class PairedPortion extends Portion
-	{
-		int _pos1;
-		int _pos2;
-		int _len;
-		RNATree _r;
-		
-		public PairedPortion(int pos1,int pos2, int len, RNATree r)
-		{
-			_pos1 = pos1;
-			_pos2 = pos2;
-			_len = len;
-			_r =r;
-		}
-
-		@Override
-		public ArrayList<Integer> getBaseList() {
-			// TODO Auto-generated method stub
-			return null;
-		}
-		
-		public String toString()
-		{
-			return "H["+_pos1+","+(_pos1+_len-1)+"]["+(_pos2-_len+1)+","+(_pos2)+"]\n"+_r.toString();
-		}
-
-		@Override
-		public int getNumBases() {
-			return 2*_len;
-		}
-
-		public GeneralPath getLocalOutline(RNA r) {
-			GeneralPath gp = new GeneralPath();
-			if (_len>0)
-			{
-				ArrayList<ModeleBase> l = r.get_listeBases();
-				Point2D.Double p1 = l.get(_pos1).getCoords();
-				Point2D.Double p2 = l.get(_pos1+_len-1).getCoords();
-				Point2D.Double p3 = l.get(_pos2-_len+1).getCoords();
-				Point2D.Double p4 = l.get(_pos2).getCoords();
-				gp.moveTo((float)p1.x, (float)p1.y);
-				gp.lineTo((float)p2.x, (float)p2.y);
-				gp.lineTo((float)p3.x, (float)p3.y);
-				gp.lineTo((float)p4.x, (float)p4.y);
-			}
-			return gp;
-		}
-
-
-		public GeneralPath getOutline(RNA r) {
-			return getOutline(r,false);
-		}
-
-		public GeneralPath getOutline(RNA r, boolean local) {
-			ArrayList<ModeleBase> l = r.get_listeBases();
-			Point2D.Double p1 = l.get(_pos1).getCoords();
-			Point2D.Double p2 = l.get(_pos1+_len-1).getCoords();
-			Point2D.Double p3 = l.get(_pos2-_len+1).getCoords();
-			Point2D.Double p4 = l.get(_pos2).getCoords();
-			GeneralPath gp = new GeneralPath();
-			gp.moveTo((float)p1.x, (float)p1.y);
-			gp.lineTo((float)p2.x, (float)p2.y);
-			if (!local)
-				gp.append(_r.getOutline(r), true);
-			gp.lineTo((float)p3.x, (float)p3.y);
-			gp.lineTo((float)p4.x, (float)p4.y);
-			
-			return gp;
-			
-		}
-	};
-	public 	int   _depth = 0;
-
-	
-	public class RNATree
-	{
-		ArrayList<Portion> _portions = new ArrayList<Portion>();
-		int _numPairedPortions=0;
-		public RNATree()
-		{
-			
-		}
-		
-		
-		public void addPortion(Portion p)
-		{
-			_portions.add(p);
-			if (p instanceof PairedPortion)
-			{
-				_numPairedPortions++;
-			}
-		}
-
-		public int getNumPortions()
-		{
-			return _portions.size();
-		}
-
-		public Portion getPortion(int i)
-		{
-			return _portions.get(i);
-		}
-		
-		public String toString()
-		{
-			String result = "";
-			_depth++;
-			for (int i=0;i<_portions.size();i++ )
-			{
-				result += String.format("%1$#" + _depth + "s", ' ');
-				result += _portions.get(i).toString();
-				if (i<_portions.size()-1)
-				  result += "\n";
-			}
-			_depth--;
-			return result;
-		}
-
-		public GeneralPath getOutline(RNA r) {
-			GeneralPath result = new GeneralPath();
-			for (int i=0;i<_portions.size();i++)
-			{
-				result.append(_portions.get(i).getOutline(r),true);
-			}
-			return result;
-		}
-	};
-	
-	
-	private void buildTree(int i, int j, RNATree parent,  RNA r) 
-	{
-		//LinkedList<BuildTreeArgs> s = new LinkedList<BuildTreeArgs>();
-		//s.add(new BuildTreeArgs(xi, xj, xparent,xr));
-		//while(s.size()!=0)
-		//{
-			
-			//BuildTreeArgs a = s.removeLast();
-			if (i >= j) {
-				parent.addPortion(new UnpairedPortion(i,j-i+1));
-			}
-			// BasePaired
-			if (r.get_listeBases().get(i).getElementStructure() == j) 
-			{
-				int i1 = i;
-				int j1 = j;
-				boolean over = false;
-				while( (i+1<r.get_listeBases().size())	&&  (j-1>=0)&&  (i+1<=j-1) && !over)
-				{
-					if (r.get_listeBases().get(i).getElementStructure() != j)
-					{ over = true; }
-					else
-					{ i++;j--; }
-				}
-				int i2 = i;
-				int j2 = j;
-				RNATree t = new RNATree();
-				if (i<j-1)
-				  buildTree(i2,j2,t,r);
-				PairedPortion p = new PairedPortion(i1,j1,i2-i1,t);
-				parent.addPortion(p);
-			} else 
-			{
-				int k = i;
-				int l;
-				int start = k;
-				int len = 0;
-				while (k <= j) {
-					l = r.get_listeBases().get(k).getElementStructure();
-					if (l != -1) 
-					{
-						if (len>0)
-						{ parent.addPortion(new UnpairedPortion(start,len)); }
-						buildTree(k, l, parent,  r);
-						k = l + 1;
-						start = k;
-						len = 0;
-					} else {
-						len++;
-						k++;
-					}
-				}
-				if (len>0)
-				{
-					parent.addPortion(new UnpairedPortion(start,len));
-				}
-			}
-		}
-
-	/*
-	public void drawTree(double x0, double y0, RNATree t, double dir, RNA r, double straightness)
-	{
-		boolean collision = true;
-		double x=x0;
-		double y=y0;
-		double multRadius = 1.0;
-		double initCirc = r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE;
-		for (int i=0;i<t.getNumPortions();i++ )
-		{
-			Portion p = t.getPortion(i);
-			if (p instanceof PairedPortion)
-			{
-				initCirc += (r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE);				
-			}
-			else
-			{
-				initCirc += r.LOOP_DISTANCE*(p.getNumBases());
-			}
-		}
-		while(collision)
-		{
-				double totCirc = r.BASE_PAIR_DISTANCE+straightness*r.LOOP_DISTANCE;
-				for (int i=0;i<t.getNumPortions();i++ )
-				{
-					Portion p = t.getPortion(i);
-					if (p instanceof PairedPortion)
-					{
-						totCirc += (r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE);				
-					}
-					else
-					{
-						double mod = 1.0;
-						if ((i==0) || (i==t.getNumPortions()-1))
-							mod = straightness;
-						  totCirc += mod*r.LOOP_DISTANCE*(p.getNumBases());
-					}
-				}
-				double radius = multRadius*initCirc/(2.0*Math.PI);
-			//radius = 2.0;
-			x = x0+radius*Math.cos(dir+Math.PI);
-			y = y0+radius*Math.sin(dir+Math.PI);
-			dir += 2.0*Math.PI;
-			double angleIncr = (2.0*Math.PI)/(totCirc);
-			double circ = r.BASE_PAIR_DISTANCE/2.0+straightness*r.LOOP_DISTANCE;
-			double ndir;
-			ArrayList<GeneralPath> shapes = new ArrayList<GeneralPath>(); 
-			for (int i=0;i<t.getNumPortions();i++ )
-			{
-				Portion p = t.getPortion(i);
-				if (p instanceof PairedPortion)
-				{
-					circ+=r.BASE_PAIR_DISTANCE/2.0;
-					ndir = dir + circ*angleIncr;
-					PairedPortion pp = (PairedPortion) p; 
-					for(int j=0;j<pp._len;j++)
-					{
-						int i1 = pp._pos1+j;
-						int i2 = pp._pos2-j;
-						double vx = Math.cos(ndir);
-						double vy = Math.sin(ndir);
-						double nx = x+((j*r.LOOP_DISTANCE+radius)*vx);
-						double ny = y+((j*r.LOOP_DISTANCE+radius)*vy);
-						r.get_listeBases().get(i1).set_coords(new Point2D.Double(nx+r.BASE_PAIR_DISTANCE*vy/ 2.0,ny-r.BASE_PAIR_DISTANCE*vx/ 2.0));
-						r.get_listeBases().get(i2).set_coords(new Point2D.Double(nx-r.BASE_PAIR_DISTANCE*vy/ 2.0,ny+r.BASE_PAIR_DISTANCE*vx/ 2.0));
-					}
-					double nx = x+(((pp._len-1)*r.LOOP_DISTANCE+radius)*Math.cos(ndir));
-					double ny = y+(((pp._len-1)*r.LOOP_DISTANCE+radius)*Math.sin(ndir));
-					drawTree(nx, ny, pp._r, ndir+Math.PI, r, straightness);
-					shapes.add(pp.getOutline(r));
-					circ += r.LOOP_DISTANCE + r.BASE_PAIR_DISTANCE/2.0;
-				}
-				else if (p instanceof UnpairedPortion)
-				{
-					UnpairedPortion up = (UnpairedPortion) p;
-					double mod = 1.0;
-					if ((i==0) || (i==t.getNumPortions()-1))
-						  mod = straightness;
-					for(int j=0;j<up._len;j++)
-					{
-						ndir = dir + circ*angleIncr;
-						double vx = Math.cos(ndir);
-						double vy = Math.sin(ndir);
-						double nx = x+((radius)*vx);
-						double ny = y+((radius)*vy);
-						r.get_listeBases().get(up._pos+j).set_coords(new Point2D.Double(nx,ny));
-						circ += mod*r.LOOP_DISTANCE;
-					}
-				}
-				//System.out.println(dir);
-			}
-			circ += r.BASE_PAIR_DISTANCE/2.0;
-			System.out.println(""+circ+"/"+totCirc);
-			if(shapes.size()>0)
-			{
-				collision = false;
-				for (int i=0;(i<shapes.size()) && !collision;i++)
-				{	
-					Area a1 = new Area(shapes.get(i));
-					for (int j=i+1;(j<shapes.size())&& !collision;j++)
-					{	
-						Area a2 = new Area(shapes.get(j));
-						a1.intersect(a2);
-						if (!a1.isEmpty())
-						{
-							collision = true;
-						}
-					}
-				}
-				if (collision)
-				{
-					straightness *= 1.2;
-					multRadius *= 1.5;
-				}
-					
-			}
-			else 
-			{
-				collision = false;
-			}
-		}
-	}
-	*/
-	
-	public int[] nextPlacement(int[] p) throws Exception
-	{
-		 //System.out.println(Arrays.toString(p));
-		int i=p.length-1;
-		int prev = MAX_NUM_DIR;
-		boolean stop = false;
-		while((i>=0) && !stop)
-		{
-			if (p[i]==prev-1)
-			{ 
-				prev = p[i]; 
-				i--; 
-			}
-			else
-			{ stop = true; }
-		}
-		if (i<0)
-			throw new Exception("No more placement available"); 
-		p[i]++;
-		i++;
-		while(i<p.length)
-		{
-			p[i] = p[i-1]+1;
-			i++;
-		}
-		 //System.out.println(Arrays.toString(p));		
-		return p;
-	}
-	
-	
-	public void drawTree(double x0, double y0, RNATree t, double dir, RNA r) throws Exception
-	{
-		boolean collision = true;
-		double x=x0;
-		double y=y0;
-		int numHelices = 0;
-		int nbHel = 1;
-		int nbUn = 0;
-		double totCirc = r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE;
-		for (int i=0;i<t.getNumPortions();i++ )
-		{
-			Portion p = t.getPortion(i);
-			if (p instanceof PairedPortion)
-			{
-				totCirc += (r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE);
-				nbHel += 1;
-			}
-			else
-			{
-				totCirc += r.LOOP_DISTANCE*(p.getNumBases());
-				nbUn += p.getNumBases()+1;
-			}
-		}
-		double radius = r.determineRadius(nbHel, nbUn, totCirc/(2.0*Math.PI));
-
-		for (int i=0;i<t.getNumPortions();i++ )
-		{
-			Portion p = t.getPortion(i);
-			if (p instanceof PairedPortion)
-			{
-				numHelices++;				
-			}
-		}
-		int[] placement = new int[numHelices];
-		double inc = ((double)MAX_NUM_DIR)/((double)numHelices+1);
-		double val = inc;
-		for (int i=0;i<numHelices;i++ )
-		{
-			placement[i] = (int)Math.round(val);
-			val += inc;
-		}
-		System.out.println();
-		double angleIncr = 2.0*Math.PI/(double)MAX_NUM_DIR;
-		while(collision)
-		{
-			x = x0+radius*Math.cos(dir+Math.PI);
-			y = y0+radius*Math.sin(dir+Math.PI);
-			ArrayList<GeneralPath> shapes = new ArrayList<GeneralPath>();
-			int curH = 0;
-			for (int i=0;i<t.getNumPortions();i++ )
-			{
-				Portion p = t.getPortion(i);
-				if (p instanceof PairedPortion)
-				{
-					double ndir = dir + placement[curH]*angleIncr;
-					curH++;
-					PairedPortion pp = (PairedPortion) p; 
-					for(int j=0;j<pp._len;j++)
-					{
-						int i1 = pp._pos1+j;
-						int i2 = pp._pos2-j;
-						double vx = Math.cos(ndir);
-						double vy = Math.sin(ndir);
-						double nx = x+(((j)*r.LOOP_DISTANCE+radius)*vx);
-						double ny = y+(((j)*r.LOOP_DISTANCE+radius)*vy);
-						r.get_listeBases().get(i1).setCoords(new Point2D.Double(nx+r.BASE_PAIR_DISTANCE*vy/ 2.0,ny-r.BASE_PAIR_DISTANCE*vx/ 2.0));
-						r.get_listeBases().get(i2).setCoords(new Point2D.Double(nx-r.BASE_PAIR_DISTANCE*vy/ 2.0,ny+r.BASE_PAIR_DISTANCE*vx/ 2.0));
-					}
-					double nx = x+(((pp._len-1)*r.LOOP_DISTANCE+radius)*Math.cos(ndir));
-					double ny = y+(((pp._len-1)*r.LOOP_DISTANCE+radius)*Math.sin(ndir));
-					drawTree(nx, ny, pp._r, ndir+Math.PI, r);
-					shapes.add(pp.getOutline(r));
-				}
-				else if (p instanceof UnpairedPortion)
-				{
-					UnpairedPortion up = (UnpairedPortion) p;
-					for(int j=0;j<up._len;j++)
-					{
-						/*ndir = dir + circ*angleIncr;
-							double vx = Math.cos(ndir);
-							double vy = Math.sin(ndir);
-							double nx = x+((radius)*vx);
-							double ny = y+((radius)*vy);
-							r.get_listeBases().get(up._pos+j).set_coords(new Point2D.Double(nx,ny));
-							circ += mod*r.LOOP_DISTANCE;*/
-						r.get_listeBases().get(up._pos+j).setCoords(new Point2D.Double(x,y));
-					}
-				}
-				//System.out.println(dir);
-			}
-			if(shapes.size()>0)
-			{
-				collision = false;
-				for (int i=0;(i<shapes.size()) && !collision;i++)
-				{	
-					Area a1 = new Area(shapes.get(i));
-					for (int j=i+1;(j<shapes.size())&& !collision;j++)
-					{	
-						Area a2 = new Area(shapes.get(j));
-						a1.intersect(a2);
-						if (!a1.isEmpty())
-						{
-							collision = true;
-						}
-					}
-				}
-				if (collision)
-				{
-					placement = nextPlacement(placement);
-				}
-					
-			}
-			else 
-			{
-				collision = false;
-			}
-		}
-	}
-
-
-	private class HelixEmbedding
-	{
-		private GeneralPath _clip;
-		Point2D.Double _support;
-		ArrayList<HelixEmbedding> _children = new ArrayList<HelixEmbedding>();
-		ArrayList<Integer> _indices = new ArrayList<Integer>();
-		PairedPortion _p;
-		RNA _r;
-		HelixEmbedding _parent;
-		
-		public HelixEmbedding(Point2D.Double support, PairedPortion p, RNA r, HelixEmbedding parent)
-		{
-			_support = support;
-			_clip = p.getLocalOutline(r);
-			_p = p;
-			_r = r;
-			_parent = parent;
-		}
-		
-		public void addHelixEmbedding(HelixEmbedding h, int index)
-		{
-			_children.add(h);
-			_indices.add(index);
-		}
-		
-		public GeneralPath getShape()
-		{
-			return _clip;
-		}
-		
-		
-		public int chooseNextMove()
-		{
-			int i = _parent._children.indexOf(this);
-			int min;
-			int max;
-			if (_parent._children.size()<VARNASecDraw.MAX_NUM_DIR-1)
-			{
-				if (_parent._children.size()==1)
-				{ min=1;max=VARNASecDraw.MAX_NUM_DIR-1;	}
-				else 
-				{
-					if (i==0)
-					{ min = 1; }
-					else
-					{ min = _parent._indices.get(i-1)+1;}
-					if (i==_parent._children.size()-1)
-					{ max = VARNASecDraw.MAX_NUM_DIR-1; }
-					else
-					{ max = _parent._indices.get(i+1)-1;}
-				}
-				int prevIndex = _parent._indices.get(i);
-				int newIndex = min+_rnd.nextInt(max+1-min);
-				double rot = ((double)(newIndex-prevIndex)*Math.PI*2.0)/MAX_NUM_DIR;
-				_parent._indices.set(i, newIndex);
-				rotate(rot);
-				return newIndex-prevIndex;
-			}
-			return 0;
-		}
-		
-		public void cancelMove(int delta)
-		{
-			int i = _parent._children.indexOf(this);
-			int prevIndex = _parent._indices.get(i);
-			double rot = ((double)(-delta)*Math.PI*2.0)/MAX_NUM_DIR;
-			_parent._indices.set(i, prevIndex-delta);
-			rotate(rot);
-		}
-		
-		public void rotate(double angle)
-		{
-			transform(AffineTransform.getRotateInstance(angle, _support.x, _support.y));
-		}
-		
-		private void transform(AffineTransform a)
-		{
-			_clip.transform(a);
-			Point2D p = a.transform(_support, null);
-			_support.setLocation(p.getX(), p.getY());
-			for (int i=0;i<_children.size();i++)
-			{
-				_children.get(i).transform(a);
-			}
-		}
-		
-		public void reflectCoordinates()
-		{
-			ArrayList<ModeleBase> mbl = _r.get_listeBases();
-
-			if (_p._len>0)
-			{
-				PathIterator pi = _clip.getPathIterator(AffineTransform.getRotateInstance(0.0));
-				ArrayList<Point2D.Double> p = new ArrayList<Point2D.Double>(); 
-				while(!pi.isDone())
-				{
-					double[] args = new double[6];
-					int type= pi.currentSegment(args);
-					if ((type == PathIterator.SEG_MOVETO)  || (type == PathIterator.SEG_LINETO))
-					{
-
-						Point2D.Double np = new Point2D.Double(args[0],args[1]); 
-						p.add(np);
-						System.out.println(Arrays.toString(args));
-					}
-					pi.next();
-				}
-				if (p.size()<4)
-				{ return; }
-				
-				Point2D.Double startLeft = p.get(0);
-				Point2D.Double endLeft = p.get(1);
-				Point2D.Double endRight = p.get(2);
-				Point2D.Double startRight = p.get(3);
-				
-				double d = startLeft.distance(endLeft);
-				double vx = endLeft.x-startLeft.x;
-				double vy = endLeft.y-startLeft.y;
-				double interval = 0.0;
-				if (_p._len>1)
-				{
-					vx/=d;
-					vy/=d;
-					interval = d/((double)_p._len-1);
-					System.out.println("DELTA: "+interval+" "+_r.LOOP_DISTANCE);
-				}
-				for (int n=0;n<_p._len;n++)
-				{
-					int i = _p._pos1 + n;
-					int j = _p._pos2 - n;
-					ModeleBase mbLeft = mbl.get(i);
-					mbLeft.setCoords(new Point2D.Double(startLeft.x+n*vx*interval, startLeft.y+n*vy*interval));
-					ModeleBase mbRight = mbl.get(j);
-					mbRight.setCoords(new Point2D.Double(startRight.x+n*vx*interval, startRight.y+n*vy*interval));
-				}
-			}
-			for (int i=0;i<_children.size();i++)
-			{
-				_children.get(i).reflectCoordinates();
-			}
-			if (_children.size()>0)
-			{
-				Point2D.Double center = _children.get(0)._support;
-				for (int i=0;i<_p._r.getNumPortions();i++)
-				{
-					Portion p = _p._r.getPortion(i);
-					if (p instanceof UnpairedPortion)
-					{
-						UnpairedPortion up = (UnpairedPortion) p;
-						for (int j=0;j<up._len;j++)
-						{
-							int n = up._pos + j;
-							ModeleBase mbLeft = mbl.get(n);
-							mbLeft.setCoords(center);
-						}
-					}
-				}	
-			}
-			else
-			{
-				placeTerminalLoop(mbl,_r);
-			}
-		}
-		
-		private void placeTerminalLoop(ArrayList<ModeleBase> mbl, RNA r)
-		{
-			if ((_children.size()==0)&&(_p._r.getNumPortions()==1))
-			{
-				Portion p = _p._r.getPortion(0);
-				if (p instanceof UnpairedPortion)
-				{
-					UnpairedPortion up = (UnpairedPortion) p;
-					double rad = determineRadius(1,up.getNumBases(),_r);
-					int a = _p._pos1+_p._len-1;
-					int b = _p._pos2-(_p._len-1);
-					ModeleBase mbLeft = mbl.get(a);
-					ModeleBase mbRight = mbl.get(b);
-					Point2D.Double pl = mbLeft.getCoords();
-					Point2D.Double pr = mbRight.getCoords();
-					Point2D.Double pm = new Point2D.Double((pl.x+pr.x)/2.0,(pl.y+pr.y)/2.0);
-					double vx = (pl.x-pr.x)/pl.distance(pr);
-					double vy = (pl.y-pr.y)/pl.distance(pr);
-					double vnx = -vy, vny = vx;
-					Point2D.Double pc = new Point2D.Double(pm.x+rad*vnx,pm.y+rad*vny);
-					double circ = r.LOOP_DISTANCE*(1.0+up.getNumBases())+r.BASE_PAIR_DISTANCE; 
-					double incrLoop = Math.PI*2.0*r.LOOP_DISTANCE/circ;  
-					double angle = Math.PI*2.0*r.BASE_PAIR_DISTANCE/(2.0*circ);
-					for (int j=0;j<up._len;j++)
-					{
-						int n = up._pos + j;
-						ModeleBase mb = mbl.get(n);
-						angle += incrLoop;
-						double dx = -Math.cos(angle)*vnx+Math.sin(angle)*vx;
-						double dy = -Math.cos(angle)*vny+Math.sin(angle)*vy;
-//						Point2D.Double pf = new Point2D.Double(pc.x,pc.y);
-						Point2D.Double pf = new Point2D.Double(pc.x+rad*dx,pc.y+rad*dy);
-						mb.setCoords(pf);
-					}
-					
-				}
-			}
-		}
-		
-		
-		
-		public String toString()
-		{
-			return "Emb.Hel.: "+_p.toString();
-		}
-	}
-	
-	public double determineRadius(int numHelices, int numUnpaired, RNA r)
-	{
-		double circ = numHelices*r.BASE_PAIR_DISTANCE+(numHelices+numUnpaired)*r.LOOP_DISTANCE;
-		return circ/(2.0*Math.PI);
-	}
-	
-	
-	public void predrawTree(double x0, double y0, RNATree t, double dir, RNA r, HelixEmbedding parent, ArrayList<HelixEmbedding> all) throws Exception
-	{
-		double x=x0;
-		double y=y0;
-		int numHelices = 0;
-		int numUBases = 0;
-		double totCirc = r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE;
-		for (int i=0;i<t.getNumPortions();i++ )
-		{
-			Portion p = t.getPortion(i);
-			if (p instanceof PairedPortion)
-			{
-				totCirc += (r.BASE_PAIR_DISTANCE+r.LOOP_DISTANCE);
-				numHelices++;	
-			}
-			else
-			{
-				  totCirc += r.LOOP_DISTANCE*(p.getNumBases());
-				  numUBases += p.getNumBases();
-			}
-		}
-		double radius = determineRadius(numHelices+1,numUBases,r);
-
-		int[] placement = new int[numHelices];
-		double inc = ((double)MAX_NUM_DIR)/((double)numHelices+1);
-		double val = inc;
-		for (int i=0;i<numHelices;i++ )
-		{
-			placement[i] = (int)Math.round(val);
-			val += inc;
-		}
-		double angleIncr = 2.0*Math.PI/(double)MAX_NUM_DIR;
-			x = x0+radius*Math.cos(dir+Math.PI);
-			y = y0+radius*Math.sin(dir+Math.PI);
-			int curH = 0;
-			for (int i=0;i<t.getNumPortions();i++ )
-			{
-				Portion p = t.getPortion(i);
-				if (p instanceof PairedPortion)
-				{
-					double ndir = dir + placement[curH]*angleIncr;
-					PairedPortion pp = (PairedPortion) p; 
-					for(int j=0;j<pp._len;j++)
-					{
-						int i1 = pp._pos1+j;
-						int i2 = pp._pos2-j;
-						double vx = Math.cos(ndir);
-						double vy = Math.sin(ndir);
-						double nx = x+(((j)*r.LOOP_DISTANCE+radius)*vx);
-						double ny = y+(((j)*r.LOOP_DISTANCE+radius)*vy);
-						r.get_listeBases().get(i1).setCoords(new Point2D.Double(nx+r.BASE_PAIR_DISTANCE*vy/ 2.0,ny-r.BASE_PAIR_DISTANCE*vx/ 2.0));
-						r.get_listeBases().get(i2).setCoords(new Point2D.Double(nx-r.BASE_PAIR_DISTANCE*vy/ 2.0,ny+r.BASE_PAIR_DISTANCE*vx/ 2.0));
-					}
-					double nx = x+(((pp._len-1)*r.LOOP_DISTANCE+radius)*Math.cos(ndir));
-					double ny = y+(((pp._len-1)*r.LOOP_DISTANCE+radius)*Math.sin(ndir));
-					HelixEmbedding nh = new HelixEmbedding(new Point2D.Double(x,y),pp,r,parent);
-					parent.addHelixEmbedding(nh,placement[curH]);
-					all.add(nh);
-					predrawTree(nx, ny, pp._r, ndir+Math.PI, r, nh, all);
-					curH++;
-				}
-				else if (p instanceof UnpairedPortion)
-				{
-					UnpairedPortion up = (UnpairedPortion) p;
-					for(int j=0;j<up._len;j++)
-					{
-						r.get_listeBases().get(up._pos+j).setCoords(new Point2D.Double(x,y));
-					}
-				}
-				//System.out.println(dir);
-			}
-	}
-	
-	
-	public static Random _rnd = new Random();
-	
-	private static int MAX_NUM_DIR = 8;
-
-	public RNATree drawRNA(double dirAngle, RNA r) {
-		RNATree t = new RNATree();
-		buildTree(0, r.get_listeBases().size() - 1, t,  r );
-		System.out.println(t);
-		ArrayList<HelixEmbedding> all = new ArrayList<HelixEmbedding>();
-		HelixEmbedding root = null;
-		try {
-			root = new HelixEmbedding(new Point2D.Double(0.0,0.0),new PairedPortion(0,0,0,t),r,null); 
-			predrawTree(0,0,t,0.0,r,root,all);
-			int steps=1000;
-			double prevbadness = Double.MAX_VALUE;
-			while((steps>0)&&(prevbadness>0))
-			{
-
-				// Generating new structure
-				HelixEmbedding chosen = all.get(_rnd.nextInt(all.size()));
-				int delta =  chosen.chooseNextMove();
-				// Draw current
-				if (_vp!=null)
-					{ 
-						GeneralPath p = new GeneralPath();
-						for (int i=0;i<all.size();i++)
-						{ p.append(all.get(i).getShape(),false); }
-						r._debugShape = p;
-						_vp.paintImmediately(0, 0, _vp.getWidth(), _vp.getHeight());	
-					}				
-
-				//Evaluating solution
-				double badness = 0.0;
-				for (int i=0;i<all.size();i++)
-				{ 
-					Shape s1 = all.get(i).getShape();
-					for (int j=i+1;j<all.size();j++)
-					{ 
-						Shape s2 = all.get(j).getShape();
-						Area a = new Area(s1);
-						a.intersect(new Area(s2));
-						if (!a.isEmpty())
-						{
-							badness ++;
-						}
-					}
-				}
-
-				if (badness-prevbadness>0)
-				{
-					chosen.cancelMove(delta);
-				}
-				else
-				{
-					prevbadness = badness;
-				}
-
-				System.out.println(badness);
-
-				steps--;
-			}
-			if (root!=null)
-			{ root.reflectCoordinates(); }
-		} catch (Exception e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return t;
-	};
-	
-}
\ No newline at end of file