+++ /dev/null
-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
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