fr.orsay.lri.varna.models.rna
Class VARNASecDraw

java.lang.Object
  extended by fr.orsay.lri.varna.models.rna.VARNASecDraw

public class VARNASecDraw
extends Object


Nested Class Summary
private  class VARNASecDraw.HelixEmbedding
           
 class VARNASecDraw.PairedPortion
           
 class VARNASecDraw.Portion
           
 class VARNASecDraw.RNATree
           
 class VARNASecDraw.UnpairedPortion
           
 
Field Summary
 int _depth
           
static Random _rnd
           
static VARNAPanel _vp
           
private static int MAX_NUM_DIR
           
 
Constructor Summary
VARNASecDraw()
           
 
Method Summary
private  void buildTree(int i, int j, VARNASecDraw.RNATree parent, RNA r)
           
 double determineRadius(int numHelices, int numUnpaired, RNA r)
           
 VARNASecDraw.RNATree drawRNA(double dirAngle, RNA r)
           
 void drawTree(double x0, double y0, VARNASecDraw.RNATree t, double dir, RNA r)
           
 int[] nextPlacement(int[] p)
           
 void predrawTree(double x0, double y0, VARNASecDraw.RNATree t, double dir, RNA r, VARNASecDraw.HelixEmbedding parent, ArrayList<VARNASecDraw.HelixEmbedding> all)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

_vp

public static VARNAPanel _vp

_depth

public int _depth

_rnd

public static Random _rnd

MAX_NUM_DIR

private static int MAX_NUM_DIR
Constructor Detail

VARNASecDraw

public VARNASecDraw()
Method Detail

buildTree

private void buildTree(int i,
                       int j,
                       VARNASecDraw.RNATree parent,
                       RNA r)

nextPlacement

public int[] nextPlacement(int[] p)
                    throws Exception
Throws:
Exception

drawTree

public void drawTree(double x0,
                     double y0,
                     VARNASecDraw.RNATree t,
                     double dir,
                     RNA r)
              throws Exception
Throws:
Exception

determineRadius

public double determineRadius(int numHelices,
                              int numUnpaired,
                              RNA r)

predrawTree

public void predrawTree(double x0,
                        double y0,
                        VARNASecDraw.RNATree t,
                        double dir,
                        RNA r,
                        VARNASecDraw.HelixEmbedding parent,
                        ArrayList<VARNASecDraw.HelixEmbedding> all)
                 throws Exception
Throws:
Exception

drawRNA

public VARNASecDraw.RNATree drawRNA(double dirAngle,
                                    RNA r)