src2/fr/orsay/lri/varna/models/templates/Benchmark.java

   1 package fr.orsay.lri.varna.models.templates;
   2
   3 import java.awt.geom.Line2D;
   4 import java.util.Arrays;
   5
   6 import fr.orsay.lri.varna.models.geom.LinesIntersect;
   7 import fr.orsay.lri.varna.models.rna.RNA;
   8
   9 /**
  10  * @author Raphael Champeimont
  11  *
  12  */
  13 public class Benchmark {
  14         private RNA rna;
  15
  16         // number of backbone crossings
  17         public int backboneCrossings;
  18         // average distance between unpaired consecutive bases
  19         public double averageUnpairedDistance;
  20         // median distance between consecutive bases
  21         public double medianConsecutiveBaseDistance;
  22         // Number of consecutive bases that are too near from each other
  23         public int tooNearConsecutiveBases;
  24         // Number of consecutive bases that are too far from each other
  25         public int tooFarConsecutiveBases;
  26
  27
  28
  29         // Parameters
  30         public double targetConsecutiveBaseDistance = RNA.LOOP_DISTANCE;
  31         // If consecutive bases are nearer that tooNearFactor * target distance, we call them too near.
  32         public double tooNearFactor = 0.5;
  33         // If consecutive bases are further that tooFarFactor * target distance, we call them too far.
  34         public double tooFarFactor = 2;
  35
  36
  37
  38         public Benchmark(RNA rna) {
  39                 this.rna = rna;
  40                 computeAll();
  41         }
  42
  43         private void computeAll() {
  44                 // Compute number of backbone crossings
  45                 {
  46                         int n = rna.getSize();
  47                         Line2D.Double[] lines = new Line2D.Double[n-1];
  48                         for (int i=0; i<n-1; i++) {
  49                                 lines[i] = new Line2D.Double(rna.getCoords(i), rna.getCoords(i+1));
  50                         }
  51                         int intersectLines = 0;
  52                         for (int i=0; i<n-1; i++) {
  53                                 for (int j=i+2; j<n-1; j++) {
  54                                         if (LinesIntersect.linesIntersect(lines[i], lines[j])) {
  55                                                 intersectLines++;
  56                                         }
  57                                 }
  58                         }
  59                         backboneCrossings = intersectLines;
  60                 }
  61
  62                 // Stats about distances between consecutive bases not both part of an helix
  63                 {
  64                         int n = rna.getSize();
  65                         double sum = 0;
  66                         int count = 0;
  67                         for (int i=0; i<n-1; i++) {
  68                                 int indexOfAssociatedBase1 = rna.getBaseAt(i).getElementStructure();
  69                                 int indexOfAssociatedBase2 = rna.getBaseAt(i+1).getElementStructure();
  70                                 if (indexOfAssociatedBase1 != -1 || indexOfAssociatedBase2 != -1) {
  71                                         // If they are not both associated (ie. not part of an helix)
  72                                         sum += rna.getBaseAt(i).getCoords().distance(rna.getBaseAt(i+1).getCoords());
  73                                         count++;
  74                                 }
  75                         }
  76                         averageUnpairedDistance = sum / count;
  77                 }
  78
  79                 // Stats about base distances
  80                 {
  81                         int n = rna.getSize();
  82                         double distances[] = new double[n-1];
  83                         for (int i=0; i<n-1; i++) {
  84                                 // If they are not both associated (ie. not part of an helix)
  85                                 distances[i] = rna.getBaseAt(i).getCoords().distance(rna.getBaseAt(i+1).getCoords());
  86                         }
  87                         Arrays.sort(distances);
  88                         double median = distances[distances.length/2];
  89                         medianConsecutiveBaseDistance = median;
  90
  91                         // We take the median as target distance, and count
  92                         // the number of consecutive bases with a distance too different
  93                         tooNearConsecutiveBases = 0;
  94                         tooFarConsecutiveBases = 0;
  95                         for (int i=0; i<n-1; i++) {
  96                                 if (distances[i] < tooNearFactor*targetConsecutiveBaseDistance) {
  97                                         tooNearConsecutiveBases++;
  98                                 }
  99                                 if (distances[i] > tooFarFactor*targetConsecutiveBaseDistance) {
 100                                         tooFarConsecutiveBases++;
 101                                 }
 102                         }
 103                 }
 104         }
 105
 106         @SuppressWarnings("unused")
 107         private int percent(int a, int b) {
 108                 return (int) Math.round((double) a / (double) b * 100.0);
 109         }
 110
 111         public void printAll() {
 112                 System.out.println("Benchmark:");
 113                 System.out.println("\tBackbone crossings = " + backboneCrossings);
 114                 System.out.println("\tAverage unpaired distance = " + averageUnpairedDistance);
 115                 System.out.println("\tMedian of consecutive base distance = " + medianConsecutiveBaseDistance);
 116                 System.out.println("\tNumber of too near consecutive bases = " + tooNearConsecutiveBases); // + " ie. " + percent(tooNearConsecutiveBases, rna.getSize()-1) + " %");
 117                 System.out.println("\tNumber of too far consecutive bases = " + tooFarConsecutiveBases); // + " ie. " + percent(tooFarConsecutiveBases, rna.getSize()-1) + " %");
 118         }
 119 }
 120