JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

[jalview.git] / src2 / fr / orsay / lri / varna / models / templates / Benchmark.java

diff --git a/src2/fr/orsay/lri/varna/models/templates/Benchmark.java b/src2/fr/orsay/lri/varna/models/templates/Benchmark.java
deleted file mode 100644 (file)
index b3db1fd..0000000
--- a/src2/fr/orsay/lri/varna/models/templates/Benchmark.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package fr.orsay.lri.varna.models.templates;
-
-import java.awt.geom.Line2D;
-import java.util.Arrays;
-
-import fr.orsay.lri.varna.models.geom.LinesIntersect;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-/**
- * @author Raphael Champeimont
- *
- */
-public class Benchmark {
-       private RNA rna;
-       
-       // number of backbone crossings
-       public int backboneCrossings;
-       // average distance between unpaired consecutive bases
-       public double averageUnpairedDistance;
-       // median distance between consecutive bases
-       public double medianConsecutiveBaseDistance;
-       // Number of consecutive bases that are too near from each other
-       public int tooNearConsecutiveBases;
-       // Number of consecutive bases that are too far from each other
-       public int tooFarConsecutiveBases;
-       
-       
-       
-       // Parameters
-       public double targetConsecutiveBaseDistance = RNA.LOOP_DISTANCE;
-       // If consecutive bases are nearer that tooNearFactor * target distance, we call them too near.
-       public double tooNearFactor = 0.5;
-       // If consecutive bases are further that tooFarFactor * target distance, we call them too far.
-       public double tooFarFactor = 2;
-       
-       
-       
-       public Benchmark(RNA rna) {
-               this.rna = rna;
-               computeAll();
-       }
-       
-       private void computeAll() {
-               // Compute number of backbone crossings
-               {
-                       int n = rna.getSize();
-                       Line2D.Double[] lines = new Line2D.Double[n-1];
-                       for (int i=0; i<n-1; i++) {
-                               lines[i] = new Line2D.Double(rna.getCoords(i), rna.getCoords(i+1));
-                       }
-                       int intersectLines = 0;
-                       for (int i=0; i<n-1; i++) {
-                               for (int j=i+2; j<n-1; j++) {
-                                       if (LinesIntersect.linesIntersect(lines[i], lines[j])) {
-                                               intersectLines++;
-                                       }
-                               }
-                       }
-                       backboneCrossings = intersectLines;
-               }
-               
-               // Stats about distances between consecutive bases not both part of an helix
-               {
-                       int n = rna.getSize();
-                       double sum = 0;
-                       int count = 0;
-                       for (int i=0; i<n-1; i++) {
-                               int indexOfAssociatedBase1 = rna.getBaseAt(i).getElementStructure();
-                               int indexOfAssociatedBase2 = rna.getBaseAt(i+1).getElementStructure();
-                               if (indexOfAssociatedBase1 != -1 || indexOfAssociatedBase2 != -1) {
-                                       // If they are not both associated (ie. not part of an helix)
-                                       sum += rna.getBaseAt(i).getCoords().distance(rna.getBaseAt(i+1).getCoords());
-                                       count++;
-                               }
-                       }
-                       averageUnpairedDistance = sum / count;
-               }
-               
-               // Stats about base distances
-               {
-                       int n = rna.getSize();
-                       double distances[] = new double[n-1];
-                       for (int i=0; i<n-1; i++) {
-                               // If they are not both associated (ie. not part of an helix)
-                               distances[i] = rna.getBaseAt(i).getCoords().distance(rna.getBaseAt(i+1).getCoords());
-                       }
-                       Arrays.sort(distances);
-                       double median = distances[distances.length/2];
-                       medianConsecutiveBaseDistance = median;
-                       
-                       // We take the median as target distance, and count
-                       // the number of consecutive bases with a distance too different
-                       tooNearConsecutiveBases = 0;
-                       tooFarConsecutiveBases = 0;
-                       for (int i=0; i<n-1; i++) {
-                               if (distances[i] < tooNearFactor*targetConsecutiveBaseDistance) {
-                                       tooNearConsecutiveBases++;
-                               }
-                               if (distances[i] > tooFarFactor*targetConsecutiveBaseDistance) {
-                                       tooFarConsecutiveBases++;
-                               }
-                       }
-               }
-       }
-       
-       @SuppressWarnings("unused")
-       private int percent(int a, int b) {
-               return (int) Math.round((double) a / (double) b * 100.0);
-       }
-
-       public void printAll() {
-               System.out.println("Benchmark:");
-               System.out.println("\tBackbone crossings = " + backboneCrossings);
-               System.out.println("\tAverage unpaired distance = " + averageUnpairedDistance);
-               System.out.println("\tMedian of consecutive base distance = " + medianConsecutiveBaseDistance);
-               System.out.println("\tNumber of too near consecutive bases = " + tooNearConsecutiveBases); // + " ie. " + percent(tooNearConsecutiveBases, rna.getSize()-1) + " %");
-               System.out.println("\tNumber of too far consecutive bases = " + tooFarConsecutiveBases); // + " ie. " + percent(tooFarConsecutiveBases, rna.getSize()-1) + " %");
-       }
-}
-