JAL-3026 srcjar files for VARNA and log4j

[jalview.git] / srcjar / fr / orsay / lri / varna / models / geom / ComputeEllipseAxis.java

diff --git a/srcjar/fr/orsay/lri/varna/models/geom/ComputeEllipseAxis.java b/srcjar/fr/orsay/lri/varna/models/geom/ComputeEllipseAxis.java
new file mode 100644 (file)
index 0000000..b8d699b
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/geom/ComputeEllipseAxis.java
@@ -0,0 +1,92 @@
+/**
+ * File written by Raphael Champeimont
+ * UMR 7238 Genomique des Microorganismes
+ */
+package fr.orsay.lri.varna.models.geom;
+
+public class ComputeEllipseAxis {
+       public static boolean debug = false;
+       
+       /**
+        * Given one axis half-length b and the circumference l,
+        * find the other axis half-length a.
+        * Returns 0 if there is no solution.
+        * Implemented with Newton's method.
+        */
+       public static double computeEllipseAxis(double b, double l) {
+               if (l/4 <= b || b <= 0 || l <= 0) {
+                       // No such ellipse can exist.
+                       return 0;
+               } else {
+                       int steps = 0;
+                       double x_n = 10;
+                       double x_n_plus_1, f_x_n, f_x_n_plus_1;
+                       f_x_n = f(x_n,b) - l;
+                       while (true) {
+                               //System.out.println("x_n = " + x_n + "  f(x_n)=" + f_x_n);
+                               x_n_plus_1 = x_n - f_x_n/fprime(x_n,b);
+                               f_x_n_plus_1 = f(x_n_plus_1,b) - l;
+                               if (x_n_plus_1 < 0) {
+                                       System.out.println("ComputeEllipseAxis: x_n < 0 => returning 0");
+                                       return 0;
+                               }
+                               // We want a precision of 0.01 on arc length
+                               if (Math.abs(f_x_n_plus_1 - f_x_n) < 0.01) {
+                                       if (debug) System.out.println("#steps = " + steps);
+                                       return x_n_plus_1;
+                               }
+                               x_n = x_n_plus_1;
+                               f_x_n = f_x_n_plus_1;
+                               steps++;
+                       }
+               }
+       }
+       
+       
+       
+       private static double f(double a, double b) {
+               // This is Ramanujan's approximation of an ellipse circumference
+               // Nice because it is fast to compute (no need to compute an integral)
+               // and the derivative is also simple (and fast to compute).
+               return Math.PI*(3*(a+b) - Math.sqrt(10*a*b + 3*(a*a + b*b)));
+       }
+       
+       private static double fprime(double a, double b) {
+               return Math.PI*(3 - (5*b + 3*a)/Math.sqrt(10*a*b + 3*(a*a + b*b)));
+       }
+       
+       
+       /*
+       private static void test(double a, double b, double l) {
+               double a2 = computeEllipseAxis(b, l);
+               System.out.println("true a=" + a + " l=" + l + "   estimated a=" + a2 + " l(from true a)=" + f(a,b));
+       }
+       
+       private static void test(double b, double l) {
+               double a2 = computeEllipseAxis(b, l);
+               System.out.println("true l=" + l + "   estimated a=" + a2);
+       }
+       
+       
+       public static void main(String[] args) {
+               double b = 4;
+               test(100, b, 401.3143);
+               test(7, b, 35.20316);
+               test(4, b, 25.13274);
+               test(1, b, 17.15684);
+               test(0.5, b, 16.37248);
+               test(0.25, b, 16.11448);
+               test(0.1, b, 16.02288);
+               test(0.01, b, 16.00034);
+               test(0, b, 16);
+               test(10000, b, 40000.03);
+       }
+       */
+       
+       /*
+       public static void main(String[] args) {
+               test(222.89291150684895, 2240);
+       }
+       */
+       
+}