add DirichletSimulator #1199

Author: walterxie

src/beast/base/inference/distribution/DirichletSimulator.java

@@ -0,0 +1,62 @@
+package beast.base.inference.distribution;
+
+import beast.base.inference.parameter.RealParameter;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+public class DirichletSimulator {
+
+    static String homePath = System.getProperty("user.home");
+    static Path outFilePath = Paths.get(homePath, "WorkSpace", "tmp", "simDirichletA1111.log");
+
+    public static void main(String[] args) {
+        Dirichlet dirichlet = new Dirichlet();
+        RealParameter alphaParam = new RealParameter(new Double[]{1.0,1.0,1.0,1.0});
+
+        dirichlet.initByName("alpha", alphaParam);
+
+        final int size = 100000;
+        Double[][] val2d = dirichlet.sample(size);
+        System.out.println("Simulate " + size + " samples");
+
+        try (BufferedWriter writer = new BufferedWriter(new FileWriter(outFilePath.toFile()))) {
+            // header
+            writer.write("Sample\t");
+            if (alphaParam.getDimension() == 4) {
+                writer.write("pi.A\tpi.C\tpi.G\tpi.T");
+            } else {
+                for (int i = 0; i < val2d[0].length; i++) {
+                    writer.write("Var" + (i + 1));
+                    if (i < val2d[0].length - 1) {
+                        writer.write('\t'); // tab delimiter
+                    }
+                }
+            }
+            writer.newLine(); // new line after each row
+
+            for (int n = 0; n < val2d.length; n++) {
+                writer.write(Integer.toString(n) + '\t');
+                for (int i = 0; i < val2d[n].length; i++) {
+                    writer.write(Double.toString(val2d[n][i]));
+                    if (i < val2d[n].length - 1) {
+                        writer.write('\t'); // tab delimiter
+                    }
+                }
+                writer.newLine(); // new line after each row
+
+                if (n % 1000 == 0) {
+                    System.out.println("Wrote " + n + " lines...");
+                }
+            }
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+
+        System.out.println("Finish writing file to " + outFilePath.toFile());
+    }
+
+}