Merge branch 'master' of https://github.com/CompEvol/sampled-ancestors

src/beast/app/tools/SATreeToBinaryTreeConverter.java

@@ -0,0 +1,84 @@
+package beast.app.tools;
+
+import beast.evolution.tree.Tree;
+import beast.evolution.tree.ZeroBranchSANode;
+import beast.util.SANexusParser;
+
+import java.io.BufferedOutputStream;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * @author Alexandra Gavryushkina
+ */
+
+/** converts nexus files with SA trees to nexus file of binary trees 
+ * Usage: SATreeToBinaryTreeConverter <inputFile> <outpuFile>
+ * Default outputFile = /tmp/x.trees
+ * **/
+public class SATreeToBinaryTreeConverter {
+
+    public static void perform(SampledAncestorTreeTrace trace, boolean useNumbers, String outputFile) throws Exception {
+    	PrintStream out = new PrintStream(new BufferedOutputStream(new FileOutputStream(outputFile)));
+
+    	trace.beastTrees.get(0).init(out);
+    	out.println();
+    	for (int i=0; i< trace.beastTrees.size(); i++) {
+    		out.print("tree STATE_" + i + " = ");
+    	    out.print(((ZeroBranchSANode)trace.beastTrees.get(i).getRoot()).toSortedNewickWithZeroBranches(new int[]{0}));
+    	    out.println(";");
+    	}
+    	out.println("End;");
+    	out.close();
+    }
+
+    public static void main(String[] args) throws IOException, Exception {
+
+        boolean useNumbers = false;
+
+        java.io.File file;
+        String outputFile = "/tmp/x.trees";
+        if (args != null && args.length > 0) {
+            file = new java.io.File(args[0]);
+            if (args.length == 2) {
+            	outputFile = args[1];
+            }
+        } else {
+            String message = "Choose file .trees";
+            java.awt.Frame frame = new java.awt.Frame();
+            java.awt.FileDialog chooser = new java.awt.FileDialog(frame, message,
+                    java.awt.FileDialog.LOAD);
+            chooser.setVisible(true);
+            if (chooser.getFile() == null) {
+                System.out.println("The file was not chosen.");
+                System.exit(0);
+            }
+            file = new java.io.File(chooser.getDirectory(), chooser.getFile());
+            chooser.dispose();
+            frame.dispose();
+        }
+
+        FileReader reader = null;
+
+        try {
+            System.err.println("Reading file " + file.getName());
+            reader = new FileReader(file);
+            SANexusParser parser = new SANexusParser();
+            parser.parseFile(file);
+            SampledAncestorTreeTrace trace = new SampledAncestorTreeTrace(parser);
+            perform(trace, useNumbers, outputFile);
+        }
+        catch (IOException e) {
+            //
+        }
+        finally {
+            if (reader != null) {
+                reader.close();
+            }
+        }
+    }
+
+}