X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FTreeGraphviz.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FTreeGraphviz.java;h=be22782a44f01a22619a16a71166f7351eb853bc;hp=0000000000000000000000000000000000000000;hb=665d2c2f4c1310e6985b93b7c2c8a8eec2fa9086;hpb=0e684f72690bd6532272a39ab6c188a27559fd09

diff --git a/src2/fr/orsay/lri/varna/models/treealign/TreeGraphviz.java b/src2/fr/orsay/lri/varna/models/treealign/TreeGraphviz.java
new file mode 100644
index 0000000..be22782
--- /dev/null
+++ b/src2/fr/orsay/lri/varna/models/treealign/TreeGraphviz.java
@@ -0,0 +1,114 @@
+package fr.orsay.lri.varna.models.treealign;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+
+
+
+/**
+ * This class translates a Tree to a graphviz file.
+ * @author Raphael Champeimont
+ *
+ * @param <? extends GraphvizDrawableNodeValue> the type of values in the tree
+ */
+public class TreeGraphviz {
+
+	/**
+	 * Generates a PostScript file using graphviz.
+	 * The dot command must be available.
+	 */
+	public static void treeToGraphvizPostscript(Tree<? extends GraphvizDrawableNodeValue> tree, String filename, String title) throws IOException {
+		// generate graphviz source
+		String graphvizSource = treeToGraphviz(tree, title);
+		
+		// open output file
+		BufferedWriter fbw;
+		fbw = new BufferedWriter(new FileWriter(filename));
+    	
+    	// execute graphviz
+		Process proc = Runtime.getRuntime().exec("dot -Tps");
+    	BufferedWriter bw  = new BufferedWriter(new OutputStreamWriter(proc.getOutputStream()));
+    	BufferedReader br  = new BufferedReader(new InputStreamReader(proc.getInputStream()));
+    	BufferedReader bre = new BufferedReader(new InputStreamReader(proc.getErrorStream()));
+    	bw.write(graphvizSource);
+    	bw.close();
+    	{
+	    	String line = null;
+            while ((line = br.readLine()) != null) {
+            	fbw.write(line + "\n");
+            }
+    	}
+    	{
+	    	String line = null;
+            while ((line = bre.readLine()) != null) {
+            	System.err.println(line);
+            }
+    	}
+    	
+    	// wait for graphviz to end
+        try {
+			proc.waitFor();
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+		}
+
+        // close file
+		fbw.close();
+	}
+	
+	/**
+	 * Like treeToGraphvizPostscript(Tree,String,String) but with the title
+	 * equal to the filename.
+	 */
+	public static void treeToGraphvizPostscript(Tree<? extends GraphvizDrawableNodeValue> tree, String filename) throws IOException {
+		treeToGraphvizPostscript(tree, filename, filename);
+	}
+	
+	/**
+	 * Creates a graphviz source file from a Tree.
+	 * @param title the title of the graph
+	 */
+	public static void treeToGraphvizFile(Tree<? extends GraphvizDrawableNodeValue> tree, String filename, String title) throws IOException {
+		BufferedWriter bw;
+		bw = new BufferedWriter(new FileWriter(filename));
+    	bw.write(treeToGraphviz(tree, filename));
+    	bw.close();
+	}
+	
+	/**
+	 * Like treeToGraphvizFile(Tree,String,String) but with the title
+	 * equal to the filename.
+	 */
+	public static void treeToGraphvizFile(Tree<? extends GraphvizDrawableNodeValue> tree, String filename) throws IOException {
+		treeToGraphvizFile(tree, filename, filename);
+	}
+	
+	/**
+	 * Creates a graphviz source from a Tree.
+	 * @param title the title of the graph
+	 */
+	public static String treeToGraphviz(Tree<? extends GraphvizDrawableNodeValue> tree, String title) {
+		return "digraph \"" + title + "\" {\n" + subtreeToGraphviz(tree) + "}\n";
+	}
+	
+	private static String subtreeToGraphviz(Tree<? extends GraphvizDrawableNodeValue> tree) {
+		String s = "";
+		String myId = tree.toGraphvizNodeId();
+		
+		s +=
+			"\""
+			+ myId
+			+ "\" [label=\""
+			+ ((tree.getValue() != null) ? tree.getValue().toGraphvizNodeName() : "null")
+			+ "\"]\n";
+		for (Tree<? extends GraphvizDrawableNodeValue> child: tree.getChildren()) {
+			s += "\"" + myId + "\" -> \"" + child.toGraphvizNodeId() + "\"\n";
+			s += subtreeToGraphviz(child);
+		}
+		
+		return s;
+	}
+}