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=0000000000000000000000000000000000000000;hp=be22782a44f01a22619a16a71166f7351eb853bc;hb=a1225b9392dc7657d5cef12907385b07527d6122;hpb=b513684c725997c77341f30ce4e584cf9f7cdfed

diff --git a/src2/fr/orsay/lri/varna/models/treealign/TreeGraphviz.java b/src2/fr/orsay/lri/varna/models/treealign/TreeGraphviz.java
deleted file mode 100644
index be22782..0000000
--- a/src2/fr/orsay/lri/varna/models/treealign/TreeGraphviz.java
+++ /dev/null
@@ -1,114 +0,0 @@
-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;
-	}
-}