JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

[jalview.git] / src2 / fr / orsay / lri / varna / models / treealign / TreeGraphviz.java

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 (file)
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;
-       }
-}