Edited wiki page forester through web user interface.

[jalview.git] / wiki / forester.wiki

diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index f74ebcf..3e4c70f 100644 (file)
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -271,7 +271,7 @@ public class Example {
 
 }}}
 
-= ddd =
+= Writing a phylogenetic tree to a graphics file (e.g. png, jpg) =
 
 {{{
 
@@ -289,24 +289,31 @@ import org.forester.archaeopteryx.TreeColorSet;
 
 public class phylo2graphics {
 
-    public static void main(final String[] args) {
-       try {
-           Configuration config = new Configuration();
-           // Could also read a configuration file with:
-           // Configuration config = new Configuration("my_configuration_file.txt", false, false, false);
-           config.putDisplayColors(TreeColorSet.BACKGROUND, new Color(255, 255, 255));
-           config.putDisplayColors(TreeColorSet.BRANCH, new Color(0, 0, 0));
-           config.putDisplayColors(TreeColorSet.TAXONOMY, new Color(0, 0, 0));
-          config.setPhylogenyGraphicsType(
-                Options.PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR);
-
-           AptxUtil.writePhylogenyToGraphicsFileNonInteractive(new File(
-                                       "/home/czmasek/tol_117_TEST.xml"), new File(
-                                       "/home/czmasek/tol_117_TEST_.png"), 1000, 1000,
-                                       GraphicsExportType.PNG, config);
+    public static void main( final String[] args ) {
+        try {
+            final Configuration config = new Configuration();
+            // Could also read a configuration file with:
+            // Configuration config = new Configuration("my_configuration_file.txt", false, false, false);
+            config.putDisplayColors( TreeColorSet.BACKGROUND, new Color( 255, 255, 255 ) );
+            config.putDisplayColors( TreeColorSet.BRANCH, new Color( 0, 0, 0 ) );
+            config.putDisplayColors( TreeColorSet.TAXONOMY, new Color( 0, 0, 0 ) );
+            config.setPhylogenyGraphicsType( Options.PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+            AptxUtil.writePhylogenyToGraphicsFile( new File( "my_tree.xml" ),
+                                                   new File( "my_tree_graphics.png" ),
+                                                   1000,
+                                                   1000,
+                                                   GraphicsExportType.PNG,
+                                                   config );
+            // If the tree 'phy' already exists, can also use this:
+            AptxUtil.writePhylogenyToGraphicsFile( phy,
+                                                   new File( "out.png" ),
+                                                   1000,
+                                                   1000,
+                                                   GraphicsExportType.PNG,
+                                                   config );
         }
-       catch (IOException e) {
-           e.printStackTrace();
+        catch ( final IOException e ) {
+            e.printStackTrace();
         }
     }
 }