From 7cbc7481c00aa1cb161fe3373e6c3586c3e8b1c3 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 11 Feb 2012 00:31:32 +0000
Subject: [PATCH] Edited wiki page Archaeopteryx through web user interface.

---
 wiki/Archaeopteryx.wiki |  103 ++---------------------------------------------
 1 file changed, 4 insertions(+), 99 deletions(-)

diff --git a/wiki/Archaeopteryx.wiki b/wiki/Archaeopteryx.wiki
index b549b60..bb1e2c0 100644
--- a/wiki/Archaeopteryx.wiki
+++ b/wiki/Archaeopteryx.wiki
@@ -1,15 +1,11 @@
-= Archaeopteryx Tutorial and Examples =
+= Archaeopteryx Documentation =
 <wiki:toc max_depth="3" />
 
 = Introduction =
 
 Under development!
 
-Documentation, tutorial, and examples for [http://www.phylosoft.org/archaeopteryx/ Archaeopteryx] (visualization, analysis, and editing of phylogenetic trees).
-
-*All examples require jar-file "forester.jar" to be in the class-path.*
-
-Download: http://code.google.com/p/forester/downloads/list
+Documentation, tutorial, and examples for visualization, analysis, and editing of phylogenetic trees with [http://www.phylosoft.org/archaeopteryx/ Archaeopteryx].
 
 Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
 
@@ -18,97 +14,6 @@ Copyright (C) 2012 Christian M Zmasek. All rights reserved.
 
 
 
-= Reading and writing of phylogenetic trees =
-
-
-
-{{{
-
-package examples;
-
-import java.io.File;
-import java.io.IOException;
-
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.util.ParserUtils;
-import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.util.ForesterUtil;
-
-public class Example {
-
-    public static void main( final String[] args ) {
-        // Reading-in of (a) tree(s) from a file.
-        final File treefile = new File( "/path/to/tree.xml" );
-        PhylogenyParser parser = null;
-        try {
-            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
-        }
-        catch ( final IOException e ) {
-            e.printStackTrace();
-        }
-        Phylogeny[] phys = null;
-        try {
-            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
-        }
-        catch ( final IOException e ) {
-            e.printStackTrace();
-        }
-        // Writing trees to a file.
-        final File outfile = new File( "/path/to/out_tree.xml" );
-        try {
-            final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
-        }
-        catch ( final Exception e ) {
-            e.printStackTrace();
-        }
-    }
-}
-
-}}}
-
-
-
-= Reading of phylogenetic trees and displaying them with Archaeopteryx =
-
-
-{{{
-
-package examples;
-
-import java.io.File;
-import java.io.IOException;
-
-import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.io.parsers.util.ParserUtils;
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-
-public class Example {
-
-    public static void main( final String[] args ) {
-        // Reading-in of (a) tree(s) from a file.
-        final File treefile = new File( "/path/to/tree.xml" );
-        PhylogenyParser parser = null;
-        try {
-            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
-        }
-        catch ( final IOException e ) {
-            e.printStackTrace();
-        }
-        Phylogeny[] phys = null;
-        try {
-            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
-        }
-        catch ( final IOException e ) {
-            e.printStackTrace();
-        }
-        // Display of the tree(s) with Archaeopteryx.
-        Archaeopteryx.createApplication( phys );
-    }
-}
+= Frequently Asked Questions =
 
-}}}
\ No newline at end of file
+== How to read and display vector or expression data ==
-- 
1.7.10.2