From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 11 Feb 2012 00:24:16 +0000 (+0000)
Subject: Created wiki page through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0589280c5b595a33ef108deb156af561f5051d0c;p=jalview.git

Created wiki page through web user interface.
---

diff --git a/wiki/Archaeopteryx.wiki b/wiki/Archaeopteryx.wiki
new file mode 100644
index 0000000..f5fc64b
--- /dev/null
+++ b/wiki/Archaeopteryx.wiki
@@ -0,0 +1,114 @@
+= forester Tutorial and Examples =
+<wiki:toc max_depth="3" />
+
+= Introduction =
+
+Under development!
+
+Documentation, tutorial, and examples for [http://www.phylosoft.org/forester/ forester].
+
+*All examples require jar-file "forester.jar" to be in the class-path.*
+
+Download: http://code.google.com/p/forester/downloads/list
+
+Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
+
+ 
+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 );
+    }
+}
+
+}}}