some fixes

[jalview.git] / wiki / Archaeopteryx.wiki

diff --git a/wiki/Archaeopteryx.wiki b/wiki/Archaeopteryx.wiki
index f5fc64b..7700953 100644 (file)
--- a/wiki/Archaeopteryx.wiki
+++ b/wiki/Archaeopteryx.wiki
@@ -1,114 +1,33 @@
-= forester Tutorial and Examples =
+= Archaeopteryx Documentation =
 <wiki:toc max_depth="3" />
 
 = Introduction =
 
 Under development!
 
-Documentation, tutorial, and examples for [http://www.phylosoft.org/forester/ forester].
+Documentation, tutorial, and examples for visualization, analysis, and editing of phylogenetic trees with [http://www.phylosoft.org/archaeopteryx/ Archaeopteryx].
+Some (older) documentation can also be found [http://aptxevo.wordpress.com/ here].
 
-*All examples require jar-file "forester.jar" to be in the class-path.*
-
-Download: http://code.google.com/p/forester/downloads/list
+For developers: Information on the underlying [http://www.phylosoft.org/forester/ forester] framework is available [forester here].
 
 Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
 
+
  
 Copyright (C) 2012 Christian M Zmasek. All rights reserved.
 
+----
 
+= Frequently Asked Questions =
 
-= 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;
+== How to read and display vector or expression data ==
 
-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;
+Aptx can be used to display vector or expression data associated with tree nodes:
 
-public class Example {
+  # Ensure the configuration file contains this line: "show_vector_data:               display yes"
+  # Start Aptx and read in a tree ([http://forester.googlecode.com/files/apaf.xml example tree])
+  # Open "Tools" menu and select "read Vector/Expression Values" to read in a matrix (of, for example, expression values) ([http://forester.googlecode.com/files/apaf_expression.tab example expression values])
 
-    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 );
-    }
-}
+It is also possible to store vector data in phyloXML formatted files ([http://forester.googlecode.com/files/apaf_with_vector_data.xml example]).
 
-}}}
+----
\ No newline at end of file