-= forester Tutorial and Examples =
+#summary Archaeopteryx Documentation
+
+= Archaeopteryx Documentation =
<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.*
+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].
-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