From f041873052e39bebaa2cdc547f98c82848c58f2a Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 2 Jun 2011 23:40:10 +0000 Subject: [PATCH] Edited wiki page forester through web user interface. --- wiki/forester.wiki | 57 ++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 49 insertions(+), 8 deletions(-) diff --git a/wiki/forester.wiki b/wiki/forester.wiki index b52eef0..e3d39f0 100644 --- a/wiki/forester.wiki +++ b/wiki/forester.wiki @@ -1,13 +1,54 @@ -#summary One-sentence summary of this page. - = Introduction = -Add your content here. +Under development! + +Documentation, tutorial, and examples for [http://www.phylosoft.org/forester/ forester]. + +Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute + + +Copyright (C) 2011 Christian M Zmasek. All rights reserved. + + += Reading in Trees and Displaying them with Archaeopteryx = + +This needs file "forester.jar" to be in the class-path. + +{{{ + +package my.examples; + +import java.io.File; +import java.io.IOException; + +import org.forester.archaeopteryx.Archaeopteryx; +import org.forester.archaeopteryx.Util; +import org.forester.io.parsers.PhylogenyParser; +import org.forester.phylogeny.Phylogeny; +import org.forester.util.ForesterUtil; +public class Example1 { -= Details = + public static void main( final String[] args ) { + // Reads in (a) tree(s) from a file. + final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" ); + PhylogenyParser parser = null; + try { + parser = ForesterUtil.createParserDependingOnFileType( treefile, true ); + } + catch ( final IOException e ) { + e.printStackTrace(); + } + Phylogeny[] phys = null; + try { + phys = Util.readPhylogenies( parser, treefile ); + } + catch ( final IOException e ) { + e.printStackTrace(); + } + // Display of the tree(s) with Archaeopteryx. + Archaeopteryx.createApplication( phys ); + } +} -Add your content here. Format your content with: - * Text in *bold* or _italic_ - * Headings, paragraphs, and lists - * Automatic links to other wiki pages \ No newline at end of file +}}} \ No newline at end of file -- 1.7.10.2