-= 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;