2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
30 import org.forester.io.parsers.PhylogenyParser;
31 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
32 import org.forester.io.parsers.nhx.NHXParser;
33 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
34 import org.forester.io.parsers.util.ParserUtils;
35 import org.forester.phylogeny.Phylogeny;
36 import org.forester.phylogeny.PhylogenyMethods;
37 import org.forester.util.ForesterUtil;
40 public final class Archaeopteryx {
42 public static MainFrame createApplication( final Phylogeny phylogeny ) {
43 final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
44 phylogenies[ 0 ] = phylogeny;
45 return createApplication( phylogenies, "", "" );
48 public static MainFrame createApplication( final Phylogeny[] phylogenies ) {
49 return createApplication( phylogenies, "", "" );
52 public static MainFrame createApplication( final Phylogeny[] phylogenies,
53 final String config_file_name,
54 final String title ) {
55 return MainFrameApplication.createInstance( phylogenies, config_file_name, title );
58 public static void main( final String args[] ) {
59 Phylogeny[] phylogenies = null;
60 String config_filename = null;
61 Configuration conf = null;
64 int filename_index = 0;
65 if ( args.length == 0 ) {
66 conf = new Configuration( null, false, false, true );
68 else if ( args.length > 0 ) {
69 // check for a config file
70 if ( args[ 0 ].startsWith( "-c" ) ) {
71 config_filename = args[ 1 ];
74 if ( args[ 0 ].startsWith( "-open" ) ) {
77 conf = new Configuration( config_filename, false, false, true );
78 if ( args.length > filename_index ) {
79 f = new File( args[ filename_index ] );
80 final String err = ForesterUtil.isReadableFile( f );
81 if ( !ForesterUtil.isEmpty( err ) ) {
82 ForesterUtil.fatalError( Constants.PRG_NAME, err );
84 boolean nhx_or_nexus = false;
85 final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( f, conf
86 .isValidatePhyloXmlAgainstSchema() );
87 if ( p instanceof NHXParser ) {
89 final NHXParser nhx = ( NHXParser ) p;
90 nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
91 nhx.setIgnoreQuotes( false );
92 nhx.setTaxonomyExtraction( conf.getTaxonomyExtraction() );
94 else if ( p instanceof NexusPhylogeniesParser ) {
96 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
97 nex.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
98 nex.setIgnoreQuotes( false );
100 else if ( p instanceof PhyloXmlParser ) {
101 MainFrameApplication.warnIfNotPhyloXmlValidation( conf );
103 phylogenies = PhylogenyMethods.readPhylogenies( p, f );
104 if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
105 for( final Phylogeny phy : phylogenies ) {
106 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
112 catch ( final Exception e ) {
113 ForesterUtil.fatalError( Constants.PRG_NAME, "failed to start: " + e.getLocalizedMessage() );
119 File current_dir = null;
120 if ( ( phylogenies != null ) && ( phylogenies.length > 0 ) ) {
121 current_dir = new File( "." );
124 MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
126 catch ( final OutOfMemoryError e ) {
127 AptxUtil.outOfMemoryError( e );
129 catch ( final Exception e ) {
130 AptxUtil.unexpectedException( e );
132 catch ( final Error e ) {
133 AptxUtil.unexpectedError( e );