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;
39 public final class Archaeopteryx {
41 public static MainFrame createApplication( final Phylogeny phylogeny ) {
42 final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
43 phylogenies[ 0 ] = phylogeny;
44 return createApplication( phylogenies, "", "" );
47 public static MainFrame createApplication( final Phylogeny phylogeny, final Configuration config, final String title ) {
48 final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
49 phylogenies[ 0 ] = phylogeny;
50 return MainFrameApplication.createInstance( phylogenies, config, title );
53 public static MainFrame createApplication( final Phylogeny[] phylogenies ) {
54 return createApplication( phylogenies, "", "" );
57 public static MainFrame createApplication( final Phylogeny[] phylogenies,
58 final String config_file_name,
59 final String title ) {
60 return MainFrameApplication.createInstance( phylogenies, config_file_name, title );
63 public static void main( final String args[] ) {
64 Phylogeny[] phylogenies = null;
65 String config_filename = null;
66 Configuration conf = null;
69 int filename_index = 0;
70 if ( args.length == 0 ) {
71 conf = new Configuration( null, false, false, true );
73 else if ( args.length > 0 ) {
74 // check for a config file
75 if ( args[ 0 ].startsWith( "-c" ) ) {
76 config_filename = args[ 1 ];
79 if ( args[ 0 ].startsWith( "-open" ) ) {
82 conf = new Configuration( config_filename, false, false, true );
83 if ( args.length > filename_index ) {
84 f = new File( args[ filename_index ] );
85 final String err = ForesterUtil.isReadableFile( f );
86 if ( !ForesterUtil.isEmpty( err ) ) {
87 ForesterUtil.fatalError( AptxConstants.PRG_NAME, err );
89 boolean nhx_or_nexus = false;
90 final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( f, conf
91 .isValidatePhyloXmlAgainstSchema() );
92 if ( p instanceof NHXParser ) {
94 final NHXParser nhx = ( NHXParser ) p;
95 nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
96 nhx.setIgnoreQuotes( false );
97 nhx.setTaxonomyExtraction( conf.getTaxonomyExtraction() );
99 else if ( p instanceof NexusPhylogeniesParser ) {
101 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
102 nex.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
103 nex.setIgnoreQuotes( false );
105 else if ( p instanceof PhyloXmlParser ) {
106 MainFrameApplication.warnIfNotPhyloXmlValidation( conf );
108 phylogenies = PhylogenyMethods.readPhylogenies( p, f );
109 if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
110 for( final Phylogeny phy : phylogenies ) {
111 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
117 catch ( final Exception e ) {
118 ForesterUtil.fatalError( AptxConstants.PRG_NAME, "failed to start: " + e.getLocalizedMessage() );
124 File current_dir = null;
125 if ( ( phylogenies != null ) && ( phylogenies.length > 0 ) ) {
126 current_dir = new File( "." );
129 MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
131 catch ( final OutOfMemoryError e ) {
132 AptxUtil.outOfMemoryError( e );
134 catch ( final Exception e ) {
135 AptxUtil.unexpectedException( e );
137 catch ( final Error e ) {
138 AptxUtil.unexpectedError( e );