forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   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.
  13 //
  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.
  18 //
  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
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.archaeopteryx;
  27
  28 import java.io.File;
  29
  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.phylogeny.Phylogeny;
  35 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  36 import org.forester.util.ForesterUtil;
  37
  38 //
  39 // java -javaagent:shiftone-jrat.jar -cp
  40 // $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/java/forester.jar:.
  41 // org.forester.archaeopteryx.Archaeopteryx
  42 // -c $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/_aptx_configuration_file
  43 //
  44 public final class Archaeopteryx {
  45
  46     private final static boolean TEST = false; //TODO remove me!
  47
  48     public static MainFrame createApplication( final Phylogeny phylogeny ) {
  49         final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
  50         phylogenies[ 0 ] = phylogeny;
  51         return createApplication( phylogenies, "", "" );
  52     }
  53
  54     public static MainFrame createApplication( final Phylogeny[] phylogenies ) {
  55         return createApplication( phylogenies, "", "" );
  56     }
  57
  58     public static MainFrame createApplication( final Phylogeny[] phylogenies,
  59                                                final String config_file_name,
  60                                                final String title ) {
  61         return MainFrameApplication.createInstance( phylogenies, config_file_name, title );
  62     }
  63
  64     public static void main( final String args[] ) {
  65         Phylogeny[] phylogenies = null;
  66         String config_filename = null;
  67         Configuration conf = null;
  68         File f = null;
  69         try {
  70             int filename_index = 0;
  71             if ( args.length == 0 ) {
  72                 conf = new Configuration( null, false, false );
  73             }
  74             else if ( args.length > 0 ) {
  75                 // check for a config file
  76                 if ( args[ 0 ].startsWith( "-c" ) ) {
  77                     config_filename = args[ 1 ];
  78                     filename_index += 2;
  79                 }
  80                 if ( args[ 0 ].startsWith( "-open" ) ) {
  81                     filename_index += 1;
  82                 }
  83                 conf = new Configuration( config_filename, false, false );
  84                 if ( args.length > filename_index ) {
  85                     f = new File( args[ filename_index ] );
  86                     final String err = ForesterUtil.isReadableFile( f );
  87                     if ( !ForesterUtil.isEmpty( err ) ) {
  88                         ForesterUtil.fatalError( Constants.PRG_NAME, err );
  89                     }
  90                     boolean nhx_or_nexus = false;
  91                     final PhylogenyParser p = ForesterUtil.createParserDependingOnFileType( f, conf
  92                             .isValidatePhyloXmlAgainstSchema() );
  93                     if ( p instanceof NHXParser ) {
  94                         nhx_or_nexus = true;
  95                         final NHXParser nhx = ( NHXParser ) p;
  96                         nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
  97                         nhx.setIgnoreQuotes( false );
  98                         ForesterUtil.TAXONOMY_EXTRACTION te = ForesterUtil.TAXONOMY_EXTRACTION.NO;
  99                         if ( conf.isExtractPfamTaxonomyCodesInNhParsing() ) {
 100                             te = ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
 101                         }
 102                         nhx.setTaxonomyExtraction( te );
 103                     }
 104                     else if ( p instanceof NexusPhylogeniesParser ) {
 105                         nhx_or_nexus = true;
 106                         final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
 107                         nex.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
 108                         nex.setIgnoreQuotes( false );
 109                     }
 110                     else if ( p instanceof PhyloXmlParser ) {
 111                         MainFrameApplication.warnIfNotPhyloXmlValidation( conf );
 112                     }
 113                     phylogenies = ForesterUtil.readPhylogenies( p, f );
 114                     if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
 115                         for( final Phylogeny phy : phylogenies ) {
 116                             ForesterUtil.transferInternalNodeNamesToConfidence( phy );
 117                         }
 118                     }
 119                     //
 120                     //                                        Phylogeny py = phylogenies[ 0 ];
 121                     //                                        for( final PhylogenyNodeIterator iter = py.iteratorExternalForward(); iter.hasNext(); ) {
 122                     //                                            final PhylogenyNode node = iter.next();
 123                     //                                            System.out.println( node.getNodeData().getTaxonomy().getScientificName() + "\t"
 124                     //                                                    + node.getNodeData().getBinaryCharacters().getPresentCount() );
 125                     //                                        }
 126                     //                                        for( final PhylogenyNodeIterator iter = py.iteratorPreorder(); iter.hasNext(); ) {
 127                     //                                            final PhylogenyNode node = iter.next();
 128                     //                                            if ( !node.isExternal() ) {
 129                     //                                                System.out.println( node.getNodeData().getTaxonomy().getScientificName() + "\t"
 130                     //                                                        + node.getNodeData().getBinaryCharacters().getPresentCount() );
 131                     //                                            }
 132                     //                                        }
 133                     //
 134                 }
 135             }
 136         }
 137         catch ( final Exception e ) {
 138             ForesterUtil.fatalError( Constants.PRG_NAME, "failed to start: " + e.getLocalizedMessage() );
 139         }
 140         String title = "";
 141         if ( f != null ) {
 142             title = f.getName();
 143         }
 144         try {
 145             String s = "";
 146             if ( TEST ) {
 147                 s = "/home/czmasek/888.xml";
 148                 if ( ForesterUtil.isReadableFile( s ) != null ) {
 149                     s = "/Users/zma/888.xml";
 150                     if ( ForesterUtil.isReadableFile( s ) != null ) {
 151                         s = "C:\\888.xml";
 152                         if ( ForesterUtil.isReadableFile( s ) != null ) {
 153                             s = "C:\\Documents and Settings\\czmasek\\";
 154                         }
 155                     }
 156                 }
 157             }
 158             if ( !TEST ) {
 159                 MainFrameApplication.createInstance( phylogenies, conf, title );
 160             }
 161             else {
 162                 MainFrameApplication.createInstance( ParserBasedPhylogenyFactory.getInstance()
 163                                                              .create( s, new PhyloXmlParser() ),
 164                                                      conf,
 165                                                      title );
 166             }
 167         }
 168         // catch ( final IOException ex ) {
 169         //     ForesterUtil.fatalError( Constants.PRG_NAME, "failed to start: " + ex.getLocalizedMessage() );
 170         // }
 171         catch ( final Exception ex ) {
 172             Util.unexpectedException( ex );
 173         }
 174         catch ( final Error err ) {
 175             Util.unexpectedError( err );
 176         }
 177     }
 178 }