forester/java/src/org/forester/application/cladinator.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2017 Christian M. Zmasek
   6 // Copyright (C) 2017 J. Craig Venter Institute
   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: phyloxml @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.application;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.text.DecimalFormat;
  31 import java.util.ArrayList;
  32 import java.util.List;
  33
  34 import org.forester.clade_analysis.AnalysisMulti;
  35 import org.forester.clade_analysis.AnalysisSingle;
  36 import org.forester.clade_analysis.Prefix;
  37 import org.forester.clade_analysis.ResultMulti;
  38 import org.forester.clade_analysis.ResultSingle;
  39 import org.forester.io.parsers.PhylogenyParser;
  40 import org.forester.io.parsers.util.ParserUtils;
  41 import org.forester.phylogeny.Phylogeny;
  42 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  43 import org.forester.phylogeny.factories.PhylogenyFactory;
  44 import org.forester.util.CommandLineArguments;
  45 import org.forester.util.ForesterUtil;
  46
  47 public final class cladinator {
  48
  49     final static private String        PRG_NAME      = "cladinator";
  50     final static private String        PRG_VERSION   = "0.100";
  51     final static private String        PRG_DATE      = "170823";
  52     final static private String        PRG_DESC      = "clades within clades -- analysis of pplacer type outputs";
  53     final static private String        E_MAIL        = "phyloxml@gmail.com";
  54     final static private String        WWW           = "https://sites.google.com/site/cmzmasek/home/software/forester";
  55     final static private String        HELP_OPTION_1 = "help";
  56     final static private String        HELP_OPTION_2 = "h";
  57     final static private String        SEP_OPTION    = "s";
  58     private final static DecimalFormat df2           = new DecimalFormat( "0.0#" );
  59
  60     public static void main( final String args[] ) {
  61         try {
  62             ForesterUtil.printProgramInformation( PRG_NAME,
  63                                                   PRG_DESC,
  64                                                   PRG_VERSION,
  65                                                   PRG_DATE,
  66                                                   E_MAIL,
  67                                                   WWW,
  68                                                   ForesterUtil.getForesterLibraryInformation() );
  69             CommandLineArguments cla = null;
  70             try {
  71                 cla = new CommandLineArguments( args );
  72             }
  73             catch ( final Exception e ) {
  74                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  75             }
  76             if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
  77                 System.out.println();
  78                 print_help();
  79                 System.exit( 0 );
  80             }
  81             else if ( ( args.length != 2 && args.length != 3 ) ) {
  82                 System.out.println();
  83                 System.out.println( "Wrong number of arguments." );
  84                 System.out.println();
  85                 print_help();
  86                 System.exit( -1 );
  87             }
  88             final List<String> allowed_options = new ArrayList<String>();
  89             allowed_options.add( SEP_OPTION );
  90             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
  91             if ( dissallowed_options.length() > 0 ) {
  92                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
  93             }
  94             final String separator;
  95             if ( cla.isOptionSet( SEP_OPTION ) ) {
  96                 separator = cla.getOptionValue( SEP_OPTION );
  97             }
  98             else {
  99                 separator = null;
 100             }
 101             final File intreefile = cla.getFile( 0 );
 102             final String query = cla.getName( 1 );
 103             System.out.println( "Input tree: " + intreefile );
 104             System.out.println( "Query     : " + query );
 105             if ( !ForesterUtil.isEmpty( separator ) ) {
 106                 System.out.println( "Separator : " + separator );
 107             }
 108             else {
 109                 System.out.println( "Separator : none" );
 110             }
 111             Phylogeny p = null;
 112             try {
 113                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 114                 final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true );
 115                 p = factory.create( intreefile, pp )[ 0 ];
 116             }
 117             catch ( final IOException e ) {
 118                 System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" );
 119                 System.exit( -1 );
 120             }
 121
 122             final ResultMulti res = AnalysisMulti.execute( p, query, separator, 0.5 );
 123
 124             System.out.println();
 125             System.out.println( "Result:" );
 126             System.out.println( "Query                        : " + query );
 127
 128             ///////////////////
 129
 130
 131
 132             System.out.println( "Collapsed:" );
 133
 134               for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
 135                   System.out.println( prefix );
 136               }
 137               if ( _has_specifics ) {
 138
 139                   System.out.println( "Specifics:" );
 140
 141                   for( final Prefix prefix : _cleaned_spec ) {
 142                       System.out.println( prefix );
 143
 144                   }
 145
 146                   System.out.println( "Collapsed With Specifics:" );
 147
 148                   for( final Prefix prefix : _collapsed ) {
 149                       System.out.println( prefix );
 150
 151                       for( final Prefix spec : _cleaned_spec ) {
 152                           if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
 153                               System.out.println( "    " + spec );
 154
 155                           }
 156                       }
 157                   }
 158               }
 159               if ( !ForesterUtil.isEmpty( _all_down ) ) {
 160
 161                   System.out.println( "Collapsed Down:" );
 162
 163                   for( final Prefix prefix : _collapsed_down ) {
 164                       System.out.println( prefix );
 165
 166                   }
 167
 168               }
 169               if ( !ForesterUtil.isEmpty( _all_up ) ) {
 170
 171
 172                   System.out.println( "Collapsed Up:" );
 173
 174                   for( final Prefix prefix : _collapsed_up ) {
 175                       System.out.println( prefix );
 176
 177                   }
 178
 179               }
 180
 181             ///////////////////
 182
 183
 184             System.out.print( "Greatest Common Prefix       : " + res.getGreatestCommonPrefix() );
 185             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() )
 186                     && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) {
 187                 System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" );
 188             }
 189             else {
 190                 System.out.println();
 191             }
 192             System.out.print( "Greatest Common Prefix Up    : " + res.getGreatestCommonPrefixUp() );
 193             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() )
 194                     && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) {
 195                 System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" );
 196             }
 197             else {
 198                 System.out.println();
 199             }
 200             System.out.print( "Greatest Common Prefix Down  : " + res.getGreatestCommonPrefixDown() );
 201             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() )
 202                     && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) {
 203                 System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" );
 204             }
 205             else {
 206                 System.out.println();
 207             }
 208             System.out.println( "Least Encompassing Clade size: " + res.getLeastEncompassingCladeSize()
 209                     + " external nodes" );
 210             final double lec_ratio = ( 100.0 * res.getLeastEncompassingCladeSize() ) / res.getTreeSize();
 211             System.out.println( "Least Encompassing Clade size: " + df2.format( lec_ratio ) + "%" );
 212             System.out.println( "Total tree size              : " + res.getTreeSize() + " external nodes" );
 213             if ( res.getWarnings().size() > 0 ) {
 214                 System.out.println( "Warnings:" );
 215                 for( final String s : res.getWarnings() ) {
 216                     System.out.println( s );
 217                 }
 218             }
 219             System.out.println();
 220         }
 221         catch ( final IllegalArgumentException e ) {
 222             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
 223         }
 224         catch ( final Exception e ) {
 225             e.printStackTrace();
 226             ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" );
 227         }
 228     }
 229
 230     private final static void print_help() {
 231         System.out.println( "Usage:" );
 232         System.out.println();
 233         System.out.println( PRG_NAME + " [options] <gene tree file> <query>" );
 234         System.out.println();
 235         System.out.println( " options:" );
 236         System.out.println( "  -" + SEP_OPTION + "=<separator>: the separator to be used" );
 237         System.out.println();
 238         System.out.println( "Example:" );
 239         System.out.println();
 240         System.out.println( " " + PRG_NAME + " -s=. my_tree.xml A.1.1.1" );
 241         System.out.println();
 242     }
 243 }