forester/java/src/org/forester/application/decorator.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.application;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.util.ArrayList;
  31 import java.util.List;
  32 import java.util.Map;
  33
  34 import org.forester.io.parsers.PhylogenyParser;
  35 import org.forester.io.parsers.util.ParserUtils;
  36 import org.forester.io.writers.PhylogenyWriter;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.data.Identifier;
  39 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  40 import org.forester.phylogeny.factories.PhylogenyFactory;
  41 import org.forester.tools.PhylogenyDecorator;
  42 import org.forester.tools.PhylogenyDecorator.FIELD;
  43 import org.forester.util.BasicTable;
  44 import org.forester.util.BasicTableParser;
  45 import org.forester.util.CommandLineArguments;
  46 import org.forester.util.ForesterUtil;
  47
  48 public final class decorator {
  49
  50     private static final String  SEQUENCE_NAME_FIELD                    = "s";
  51     private static final String  TAXONOMY_CODE_FIELD                    = "c";
  52     private static final String  TAXONOMY_SCIENTIFIC_NAME_FIELD         = "sn";
  53     private static final String  DS_FILED                               = "d";
  54     private static final String  SEQUENCE_ANNOTATION_DESC               = "a";
  55     private static final String  NODE_NAME_FIELD                        = "n";
  56     final static private String  PICKY_OPTION                           = "p";
  57     final static private String  FIELD_OPTION                           = "f";
  58     final static private String  TRIM_AFTER_TILDE_OPTION                = "t";
  59     final static private String  MOVE_DOMAIN_NUMBER_OPTION              = "mdn";       // Hidden expert option.
  60     final static private String  TREE_NAME_OPTION                       = "pn";
  61     final static private String  TREE_ID_OPTION                         = "pi";
  62     final static private String  TREE_DESC_OPTION                       = "pd";
  63     final static private String  EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
  64     final static private String  PROCESS_NAME_INTELLIGENTLY_OPTION      = "x";
  65     final static private String  PROCESS_SIMILAR_TO_OPTION              = "xs";
  66     final static private String  CUT_NAME_AFTER_FIRST_SPACE_OPTION      = "c";
  67     final static private String  ALLOW_REMOVAL_OF_CHARS_OPTION          = "r";
  68     final static private String  ADVANCED_TABLE_OPTION                  = "table";
  69     final static private String  KEY_COLUMN                             = "k";
  70     final static private String  VALUE_COLUMN                           = "v";
  71     final static private String  MAPPING_FILE_SEPARATOR_OPTION          = "s";
  72     final static private String  MAPPING_FILE_SEPARATOR_DEFAULT         = ":";
  73     final static private boolean USE_FIRST_SEPARATOR_ONLY               = true;
  74     final static private String  PRG_NAME                               = "decorator";
  75     final static private String  PRG_VERSION                            = "1.11";
  76     final static private String  PRG_DATE                               = "2012.09.15";
  77
  78     private static void argumentsError() {
  79         System.out.println();
  80         System.out.println( decorator.PRG_NAME + " -" + ADVANCED_TABLE_OPTION + " | -f=<c> <phylogenies infile> "
  81                 + "[mapping table file] <phylogenies outfile>" );
  82         System.out.println();
  83         System.out.println( "options:" );
  84         System.out.println();
  85         System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=<c>)" );
  86         System.out.println( " -r=<n> : allow to remove up to n characters from the end of the names" );
  87         System.out.println( "          in phylogenies infile if not found (in map) otherwise" );
  88         System.out.println( " -p     : picky, fails if node name not found in mapping table" );
  89         System.out.println( " -" + TREE_NAME_OPTION + "=<s>: name for the phylogeny" );
  90         System.out.println( " -" + TREE_ID_OPTION + "=<s>: identifier for the phylogeny (in the form provider:value)" );
  91         System.out.println( " -" + TREE_DESC_OPTION + "=<s>: description for phylogenies" );
  92         System.out.println();
  93         System.out.println();
  94         System.out.println( "advanced options, only available if -" + ADVANCED_TABLE_OPTION + " is not used:" );
  95         System.out.println();
  96         System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
  97         System.out.println( "                                " + SEQUENCE_ANNOTATION_DESC
  98                 + " : sequence annotation description" );
  99         System.out.println( "                                " + DS_FILED + " : domain structure" );
 100         System.out.println( "                                " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
 101         System.out.println( "                                " + TAXONOMY_SCIENTIFIC_NAME_FIELD
 102                 + ": taxonomy scientific name" );
 103         System.out.println( "                                " + SEQUENCE_NAME_FIELD + " : sequence name" );
 104         System.out.println( " -k=<n> : key column in mapping table (0 based)," );
 105         System.out.println( "          names of the node to be decorated - default is 0" );
 106         System.out.println( " -v=<n> : value column in mapping table (0 based)," );
 107         System.out.println( "          data which with to decorate - default is 1" );
 108         System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
 109                 + "    : to extract bracketed scientific names" );
 110         System.out.println( " -s=<c> : column separator in mapping file, default is \""
 111                 + decorator.MAPPING_FILE_SEPARATOR_DEFAULT + "\"" );
 112         System.out.println( " -x     : process name \"intelligently\" (only for -f=n)" );
 113         System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION
 114                 + "    : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" );
 115         System.out.println( " -c     : cut name after first space (only for -f=n)" );
 116         System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
 117                 + "     : trim node name to be replaced after tilde" );
 118         System.out.println();
 119         System.exit( -1 );
 120     }
 121
 122     public static void main( final String args[] ) {
 123         ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE );
 124         if ( ( args.length < 4 ) || ( args.length > 12 ) ) {
 125             decorator.argumentsError();
 126         }
 127         CommandLineArguments cla = null;
 128         try {
 129             cla = new CommandLineArguments( args );
 130         }
 131         catch ( final Exception e ) {
 132             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
 133         }
 134         if ( ( cla.getNumberOfNames() < 3 ) || ( cla.getNumberOfNames() > 4 ) ) {
 135             decorator.argumentsError();
 136         }
 137         final File phylogenies_infile = cla.getFile( 0 );
 138         final File mapping_infile = cla.getFile( 1 );
 139         final File phylogenies_outfile = cla.getFile( 2 );
 140         if ( phylogenies_outfile.exists() ) {
 141             ForesterUtil.fatalError( PRG_NAME, "[" + phylogenies_outfile + "] already exists" );
 142         }
 143         final List<String> allowed_options = new ArrayList<String>();
 144         allowed_options.add( decorator.ADVANCED_TABLE_OPTION );
 145         allowed_options.add( decorator.PICKY_OPTION );
 146         allowed_options.add( decorator.FIELD_OPTION );
 147         allowed_options.add( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION );
 148         allowed_options.add( decorator.PROCESS_SIMILAR_TO_OPTION );
 149         allowed_options.add( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION );
 150         allowed_options.add( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
 151         allowed_options.add( decorator.KEY_COLUMN );
 152         allowed_options.add( decorator.VALUE_COLUMN );
 153         allowed_options.add( decorator.MAPPING_FILE_SEPARATOR_OPTION );
 154         allowed_options.add( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION );
 155         allowed_options.add( decorator.TREE_NAME_OPTION );
 156         allowed_options.add( decorator.TREE_ID_OPTION );
 157         allowed_options.add( decorator.TREE_DESC_OPTION );
 158         allowed_options.add( decorator.MOVE_DOMAIN_NUMBER_OPTION );
 159         allowed_options.add( decorator.TRIM_AFTER_TILDE_OPTION );
 160         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 161         if ( dissallowed_options.length() > 0 ) {
 162             ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options );
 163         }
 164         final boolean advanced_table = cla.isOptionSet( decorator.ADVANCED_TABLE_OPTION );
 165         if ( !advanced_table ) {
 166             final List<String> mandatory_options = new ArrayList<String>();
 167             mandatory_options.add( decorator.FIELD_OPTION );
 168             final String missing_options = cla.validateMandatoryOptionsAsString( mandatory_options );
 169             if ( missing_options.length() > 0 ) {
 170                 ForesterUtil.fatalError( decorator.PRG_NAME, "missing option(s): " + missing_options );
 171             }
 172         }
 173         final boolean picky = cla.isOptionSet( decorator.PICKY_OPTION );
 174         String separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
 175         if ( cla.isOptionSet( decorator.MAPPING_FILE_SEPARATOR_OPTION ) ) {
 176             if ( advanced_table ) {
 177                 argumentsError();
 178             }
 179             separator = cla.getOptionValue( decorator.MAPPING_FILE_SEPARATOR_OPTION );
 180         }
 181         int key_column = 0;
 182         int value_column = 1;
 183         String field_str = "";
 184         FIELD field = FIELD.NODE_NAME;
 185         int numbers_of_chars_allowed_to_remove_if_not_found_in_map = -1;
 186         boolean cut_name_after_space = false;
 187         boolean process_name_intelligently = false;
 188         boolean process_similar_to = false;
 189         boolean extract_bracketed_scientific_name = false;
 190         boolean move_domain_numbers_at_end_to_middle = false;
 191         boolean trim_after_tilde = false;
 192         String tree_name = "";
 193         String tree_id = "";
 194         String tree_desc = "";
 195         try {
 196             if ( cla.isOptionSet( decorator.TREE_NAME_OPTION ) ) {
 197                 tree_name = cla.getOptionValueAsCleanString( decorator.TREE_NAME_OPTION );
 198             }
 199             if ( cla.isOptionSet( decorator.TREE_ID_OPTION ) ) {
 200                 tree_id = cla.getOptionValueAsCleanString( decorator.TREE_ID_OPTION );
 201             }
 202             if ( cla.isOptionSet( decorator.TREE_DESC_OPTION ) ) {
 203                 tree_desc = cla.getOptionValueAsCleanString( decorator.TREE_DESC_OPTION );
 204             }
 205             if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION ) ) {
 206                 if ( advanced_table ) {
 207                     argumentsError();
 208                 }
 209                 extract_bracketed_scientific_name = true;
 210             }
 211             if ( cla.isOptionSet( decorator.KEY_COLUMN ) ) {
 212                 if ( advanced_table ) {
 213                     argumentsError();
 214                 }
 215                 key_column = cla.getOptionValueAsInt( decorator.KEY_COLUMN );
 216             }
 217             if ( cla.isOptionSet( decorator.VALUE_COLUMN ) ) {
 218                 if ( advanced_table ) {
 219                     argumentsError();
 220                 }
 221                 value_column = cla.getOptionValueAsInt( decorator.VALUE_COLUMN );
 222             }
 223             if ( cla.isOptionSet( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION ) ) {
 224                 if ( advanced_table ) {
 225                     argumentsError();
 226                 }
 227                 cut_name_after_space = true;
 228             }
 229             if ( cla.isOptionSet( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION ) ) {
 230                 if ( advanced_table ) {
 231                     argumentsError();
 232                 }
 233                 process_name_intelligently = true;
 234             }
 235             if ( cla.isOptionSet( decorator.PROCESS_SIMILAR_TO_OPTION ) ) {
 236                 if ( advanced_table ) {
 237                     argumentsError();
 238                 }
 239                 process_similar_to = true;
 240             }
 241             if ( cla.isOptionSet( decorator.TRIM_AFTER_TILDE_OPTION ) ) {
 242                 if ( advanced_table ) {
 243                     argumentsError();
 244                 }
 245                 trim_after_tilde = true;
 246             }
 247             if ( cla.isOptionSet( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ) ) {
 248                 numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla
 249                         .getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
 250             }
 251             if ( cla.isOptionSet( decorator.MOVE_DOMAIN_NUMBER_OPTION ) ) {
 252                 move_domain_numbers_at_end_to_middle = true;
 253             }
 254             if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) {
 255                 field_str = cla.getOptionValue( decorator.FIELD_OPTION );
 256                 if ( field_str.equals( NODE_NAME_FIELD ) ) {
 257                     field = FIELD.NODE_NAME;
 258                 }
 259                 else if ( field_str.equals( SEQUENCE_ANNOTATION_DESC ) ) {
 260                     field = FIELD.SEQUENCE_ANNOTATION_DESC;
 261                 }
 262                 else if ( field_str.equals( DS_FILED ) ) {
 263                     field = FIELD.DOMAIN_STRUCTURE;
 264                     extract_bracketed_scientific_name = false;
 265                 }
 266                 else if ( field_str.equals( TAXONOMY_CODE_FIELD ) ) {
 267                     field = FIELD.TAXONOMY_CODE;
 268                 }
 269                 else if ( field_str.equals( SEQUENCE_NAME_FIELD ) ) {
 270                     field = FIELD.SEQUENCE_NAME;
 271                 }
 272                 else if ( field_str.equals( TAXONOMY_SCIENTIFIC_NAME_FIELD ) ) {
 273                     field = FIELD.TAXONOMY_SCIENTIFIC_NAME;
 274                     extract_bracketed_scientific_name = false;
 275                 }
 276                 else {
 277                     ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
 278                             + "\" option: \"" + field_str + "\"" );
 279                 }
 280             }
 281         }
 282         catch ( final Exception e ) {
 283             ForesterUtil.fatalError( decorator.PRG_NAME, "error in command line: " + e.getMessage() );
 284         }
 285         if ( ( field != FIELD.NODE_NAME ) && ( cut_name_after_space || process_name_intelligently ) ) {
 286             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x or -c option without -f=n" );
 287         }
 288         if ( ( field != FIELD.NODE_NAME ) && process_similar_to ) {
 289             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
 290                     + " option without -f=n" );
 291         }
 292         if ( cut_name_after_space && process_name_intelligently ) {
 293             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x and -c option together" );
 294         }
 295         if ( process_similar_to && process_name_intelligently ) {
 296             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
 297                     + " and -x option together" );
 298         }
 299         if ( process_similar_to && cut_name_after_space ) {
 300             ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
 301                     + " and -c option together" );
 302         }
 303         Phylogeny[] phylogenies = null;
 304         try {
 305             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 306             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogenies_infile, true );
 307             phylogenies = factory.create( phylogenies_infile, pp );
 308         }
 309         catch ( final Exception e ) {
 310             ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
 311                     + "] [" + e.getMessage() + "]" );
 312         }
 313         Map<String, String> map = null;
 314         if ( !advanced_table ) {
 315             BasicTable<String> mapping_table = null;
 316             try {
 317                 mapping_table = BasicTableParser.parse( mapping_infile, separator, false, true );
 318             }
 319             catch ( final Exception e ) {
 320                 ForesterUtil.fatalError( decorator.PRG_NAME,
 321                                          "failed to read [" + mapping_infile + "] [" + e.getMessage() + "]" );
 322             }
 323             System.out.println( mapping_table.toString() );
 324             if ( ( key_column < 0 ) || ( key_column >= mapping_table.getNumberOfColumns() ) ) {
 325                 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for key column" );
 326             }
 327             if ( ( value_column < 0 ) || ( value_column >= mapping_table.getNumberOfColumns() ) ) {
 328                 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for value column" );
 329             }
 330             map = mapping_table.getColumnsAsMap( key_column, value_column );
 331         }
 332         if ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id )
 333                 || !ForesterUtil.isEmpty( tree_desc ) ) {
 334             if ( ( phylogenies.length > 1 )
 335                     && ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
 336                 ForesterUtil.fatalError( decorator.PRG_NAME,
 337                                          "attempt to set same name or id on more than one phylogeny" );
 338             }
 339             if ( !ForesterUtil.isEmpty( tree_name ) ) {
 340                 phylogenies[ 0 ].setName( tree_name );
 341             }
 342             if ( !ForesterUtil.isEmpty( tree_id ) ) {
 343                 final String[] s_ary = tree_id.split( ":" );
 344                 phylogenies[ 0 ].setIdentifier( new Identifier( s_ary[ 1 ], s_ary[ 0 ] ) );
 345             }
 346             if ( !ForesterUtil.isEmpty( tree_desc ) ) {
 347                 for( int i = 0; i < phylogenies.length; ++i ) {
 348                     phylogenies[ i ].setDescription( tree_desc );
 349                 }
 350             }
 351         }
 352         try {
 353             if ( advanced_table ) {
 354                 Map<String, Map<String, String>> table = null;
 355                 try {
 356                     table = PhylogenyDecorator.parseMappingTable( mapping_infile );
 357                 }
 358                 catch ( final IOException e ) {
 359                     ForesterUtil.fatalError( decorator.PRG_NAME,
 360                                              "failed to read \"" + mapping_infile + "\" [" + e.getMessage() + "]" );
 361                 }
 362                 PhylogenyDecorator.decorate( phylogenies,
 363                                              table,
 364                                              picky,
 365                                              numbers_of_chars_allowed_to_remove_if_not_found_in_map );
 366             }
 367             else {
 368                 PhylogenyDecorator.decorate( phylogenies,
 369                                              map,
 370                                              field,
 371                                              extract_bracketed_scientific_name,
 372                                              picky,
 373                                              cut_name_after_space,
 374                                              process_name_intelligently,
 375                                              process_similar_to,
 376                                              numbers_of_chars_allowed_to_remove_if_not_found_in_map,
 377                                              move_domain_numbers_at_end_to_middle,
 378                                              trim_after_tilde );
 379             }
 380         }
 381         catch ( final NullPointerException e ) {
 382             ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
 383         }
 384         catch ( final Exception e ) {
 385             ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() );
 386         }
 387         try {
 388             final PhylogenyWriter w = new PhylogenyWriter();
 389             w.toPhyloXML( phylogenies, 0, phylogenies_outfile, ForesterUtil.getLineSeparator() );
 390         }
 391         catch ( final IOException e ) {
 392             ForesterUtil.fatalError( decorator.PRG_NAME, "failed to write output [" + e.getMessage() + "]" );
 393         }
 394         System.out.println();
 395         ForesterUtil.programMessage( PRG_NAME, "wrote: " + phylogenies_outfile );
 396         ForesterUtil.programMessage( PRG_NAME, "OK." );
 397     }
 398 }