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 import java.util.SortedMap;
  34 import java.util.regex.Pattern;
  35 import java.util.regex.PatternSyntaxException;
  36
  37 import org.forester.clade_analysis.AnalysisMulti;
  38 import org.forester.clade_analysis.Prefix;
  39 import org.forester.clade_analysis.ResultMulti;
  40 import org.forester.io.parsers.PhylogenyParser;
  41 import org.forester.io.parsers.util.ParserUtils;
  42 import org.forester.phylogeny.Phylogeny;
  43 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  44 import org.forester.phylogeny.factories.PhylogenyFactory;
  45 import org.forester.util.BasicTable;
  46 import org.forester.util.BasicTableParser;
  47 import org.forester.util.CommandLineArguments;
  48 import org.forester.util.EasyWriter;
  49 import org.forester.util.ForesterUtil;
  50 import org.forester.util.UserException;
  51
  52 public final class cladinator {
  53
  54     final static private String        PRG_NAME                             = "cladinator";
  55     final static private String        PRG_VERSION                          = "1.07";
  56     final static private String        PRG_DATE                             = "1711xx";
  57     final static private String        PRG_DESC                             = "clades within clades of annotated labels -- analysis of pplacer-type outputs";
  58     final static private String        E_MAIL                               = "phyloxml@gmail.com";
  59     final static private String        WWW                                  = "https://sites.google.com/site/cmzmasek/home/software/forester";
  60     final static private String        HELP_OPTION_1                        = "help";
  61     final static private String        HELP_OPTION_2                        = "h";
  62     final static private String        SEP_OPTION                           = "s";
  63     final static private String        QUERY_PATTERN_OPTION                 = "q";
  64     final static private String        SPECIFICS_CUTOFF_OPTION              = "c";
  65     final static private String        MAPPING_FILE_OPTION                  = "m";
  66     final static private String        EXTRA_PROCESSING_OPTION1             = "x";
  67     final static private String        EXTRA_PROCESSING1_SEP_OPTION         = "xs";
  68     final static private String        EXTRA_PROCESSING1_KEEP_EXTRA_OPTION  = "xk";
  69     final static private String        QUIET_OPTION                         = "Q";
  70     final static private String        SPECIAL_PROCESSING_OPTION            = "S";
  71     final static private String        VERBOSE_OPTION                       = "v";
  72     final static private String        REMOVE_ANNOT_SEP_OPTION              = "rs";
  73     final static private double        SPECIFICS_CUTOFF_DEFAULT             = 0.7;
  74     final static private String        SEP_DEFAULT                          = ".";
  75     final static private Pattern       QUERY_PATTERN_DEFAULT                = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE;
  76     final static private String        EXTRA_PROCESSING1_SEP_DEFAULT        = "|";
  77     final static private boolean       EXTRA_PROCESSING1_KEEP_EXTRA_DEFAULT = false;
  78     private final static DecimalFormat df                                   = new DecimalFormat( "0.0###" );
  79
  80     public static void main( final String args[] ) {
  81         try {
  82             ForesterUtil.printProgramInformation( PRG_NAME,
  83                                                   PRG_DESC,
  84                                                   PRG_VERSION,
  85                                                   PRG_DATE,
  86                                                   E_MAIL,
  87                                                   WWW,
  88                                                   ForesterUtil.getForesterLibraryInformation() );
  89             CommandLineArguments cla = null;
  90             try {
  91                 cla = new CommandLineArguments( args );
  92             }
  93             catch ( final Exception e ) {
  94                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  95             }
  96             if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
  97                 System.out.println();
  98                 print_help();
  99                 System.exit( 0 );
 100             }
 101             if ( ( cla.getNumberOfNames() != 1 ) && ( cla.getNumberOfNames() != 2 ) ) {
 102                 print_help();
 103                 System.exit( -1 );
 104             }
 105             final List<String> allowed_options = new ArrayList<String>();
 106             allowed_options.add( SEP_OPTION );
 107             allowed_options.add( QUERY_PATTERN_OPTION );
 108             allowed_options.add( SPECIFICS_CUTOFF_OPTION );
 109             allowed_options.add( MAPPING_FILE_OPTION );
 110             allowed_options.add( EXTRA_PROCESSING_OPTION1 );
 111             allowed_options.add( EXTRA_PROCESSING1_SEP_OPTION );
 112             allowed_options.add( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION );
 113             allowed_options.add( SPECIAL_PROCESSING_OPTION );
 114             allowed_options.add( VERBOSE_OPTION );
 115             allowed_options.add( QUIET_OPTION );
 116             allowed_options.add( REMOVE_ANNOT_SEP_OPTION );
 117             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 118             if ( dissallowed_options.length() > 0 ) {
 119                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
 120             }
 121             double cutoff_specifics = SPECIFICS_CUTOFF_DEFAULT;
 122             if ( cla.isOptionSet( SPECIFICS_CUTOFF_OPTION ) ) {
 123                 if ( cla.isOptionValueSet( SPECIFICS_CUTOFF_OPTION ) ) {
 124                     cutoff_specifics = cla.getOptionValueAsDouble( SPECIFICS_CUTOFF_OPTION );
 125                     if ( cutoff_specifics < 0 ) {
 126                         ForesterUtil.fatalError( PRG_NAME, "cutoff cannot be negative" );
 127                     }
 128                 }
 129                 else {
 130                     ForesterUtil.fatalError( PRG_NAME, "no value for cutoff for specifics" );
 131                 }
 132             }
 133             String separator = SEP_DEFAULT;
 134             if ( cla.isOptionSet( SEP_OPTION ) ) {
 135                 if ( cla.isOptionValueSet( SEP_OPTION ) ) {
 136                     separator = cla.getOptionValue( SEP_OPTION );
 137                 }
 138                 else {
 139                     ForesterUtil.fatalError( PRG_NAME, "no value for separator option" );
 140                 }
 141             }
 142             Pattern compiled_query = null;
 143             if ( cla.isOptionSet( QUERY_PATTERN_OPTION ) ) {
 144                 if ( cla.isOptionValueSet( QUERY_PATTERN_OPTION ) ) {
 145                     final String query_str = cla.getOptionValue( QUERY_PATTERN_OPTION );
 146                     try {
 147                         compiled_query = Pattern.compile( query_str );
 148                     }
 149                     catch ( final PatternSyntaxException e ) {
 150                         ForesterUtil.fatalError( PRG_NAME,
 151                                                  "error in regular expression: " + query_str + ": " + e.getMessage() );
 152                     }
 153                 }
 154                 else {
 155                     ForesterUtil.fatalError( PRG_NAME, "no value for query pattern option" );
 156                 }
 157             }
 158             File mapping_file = null;
 159             if ( cla.isOptionSet( MAPPING_FILE_OPTION ) ) {
 160                 if ( cla.isOptionValueSet( MAPPING_FILE_OPTION ) ) {
 161                     final String mapping_file_str = cla.getOptionValue( MAPPING_FILE_OPTION );
 162                     final String error = ForesterUtil.isReadableFile( mapping_file_str );
 163                     if ( !ForesterUtil.isEmpty( error ) ) {
 164                         ForesterUtil.fatalError( PRG_NAME, error );
 165                     }
 166                     mapping_file = new File( mapping_file_str );
 167                 }
 168                 else {
 169                     ForesterUtil.fatalError( PRG_NAME, "no value for mapping file" );
 170                 }
 171             }
 172             final Pattern pattern = ( compiled_query != null ) ? compiled_query : QUERY_PATTERN_DEFAULT;
 173             final File intreefile = cla.getFile( 0 );
 174             final String error_intreefile = ForesterUtil.isReadableFile( intreefile );
 175             if ( !ForesterUtil.isEmpty( error_intreefile ) ) {
 176                 ForesterUtil.fatalError( PRG_NAME, error_intreefile );
 177             }
 178             final File outtablefile;
 179             if ( cla.getNumberOfNames() > 1 ) {
 180                 outtablefile = cla.getFile( 1 );
 181                 final String error_outtablefile = ForesterUtil.isWritableFile( outtablefile );
 182                 if ( !ForesterUtil.isEmpty( error_outtablefile ) ) {
 183                     ForesterUtil.fatalError( PRG_NAME, error_outtablefile );
 184                 }
 185             }
 186             else {
 187                 outtablefile = null;
 188             }
 189             final BasicTable<String> t;
 190             final SortedMap<String, String> map;
 191             if ( mapping_file != null ) {
 192                 t = BasicTableParser.parse( mapping_file, '\t' );
 193                 if ( t.getNumberOfColumns() != 2 ) {
 194                     ForesterUtil.fatalError( PRG_NAME,
 195                                              "mapping file needs to have 2 tab-separated columns, not "
 196                                                      + t.getNumberOfColumns() );
 197                 }
 198                 map = t.getColumnsAsMap( 0, 1 );
 199             }
 200             else {
 201                 t = null;
 202                 map = null;
 203             }
 204             final boolean extra_processing1;
 205             if ( cla.isOptionSet( EXTRA_PROCESSING_OPTION1 ) ) {
 206                 extra_processing1 = true;
 207             }
 208             else {
 209                 extra_processing1 = false;
 210             }
 211             String extra_processing1_sep = EXTRA_PROCESSING1_SEP_DEFAULT;
 212             if ( cla.isOptionSet( EXTRA_PROCESSING1_SEP_OPTION ) ) {
 213                 if ( !extra_processing1 ) {
 214                     ForesterUtil.fatalError( PRG_NAME,
 215                                              "extra processing is not enabled, cannot set -"
 216                                                      + EXTRA_PROCESSING1_SEP_OPTION + " option" );
 217                 }
 218                 if ( cla.isOptionValueSet( EXTRA_PROCESSING1_SEP_OPTION ) ) {
 219                     extra_processing1_sep = cla.getOptionValue( EXTRA_PROCESSING1_SEP_OPTION );
 220                 }
 221                 else {
 222                     ForesterUtil.fatalError( PRG_NAME, "no value for extra processing separator" );
 223                 }
 224             }
 225             if ( ( extra_processing1_sep != null ) && extra_processing1_sep.equals( separator ) ) {
 226                 ForesterUtil.fatalError( PRG_NAME,
 227                                          "extra processing separator must not be the same the annotation-separator" );
 228             }
 229             boolean extra_processing1_keep = EXTRA_PROCESSING1_KEEP_EXTRA_DEFAULT;
 230             if ( cla.isOptionSet( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION ) ) {
 231                 if ( !extra_processing1 ) {
 232                     ForesterUtil.fatalError( PRG_NAME,
 233                                              "extra processing is not enabled, cannot set -"
 234                                                      + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION + " option" );
 235                 }
 236                 extra_processing1_keep = true;
 237             }
 238             Pattern special_pattern = null;
 239             boolean special_processing = false;
 240             if ( cla.isOptionSet( SPECIAL_PROCESSING_OPTION ) ) {
 241                 if ( extra_processing1 == true ) {
 242                     ForesterUtil
 243                             .fatalError( PRG_NAME,
 244                                          "extra processing cannot be used together with special processing pattern" );
 245                 }
 246                 if ( cla.isOptionValueSet( SPECIAL_PROCESSING_OPTION ) ) {
 247                     final String str = cla.getOptionValue( SPECIAL_PROCESSING_OPTION );
 248                     try {
 249                         special_pattern = Pattern.compile( str );
 250                     }
 251                     catch ( final PatternSyntaxException e ) {
 252                         ForesterUtil
 253                                 .fatalError( PRG_NAME,
 254                                              "error in special processing pattern: " + str + ": " + e.getMessage() );
 255                     }
 256                     special_processing = true;
 257                 }
 258                 else {
 259                     ForesterUtil.fatalError( PRG_NAME, "no value for special processing pattern" );
 260                 }
 261             }
 262             final boolean remove_annotation_sep;
 263             if ( cla.isOptionSet( REMOVE_ANNOT_SEP_OPTION ) ) {
 264                 remove_annotation_sep = true;
 265             }
 266             else {
 267                 remove_annotation_sep = false;
 268             }
 269             final boolean verbose;
 270             if ( cla.isOptionSet( VERBOSE_OPTION ) ) {
 271                 verbose = true;
 272             }
 273             else {
 274                 verbose = false;
 275             }
 276             final boolean quit;
 277             if ( cla.isOptionSet( QUIET_OPTION ) ) {
 278                 quit = true;
 279             }
 280             else {
 281                 quit = false;
 282             }
 283             System.out.println( "Input tree                 : " + intreefile );
 284             System.out.println( "Specific-hit support cutoff: " + cutoff_specifics );
 285             if ( mapping_file != null ) {
 286                 System.out.println( "Mapping file               : " + mapping_file + " (" + t.getNumberOfRows()
 287                         + " rows)" );
 288             }
 289             System.out.println( "Annotation-separator       : " + separator );
 290             if ( remove_annotation_sep ) {
 291                 System.out.println( "Remove anno.-sep. in output: " + remove_annotation_sep );
 292             }
 293             System.out.println( "Query pattern              : " + pattern );
 294             if ( extra_processing1 ) {
 295                 System.out.println( "Extra processing           : " + extra_processing1 );
 296                 System.out.println( "Extra processing separator : " + extra_processing1_sep );
 297                 System.out.println( "Keep extra annotations     : " + extra_processing1_keep );
 298             }
 299             if ( special_processing ) {
 300                 System.out.println( "Special processing         : " + special_processing );
 301                 System.out.println( "Special processing pattern : " + special_pattern );
 302             }
 303             if ( outtablefile != null ) {
 304                 System.out.println( "Output table               : " + outtablefile );
 305             }
 306             Phylogeny phys[] = null;
 307             try {
 308                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 309                 final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true );
 310                 phys = factory.create( intreefile, pp );
 311             }
 312             catch ( final IOException e ) {
 313                 ForesterUtil.fatalError( PRG_NAME, "Could not read \"" + intreefile + "\" [" + e.getMessage() + "]" );
 314             }
 315             if ( phys.length == 0 ) {
 316                 ForesterUtil.fatalError( PRG_NAME, "\"" + intreefile + "\" does not contain any trees" );
 317             }
 318             System.out.println( "Number of input trees      : " + phys.length );
 319             if ( phys.length == 1 ) {
 320                 System.out.println( "Ext. nodes in input tree   : " + phys[ 0 ].getNumberOfExternalNodes() );
 321             }
 322             else {
 323                 System.out.println( "Ext. nodes in input tree 1 : " + phys[ 0 ].getNumberOfExternalNodes() );
 324             }
 325             final EasyWriter outtable_writer;
 326             if ( outtablefile != null ) {
 327                 outtable_writer = ForesterUtil.createEasyWriter( outtablefile );
 328                 outtable_writer.print( "#" + PRG_NAME + " " + PRG_VERSION + " " + PRG_DATE );
 329                 outtable_writer.print( " Input tree: " + intreefile );
 330                 outtable_writer.println( " Specific-hit support cutoff: " + cutoff_specifics );
 331             }
 332             else {
 333                 outtable_writer = null;
 334             }
 335             int counter = 0;
 336             for( final Phylogeny phy : phys ) {
 337                 if ( map != null ) {
 338                     AnalysisMulti.performMapping( pattern, map, phy, verbose );
 339                 }
 340                 if ( extra_processing1 ) {
 341                     AnalysisMulti.performExtraProcessing1( pattern,
 342                                                            phy,
 343                                                            extra_processing1_sep,
 344                                                            extra_processing1_keep,
 345                                                            separator,
 346                                                            verbose );
 347                 }
 348                 else if ( special_processing ) {
 349                     AnalysisMulti.performSpecialProcessing1( pattern, phy, separator, special_pattern, verbose );
 350                 }
 351                 final ResultMulti res = AnalysisMulti.execute( phy, pattern, separator, cutoff_specifics );
 352                 if ( !quit ) {
 353                     if ( phys.length == 1 ) {
 354                         printResult( res, -1, remove_annotation_sep );
 355                     }
 356                     else {
 357                         printResult( res, counter, remove_annotation_sep );
 358                     }
 359                 }
 360                 if ( outtable_writer != null ) {
 361                     writeResultToTable( res, outtable_writer, remove_annotation_sep );
 362                     outtable_writer.flush();
 363                 }
 364                 ++counter;
 365             }
 366             if ( outtable_writer != null ) {
 367                 outtable_writer.flush();
 368                 outtable_writer.close();
 369             }
 370         }
 371         catch ( final UserException e ) {
 372             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
 373         }
 374         catch ( final IOException e ) {
 375             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
 376         }
 377         catch ( final Exception e ) {
 378             e.printStackTrace();
 379             ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" );
 380         }
 381     }
 382
 383     private final static void printResult( final ResultMulti res,
 384                                            final int counter,
 385                                            final boolean remove_annotation_sep ) {
 386         System.out.println();
 387         if ( counter == -1 ) {
 388             System.out.println( "Result for " + res.getQueryNamePrefix() );
 389         }
 390         else {
 391             System.out.println( "Result for " + res.getQueryNamePrefix() + " [tree " + counter + "]" );
 392         }
 393         if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
 394             System.out.println( " No match to query pattern!" );
 395         }
 396         else {
 397             System.out.println( " Matching Clade(s):" );
 398             for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
 399                 if ( remove_annotation_sep ) {
 400                     System.out.println( " " + prefix.toStringRemovSeparator() );
 401                 }
 402                 else {
 403                     System.out.println( " " + prefix );
 404                 }
 405             }
 406             if ( res.isHasSpecificMultiHitsPrefixes() ) {
 407                 System.out.println();
 408                 System.out.println( " Specific-hit(s):" );
 409                 for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
 410                     if ( remove_annotation_sep ) {
 411                         System.out.println( " " + prefix.toStringRemovSeparator() );
 412                     }
 413                     else {
 414                         System.out.println( " " + prefix );
 415                     }
 416                 }
 417                 System.out.println();
 418                 System.out.println( " Matching Clade(s) with Specific-hit(s):" );
 419                 for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
 420                     if ( remove_annotation_sep ) {
 421                         System.out.println( " " + prefix.toStringRemovSeparator() );
 422                     }
 423                     else {
 424                         System.out.println( " " + prefix );
 425                     }
 426                     for( final Prefix spec : res.getSpecificMultiHitPrefixes() ) {
 427                         if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
 428                             if ( remove_annotation_sep ) {
 429                                 System.out.println( "     " + spec.toStringRemovSeparator() );
 430                             }
 431                             else {
 432                                 System.out.println( "     " + spec );
 433                             }
 434                         }
 435                     }
 436                 }
 437             }
 438             if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
 439                 System.out.println();
 440                 System.out.println( " Matching Down-tree Bracketing Clade(s):" );
 441                 for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
 442                     if ( remove_annotation_sep ) {
 443                         System.out.println( " " + prefix.toStringRemovSeparator() );
 444                     }
 445                     else {
 446                         System.out.println( " " + prefix );
 447                     }
 448                 }
 449             }
 450             if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
 451                 System.out.println();
 452                 System.out.println( " Matching Up-tree Bracketing Clade(s):" );
 453                 for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
 454                     if ( remove_annotation_sep ) {
 455                         System.out.println( " " + prefix.toStringRemovSeparator() );
 456                     }
 457                     else {
 458                         System.out.println( " " + prefix );
 459                     }
 460                 }
 461             }
 462             System.out.println();
 463             System.out.println( " Total Number of Matches: " + res.getNumberOfMatches() + "/"
 464                     + res.getReferenceTreeNumberOfExternalNodes() );
 465         }
 466         System.out.println();
 467     }
 468
 469     private final static void writeResultToTable( final ResultMulti res,
 470                                                   final EasyWriter w,
 471                                                   final boolean remove_annotation_sep )
 472             throws IOException {
 473         if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
 474             w.print( res.getQueryNamePrefix() );
 475             w.print( "\t" );
 476             w.println( "No match to query pattern!" );
 477         }
 478         else {
 479             for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
 480                 w.print( res.getQueryNamePrefix() );
 481                 w.print( "\t" );
 482                 w.print( "Matching Clades" );
 483                 w.print( "\t" );
 484                 if ( remove_annotation_sep ) {
 485                     w.print( prefix.getPrefixRemovSeparator() );
 486                 }
 487                 else {
 488                     w.print( prefix.getPrefix() );
 489                 }
 490                 w.print( "\t" );
 491                 w.print( df.format( prefix.getConfidence() ) );
 492                 w.print( "\t" );
 493                 w.print( String.valueOf( res.getNumberOfMatches() ) );
 494                 w.print( "\t" );
 495                 w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
 496                 w.println();
 497             }
 498             if ( res.isHasSpecificMultiHitsPrefixes() ) {
 499                 for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
 500                     w.print( res.getQueryNamePrefix() );
 501                     w.print( "\t" );
 502                     w.print( "Specific-hits" );
 503                     w.print( "\t" );
 504                     if ( remove_annotation_sep ) {
 505                         w.print( prefix.getPrefixRemovSeparator() );
 506                     }
 507                     else {
 508                         w.print( prefix.getPrefix() );
 509                     }
 510                     w.print( "\t" );
 511                     w.print( df.format( prefix.getConfidence() ) );
 512                     w.print( "\t" );
 513                     w.print( String.valueOf( res.getNumberOfMatches() ) );
 514                     w.print( "\t" );
 515                     w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
 516                     w.println();
 517                 }
 518             }
 519             if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
 520                 for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
 521                     w.print( res.getQueryNamePrefix() );
 522                     w.print( "\t" );
 523                     w.print( "Matching Down-tree Bracketing Clades" );
 524                     w.print( "\t" );
 525                     if ( remove_annotation_sep ) {
 526                         w.print( prefix.getPrefixRemovSeparator() );
 527                     }
 528                     else {
 529                         w.print( prefix.getPrefix() );
 530                     }
 531                     w.print( "\t" );
 532                     w.print( df.format( prefix.getConfidence() ) );
 533                     w.print( "\t" );
 534                     w.print( String.valueOf( res.getNumberOfMatches() ) );
 535                     w.print( "\t" );
 536                     w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
 537                     w.println();
 538                 }
 539             }
 540             if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
 541                 for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
 542                     w.print( res.getQueryNamePrefix() );
 543                     w.print( "\t" );
 544                     w.print( "Matching Up-tree Bracketing Clades" );
 545                     w.print( "\t" );
 546                     if ( remove_annotation_sep ) {
 547                         w.print( prefix.getPrefixRemovSeparator() );
 548                     }
 549                     else {
 550                         w.print( prefix.getPrefix() );
 551                     }
 552                     w.print( "\t" );
 553                     w.print( df.format( prefix.getConfidence() ) );
 554                     w.print( "\t" );
 555                     w.print( String.valueOf( res.getNumberOfMatches() ) );
 556                     w.print( "\t" );
 557                     w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
 558                     w.println();
 559                 }
 560             }
 561         }
 562     }
 563
 564     private final static void print_help() {
 565         System.out.println( "Usage:" );
 566         System.out.println();
 567         System.out.println( PRG_NAME + " [options] <input tree(s) file> [output table file]" );
 568         System.out.println();
 569         System.out.println( " options:" );
 570         System.out.println( "  -" + SPECIFICS_CUTOFF_OPTION
 571                 + "=<double>        : the minimal confidence value for \"specific-hits\" to be reported (default: "
 572                 + SPECIFICS_CUTOFF_DEFAULT + ")" );
 573         System.out.println( "  -" + SEP_OPTION + "=<separator>     : the annotation-separator to be used (default: \""
 574                 + SEP_DEFAULT + "\")" );
 575         System.out.println( "  -" + MAPPING_FILE_OPTION
 576                 + "=<mapping table> : to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" );
 577         System.out.println( "  -" + EXTRA_PROCESSING_OPTION1
 578                 + "                 : to enable extra processing of annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1\")" );
 579         System.out.println( "  -" + EXTRA_PROCESSING1_SEP_OPTION
 580                 + "=<separator>    : the separator for extra annotations (default: \"" + EXTRA_PROCESSING1_SEP_DEFAULT
 581                 + "\")" );
 582         System.out.println( "  -" + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION
 583                 + "                : to keep extra annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1.Q16611\")" );
 584         System.out.println( "  -" + SPECIAL_PROCESSING_OPTION
 585                 + "=<pattern>       : special processing with pattern (e.g. \"(\\d+)([a-z]+)_.+\" for changing \"6q_EF42\" to \"6.q\")" );
 586         System.out.println( "  -" + REMOVE_ANNOT_SEP_OPTION
 587                 + "                : to remove the annotation-separator in the output (e.g. the \"" + SEP_DEFAULT
 588                 + "\")" );
 589         System.out.println( "  -" + VERBOSE_OPTION + "                 : verbose" );
 590         System.out.println( "  -" + QUIET_OPTION
 591                 + "                 : quiet (no output to console, for when used in a pipeline)" );
 592         System.out.println( "  --" + QUERY_PATTERN_OPTION
 593                 + "=<pattern>      : expert option: the regular expression pattern for the query (default: \""
 594                 + QUERY_PATTERN_DEFAULT + "\" for pplacer output)" );
 595         System.out.println();
 596         System.out.println( "Examples:" );
 597         System.out.println();
 598         System.out.println( " " + PRG_NAME + " pp_out_tree.sing.tre result.tsv" );
 599         System.out.println( " " + PRG_NAME + " -c=0.5 -s=. pp_out_tree.sing.tre result.tsv" );
 600         System.out.println( " " + PRG_NAME + " -c=0.9 -s=_ -m=map.tsv pp_out_trees.sing.tre result.tsv" );
 601         System.out.println( " " + PRG_NAME + " -x -xs=& -xk pp_out_trees.sing.tre result.tsv" );
 602         System.out.println( " " + PRG_NAME + " -x -xs=\"|\" pp_out_trees.sing.tre result.tsv" );
 603         System.out.println( " " + PRG_NAME + " -x -xk -m=map.tsv pp_out_trees.sing.tre result.tsv" );
 604         System.out.println( " " + PRG_NAME + " -m=map.tsv -S='(\\d+)([a-z?]*)_.+' pp_out_trees.sing.tre result.tsv" );
 605         System.out.println();
 606     }
 607 }