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.application;
29 import java.io.IOException;
30 import java.util.ArrayList;
31 import java.util.List;
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;
48 public final class decorator {
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 TREE_NAME_OPTION = "pn";
60 final static private String TREE_ID_OPTION = "pi";
61 final static private String TREE_DESC_OPTION = "pd";
62 final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
63 final static private String EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION = "tc";
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 char MAPPING_FILE_SEPARATOR_DEFAULT = '\t';
73 final static private String PRG_NAME = "decorator";
74 final static private String PRG_VERSION = "1.13";
75 final static private String PRG_DATE = "2013.01.19";
77 public static void main( final String args[] ) {
78 ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE );
79 if ( ( args.length < 4 ) || ( args.length > 12 ) ) {
80 decorator.argumentsError();
82 CommandLineArguments cla = null;
84 cla = new CommandLineArguments( args );
86 catch ( final Exception e ) {
87 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
89 if ( ( cla.getNumberOfNames() < 3 ) || ( cla.getNumberOfNames() > 4 ) ) {
90 decorator.argumentsError();
92 final File phylogenies_infile = cla.getFile( 0 );
93 final File mapping_infile = cla.getFile( 1 );
94 final File phylogenies_outfile = cla.getFile( 2 );
95 if ( phylogenies_outfile.exists() ) {
96 ForesterUtil.fatalError( PRG_NAME, "[" + phylogenies_outfile + "] already exists" );
98 final List<String> allowed_options = new ArrayList<String>();
99 allowed_options.add( decorator.ADVANCED_TABLE_OPTION );
100 allowed_options.add( decorator.PICKY_OPTION );
101 allowed_options.add( decorator.FIELD_OPTION );
102 allowed_options.add( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION );
103 allowed_options.add( decorator.PROCESS_SIMILAR_TO_OPTION );
104 allowed_options.add( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION );
105 allowed_options.add( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
106 allowed_options.add( decorator.KEY_COLUMN );
107 allowed_options.add( decorator.VALUE_COLUMN );
108 allowed_options.add( decorator.MAPPING_FILE_SEPARATOR_OPTION );
109 allowed_options.add( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION );
110 allowed_options.add( decorator.EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION );
111 allowed_options.add( decorator.TREE_NAME_OPTION );
112 allowed_options.add( decorator.TREE_ID_OPTION );
113 allowed_options.add( decorator.TREE_DESC_OPTION );
114 allowed_options.add( decorator.TRIM_AFTER_TILDE_OPTION );
115 final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
116 if ( dissallowed_options.length() > 0 ) {
117 ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options );
119 final boolean advanced_table = cla.isOptionSet( decorator.ADVANCED_TABLE_OPTION );
120 if ( !advanced_table ) {
121 final List<String> mandatory_options = new ArrayList<String>();
122 mandatory_options.add( decorator.FIELD_OPTION );
123 final String missing_options = cla.validateMandatoryOptionsAsString( mandatory_options );
124 if ( missing_options.length() > 0 ) {
125 ForesterUtil.fatalError( decorator.PRG_NAME, "missing option(s): " + missing_options );
128 final boolean picky = cla.isOptionSet( decorator.PICKY_OPTION );
129 char separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
130 if ( cla.isOptionSet( decorator.MAPPING_FILE_SEPARATOR_OPTION ) ) {
131 if ( advanced_table ) {
134 separator = cla.getOptionValueAsChar( decorator.MAPPING_FILE_SEPARATOR_OPTION );
137 int value_column = 1;
138 String field_str = "";
139 FIELD field = FIELD.NODE_NAME;
140 int numbers_of_chars_allowed_to_remove_if_not_found_in_map = -1;
141 boolean cut_name_after_space = false;
142 boolean process_name_intelligently = false;
143 boolean process_similar_to = false;
144 boolean extract_bracketed_scientific_name = false;
145 boolean extract_bracketed_tax_code = false;
146 boolean trim_after_tilde = false;
147 String tree_name = "";
149 String tree_desc = "";
151 if ( cla.isOptionSet( decorator.TREE_NAME_OPTION ) ) {
152 tree_name = cla.getOptionValueAsCleanString( decorator.TREE_NAME_OPTION );
154 if ( cla.isOptionSet( decorator.TREE_ID_OPTION ) ) {
155 tree_id = cla.getOptionValueAsCleanString( decorator.TREE_ID_OPTION );
157 if ( cla.isOptionSet( decorator.TREE_DESC_OPTION ) ) {
158 tree_desc = cla.getOptionValueAsCleanString( decorator.TREE_DESC_OPTION );
160 if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION ) ) {
161 if ( advanced_table ) {
164 extract_bracketed_scientific_name = true;
166 if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION ) ) {
167 if ( advanced_table ) {
170 extract_bracketed_tax_code = true;
172 if ( cla.isOptionSet( decorator.KEY_COLUMN ) ) {
173 if ( advanced_table ) {
176 key_column = cla.getOptionValueAsInt( decorator.KEY_COLUMN );
178 if ( cla.isOptionSet( decorator.VALUE_COLUMN ) ) {
179 if ( advanced_table ) {
182 value_column = cla.getOptionValueAsInt( decorator.VALUE_COLUMN );
184 if ( cla.isOptionSet( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION ) ) {
185 if ( advanced_table ) {
188 cut_name_after_space = true;
190 if ( cla.isOptionSet( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION ) ) {
191 if ( advanced_table ) {
194 process_name_intelligently = true;
196 if ( cla.isOptionSet( decorator.PROCESS_SIMILAR_TO_OPTION ) ) {
197 if ( advanced_table ) {
200 process_similar_to = true;
202 if ( cla.isOptionSet( decorator.TRIM_AFTER_TILDE_OPTION ) ) {
203 if ( advanced_table ) {
206 trim_after_tilde = true;
208 if ( cla.isOptionSet( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ) ) {
209 numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla
210 .getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
212 if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) {
213 field_str = cla.getOptionValue( decorator.FIELD_OPTION );
214 if ( field_str.equals( NODE_NAME_FIELD ) ) {
215 field = FIELD.NODE_NAME;
217 else if ( field_str.equals( SEQUENCE_ANNOTATION_DESC ) ) {
218 field = FIELD.SEQUENCE_ANNOTATION_DESC;
220 else if ( field_str.equals( DS_FILED ) ) {
221 field = FIELD.DOMAIN_STRUCTURE;
222 extract_bracketed_scientific_name = false;
223 extract_bracketed_tax_code = false;
225 else if ( field_str.equals( TAXONOMY_CODE_FIELD ) ) {
226 field = FIELD.TAXONOMY_CODE;
228 else if ( field_str.equals( SEQUENCE_NAME_FIELD ) ) {
229 field = FIELD.SEQUENCE_NAME;
231 else if ( field_str.equals( TAXONOMY_SCIENTIFIC_NAME_FIELD ) ) {
232 field = FIELD.TAXONOMY_SCIENTIFIC_NAME;
233 extract_bracketed_scientific_name = false;
234 extract_bracketed_tax_code = false;
237 ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
238 + "\" option: \"" + field_str + "\"" );
242 catch ( final Exception e ) {
243 ForesterUtil.fatalError( decorator.PRG_NAME, "error in command line: " + e.getMessage() );
245 if ( ( field != FIELD.NODE_NAME ) && ( cut_name_after_space || process_name_intelligently ) ) {
246 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x or -c option without -f=n" );
248 if ( ( field != FIELD.NODE_NAME ) && process_similar_to ) {
249 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
250 + " option without -f=n" );
252 if ( cut_name_after_space && process_name_intelligently ) {
253 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x and -c option together" );
255 if ( process_similar_to && process_name_intelligently ) {
256 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
257 + " and -x option together" );
259 if ( process_similar_to && cut_name_after_space ) {
260 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
261 + " and -c option together" );
263 if ( extract_bracketed_scientific_name && extract_bracketed_tax_code ) {
266 Phylogeny[] phylogenies = null;
268 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
269 final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogenies_infile, true );
270 phylogenies = factory.create( phylogenies_infile, pp );
272 catch ( final Exception e ) {
273 ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
274 + "] [" + e.getMessage() + "]" );
276 Map<String, String> map = null;
277 if ( !advanced_table ) {
278 BasicTable<String> mapping_table = null;
280 mapping_table = BasicTableParser.parse( mapping_infile, separator, true, false );
282 catch ( final Exception e ) {
283 ForesterUtil.fatalError( decorator.PRG_NAME,
284 "failed to read [" + mapping_infile + "] [" + e.getMessage() + "]" );
286 if ( ( key_column < 0 ) || ( key_column >= mapping_table.getNumberOfColumns() ) ) {
287 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for key column" );
289 if ( ( value_column < 0 ) || ( value_column >= mapping_table.getNumberOfColumns() ) ) {
290 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for value column" );
292 map = mapping_table.getColumnsAsMap( key_column, value_column );
294 if ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id )
295 || !ForesterUtil.isEmpty( tree_desc ) ) {
296 if ( ( phylogenies.length > 1 )
297 && ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
298 ForesterUtil.fatalError( decorator.PRG_NAME,
299 "attempt to set same name or id on more than one phylogeny" );
301 if ( !ForesterUtil.isEmpty( tree_name ) ) {
302 phylogenies[ 0 ].setName( tree_name );
304 if ( !ForesterUtil.isEmpty( tree_id ) ) {
305 final String[] s_ary = tree_id.split( ":" );
306 phylogenies[ 0 ].setIdentifier( new Identifier( s_ary[ 1 ], s_ary[ 0 ] ) );
308 if ( !ForesterUtil.isEmpty( tree_desc ) ) {
309 for( final Phylogeny phylogenie : phylogenies ) {
310 phylogenie.setDescription( tree_desc );
315 if ( advanced_table ) {
316 Map<String, Map<String, String>> table = null;
318 table = PhylogenyDecorator.parseMappingTable( mapping_infile );
320 catch ( final IOException e ) {
321 ForesterUtil.fatalError( decorator.PRG_NAME,
322 "failed to read \"" + mapping_infile + "\" [" + e.getMessage() + "]" );
324 PhylogenyDecorator.decorate( phylogenies,
327 numbers_of_chars_allowed_to_remove_if_not_found_in_map );
330 PhylogenyDecorator.decorate( phylogenies,
333 extract_bracketed_scientific_name,
334 extract_bracketed_tax_code,
336 cut_name_after_space,
337 process_name_intelligently,
339 numbers_of_chars_allowed_to_remove_if_not_found_in_map,
343 catch ( final NullPointerException e ) {
344 ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
346 catch ( final Exception e ) {
347 ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() );
350 final PhylogenyWriter w = new PhylogenyWriter();
351 w.toPhyloXML( phylogenies, 0, phylogenies_outfile, ForesterUtil.getLineSeparator() );
353 catch ( final IOException e ) {
354 ForesterUtil.fatalError( decorator.PRG_NAME, "failed to write output [" + e.getMessage() + "]" );
356 System.out.println();
357 ForesterUtil.programMessage( PRG_NAME, "wrote: " + phylogenies_outfile );
358 ForesterUtil.programMessage( PRG_NAME, "OK." );
361 private static void argumentsError() {
362 System.out.println();
363 System.out.println( decorator.PRG_NAME + " -" + ADVANCED_TABLE_OPTION + " | -f=<c> <phylogenies infile> "
364 + "[mapping table file] <phylogenies outfile>" );
365 System.out.println();
366 System.out.println( "options:" );
367 System.out.println();
368 System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=<c>)" );
369 System.out.println( " -r=<n> : allow to remove up to n characters from the end of the names" );
370 System.out.println( " in phylogenies infile if not found (in map) otherwise" );
371 System.out.println( " -p : picky, fails if node name not found in mapping table" );
372 System.out.println( " -" + TREE_NAME_OPTION + "=<s>: name for the phylogeny" );
373 System.out.println( " -" + TREE_ID_OPTION + "=<s>: identifier for the phylogeny (in the form provider:value)" );
374 System.out.println( " -" + TREE_DESC_OPTION + "=<s>: description for phylogenies" );
375 System.out.println();
376 System.out.println();
377 System.out.println( "advanced options, only available if -" + ADVANCED_TABLE_OPTION + " is not used:" );
378 System.out.println();
379 System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
380 System.out.println( " " + SEQUENCE_ANNOTATION_DESC
381 + " : sequence annotation description" );
382 System.out.println( " " + DS_FILED + " : domain structure" );
383 System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
384 System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD
385 + ": taxonomy scientific name" );
386 System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" );
387 System.out.println( " -k=<n> : key column in mapping table (0 based)," );
388 System.out.println( " names of the node to be decorated - default is 0" );
389 System.out.println( " -v=<n> : value column in mapping table (0 based)," );
390 System.out.println( " data which with to decorate - default is 1" );
391 System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
392 + " : to extract bracketed scientific names, e.g. [Nematostella vectensis]" );
393 System.out.println( " -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION
394 + " : to extract bracketed taxonomic codes, e.g. [NEMVE]" );
395 System.out.println( " -s=<c> : column separator in mapping file, default is \""
396 + decorator.MAPPING_FILE_SEPARATOR_DEFAULT + "\"" );
397 System.out.println( " -x : process name \"intelligently\" (only for -f=n)" );
398 System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION
399 + " : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" );
400 System.out.println( " -c : cut name after first space (only for -f=n)" );
401 System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
402 + " : trim node name to be replaced after tilde" );
403 System.out.println();