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: www.phylosoft.org/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.writers.PhylogenyWriter;
36 import org.forester.phylogeny.Phylogeny;
37 import org.forester.phylogeny.data.Identifier;
38 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
39 import org.forester.phylogeny.factories.PhylogenyFactory;
40 import org.forester.tools.PhylogenyDecorator;
41 import org.forester.tools.PhylogenyDecorator.FIELD;
42 import org.forester.util.BasicTable;
43 import org.forester.util.BasicTableParser;
44 import org.forester.util.CommandLineArguments;
45 import org.forester.util.ForesterUtil;
47 public final class decorator {
49 private static final String SEQUENCE_NAME_FIELD = "s";
50 private static final String TAXONOMY_CODE_FIELD = "c";
51 private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD = "sn";
52 private static final String DS_FILED = "d";
53 private static final String SEQUENCE_ANNOTATION_DESC = "a";
54 private static final String NODE_NAME_FIELD = "n";
55 final static private String PICKY_OPTION = "p";
56 final static private String FIELD_OPTION = "f";
57 final static private String MOVE_DOMAIN_NUMBER_OPTION = "mdn"; // Hidden expert option.
58 final static private String TREE_NAME_OPTION = "pn";
59 final static private String TREE_ID_OPTION = "pi";
60 final static private String TREE_DESC_OPTION = "pd";
61 final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
62 final static private String PROCESS_NAME_INTELLIGENTLY_OPTION = "x";
63 final static private String PROCESS_SIMILAR_TO_OPTION = "xs";
64 final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION = "c";
65 final static private String ALLOW_REMOVAL_OF_CHARS_OPTION = "r";
66 final static private String ADVANCED_TABLE_OPTION = "table";
67 final static private String KEY_COLUMN = "k";
68 final static private String VALUE_COLUMN = "v";
69 final static private String MAPPING_FILE_SEPARATOR_OPTION = "s";
70 final static private String MAPPING_FILE_SEPARATOR_DEFAULT = ":";
71 final static private boolean USE_FIRST_SEPARATOR_ONLY = true;
72 final static private String PRG_NAME = "decorator";
73 final static private String PRG_VERSION = "1.10";
74 final static private String PRG_DATE = "2009.10.08";
76 private static void argumentsError() {
78 System.out.println( decorator.PRG_NAME + " -" + ADVANCED_TABLE_OPTION + " | -f=<c> <phylogenies infile> "
79 + "[mapping table file] <phylogenies outfile>" );
81 System.out.println( "options:" );
83 System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=<c>)" );
84 System.out.println( " -r=<n> : allow to remove up to n characters from the end of the names" );
85 System.out.println( " in phylogenies infile if not found (in map) otherwise" );
86 System.out.println( " -p : for picky, fails if node name not found in mapping table, default is off" );
87 System.out.println( " -" + TREE_NAME_OPTION + "=<s>: name for the phylogeny" );
88 System.out.println( " -" + TREE_ID_OPTION + "=<s>: identifier for the phylogeny (in the form provider:value)" );
89 System.out.println( " -" + TREE_DESC_OPTION + "=<s>: description for phylogenies" );
92 System.out.println( "advanced options, only available if -" + ADVANCED_TABLE_OPTION + " is not used:" );
94 System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
95 System.out.println( " " + SEQUENCE_ANNOTATION_DESC
96 + " : sequence annotation description" );
97 System.out.println( " " + DS_FILED + " : domain structure" );
98 System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
99 System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD
100 + ": taxonomy scientific name" );
101 System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" );
102 System.out.println( " -k=<n> : key column in mapping table (0 based)," );
103 System.out.println( " names of the node to be decorated - default is 0" );
104 System.out.println( " -v=<n> : value column in mapping table (0 based)," );
105 System.out.println( " data which with to decorate - default is 1" );
106 System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
107 + " : to extract bracketed scientific names" );
108 System.out.println( " -s=<c> : column separator in mapping file, default is \""
109 + decorator.MAPPING_FILE_SEPARATOR_DEFAULT + "\"" );
110 System.out.println( " -x : process name \"intelligently\" (only for -f=n)" );
111 System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION
112 + " : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" );
113 System.out.println( " -c : cut name after first space (only for -f=n)" );
114 System.out.println();
118 public static void main( final String args[] ) {
119 ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE );
120 if ( ( args.length < 4 ) || ( args.length > 12 ) ) {
121 decorator.argumentsError();
123 CommandLineArguments cla = null;
125 cla = new CommandLineArguments( args );
127 catch ( final Exception e ) {
128 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
130 if ( ( cla.getNumberOfNames() < 3 ) || ( cla.getNumberOfNames() > 4 ) ) {
131 decorator.argumentsError();
133 final File phylogenies_infile = cla.getFile( 0 );
134 final File mapping_infile = cla.getFile( 1 );
135 final File phylogenies_outfile = cla.getFile( 2 );
136 if ( phylogenies_outfile.exists() ) {
137 ForesterUtil.fatalError( PRG_NAME, "[" + phylogenies_outfile + "] already exists" );
139 final List<String> allowed_options = new ArrayList<String>();
140 allowed_options.add( decorator.ADVANCED_TABLE_OPTION );
141 allowed_options.add( decorator.PICKY_OPTION );
142 allowed_options.add( decorator.FIELD_OPTION );
143 allowed_options.add( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION );
144 allowed_options.add( decorator.PROCESS_SIMILAR_TO_OPTION );
145 allowed_options.add( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION );
146 allowed_options.add( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
147 allowed_options.add( decorator.KEY_COLUMN );
148 allowed_options.add( decorator.VALUE_COLUMN );
149 allowed_options.add( decorator.MAPPING_FILE_SEPARATOR_OPTION );
150 allowed_options.add( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION );
151 allowed_options.add( decorator.TREE_NAME_OPTION );
152 allowed_options.add( decorator.TREE_ID_OPTION );
153 allowed_options.add( decorator.TREE_DESC_OPTION );
154 allowed_options.add( decorator.MOVE_DOMAIN_NUMBER_OPTION );
155 final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
156 if ( dissallowed_options.length() > 0 ) {
157 ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options );
159 final boolean advanced_table = cla.isOptionSet( decorator.ADVANCED_TABLE_OPTION );
160 if ( !advanced_table ) {
161 final List<String> mandatory_options = new ArrayList<String>();
162 mandatory_options.add( decorator.FIELD_OPTION );
163 final String missing_options = cla.validateMandatoryOptionsAsString( mandatory_options );
164 if ( missing_options.length() > 0 ) {
165 ForesterUtil.fatalError( decorator.PRG_NAME, "missing option(s): " + missing_options );
168 final boolean picky = cla.isOptionSet( decorator.PICKY_OPTION );
169 String separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
170 if ( cla.isOptionSet( decorator.MAPPING_FILE_SEPARATOR_OPTION ) ) {
171 if ( advanced_table ) {
174 separator = cla.getOptionValue( decorator.MAPPING_FILE_SEPARATOR_OPTION );
177 int value_column = 1;
178 String field_str = "";
179 FIELD field = FIELD.NODE_NAME;
180 int numbers_of_chars_allowed_to_remove_if_not_found_in_map = -1;
181 boolean cut_name_after_space = false;
182 boolean process_name_intelligently = false;
183 boolean process_similar_to = false;
184 boolean extract_bracketed_scientific_name = false;
185 boolean move_domain_numbers_at_end_to_middle = false;
186 String tree_name = "";
188 String tree_desc = "";
190 if ( cla.isOptionSet( decorator.TREE_NAME_OPTION ) ) {
191 tree_name = cla.getOptionValueAsCleanString( decorator.TREE_NAME_OPTION );
193 if ( cla.isOptionSet( decorator.TREE_ID_OPTION ) ) {
194 tree_id = cla.getOptionValueAsCleanString( decorator.TREE_ID_OPTION );
196 if ( cla.isOptionSet( decorator.TREE_DESC_OPTION ) ) {
197 tree_desc = cla.getOptionValueAsCleanString( decorator.TREE_DESC_OPTION );
199 if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION ) ) {
200 if ( advanced_table ) {
203 extract_bracketed_scientific_name = true;
205 if ( cla.isOptionSet( decorator.KEY_COLUMN ) ) {
206 if ( advanced_table ) {
209 key_column = cla.getOptionValueAsInt( decorator.KEY_COLUMN );
211 if ( cla.isOptionSet( decorator.VALUE_COLUMN ) ) {
212 if ( advanced_table ) {
215 value_column = cla.getOptionValueAsInt( decorator.VALUE_COLUMN );
217 if ( cla.isOptionSet( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION ) ) {
218 if ( advanced_table ) {
221 cut_name_after_space = true;
223 if ( cla.isOptionSet( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION ) ) {
224 if ( advanced_table ) {
227 process_name_intelligently = true;
229 if ( cla.isOptionSet( decorator.PROCESS_SIMILAR_TO_OPTION ) ) {
230 if ( advanced_table ) {
233 process_similar_to = true;
235 if ( cla.isOptionSet( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ) ) {
236 numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla
237 .getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
239 if ( cla.isOptionSet( decorator.MOVE_DOMAIN_NUMBER_OPTION ) ) {
240 move_domain_numbers_at_end_to_middle = true;
242 if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) {
243 field_str = cla.getOptionValue( decorator.FIELD_OPTION );
244 if ( field_str.equals( NODE_NAME_FIELD ) ) {
245 field = FIELD.NODE_NAME;
247 else if ( field_str.equals( SEQUENCE_ANNOTATION_DESC ) ) {
248 field = FIELD.SEQUENCE_ANNOTATION_DESC;
250 else if ( field_str.equals( DS_FILED ) ) {
251 field = FIELD.DOMAIN_STRUCTURE;
252 extract_bracketed_scientific_name = false;
254 else if ( field_str.equals( TAXONOMY_CODE_FIELD ) ) {
255 field = FIELD.TAXONOMY_CODE;
257 else if ( field_str.equals( SEQUENCE_NAME_FIELD ) ) {
258 field = FIELD.SEQUENCE_NAME;
260 else if ( field_str.equals( TAXONOMY_SCIENTIFIC_NAME_FIELD ) ) {
261 field = FIELD.TAXONOMY_SCIENTIFIC_NAME;
262 extract_bracketed_scientific_name = false;
265 ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
266 + "\" option: \"" + field_str + "\"" );
270 catch ( final Exception e ) {
271 ForesterUtil.fatalError( decorator.PRG_NAME, "error in command line: " + e.getMessage() );
273 if ( ( field != FIELD.NODE_NAME ) && ( cut_name_after_space || process_name_intelligently ) ) {
274 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x or -c option without -f=n" );
276 if ( ( field != FIELD.NODE_NAME ) && process_similar_to ) {
277 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
278 + " option without -f=n" );
280 if ( cut_name_after_space && process_name_intelligently ) {
281 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x and -c option together" );
283 if ( process_similar_to && process_name_intelligently ) {
284 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
285 + " and -x option together" );
287 if ( process_similar_to && cut_name_after_space ) {
288 ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
289 + " and -c option together" );
291 Phylogeny[] phylogenies = null;
293 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
294 final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogenies_infile, true );
295 phylogenies = factory.create( phylogenies_infile, pp );
297 catch ( final Exception e ) {
298 ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
299 + "] [" + e.getMessage() + "]" );
301 Map<String, String> map = null;
302 if ( !advanced_table ) {
303 BasicTable<String> mapping_table = null;
305 mapping_table = BasicTableParser.parse( mapping_infile, separator, decorator.USE_FIRST_SEPARATOR_ONLY );
307 catch ( final Exception e ) {
308 ForesterUtil.fatalError( decorator.PRG_NAME,
309 "failed to read [" + mapping_infile + "] [" + e.getMessage() + "]" );
311 if ( ( key_column < 0 ) || ( key_column >= mapping_table.getNumberOfColumns() ) ) {
312 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for key column" );
314 if ( ( value_column < 0 ) || ( value_column >= mapping_table.getNumberOfColumns() ) ) {
315 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for value column" );
317 map = mapping_table.getColumnsAsMap( key_column, value_column );
319 if ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id )
320 || !ForesterUtil.isEmpty( tree_desc ) ) {
321 if ( ( phylogenies.length > 1 )
322 && ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
323 ForesterUtil.fatalError( decorator.PRG_NAME,
324 "attempt to set same name or id on more than one phylogeny" );
326 if ( !ForesterUtil.isEmpty( tree_name ) ) {
327 phylogenies[ 0 ].setName( tree_name );
329 if ( !ForesterUtil.isEmpty( tree_id ) ) {
330 final String[] s_ary = tree_id.split( ":" );
331 phylogenies[ 0 ].setIdentifier( new Identifier( s_ary[ 1 ], s_ary[ 0 ] ) );
333 if ( !ForesterUtil.isEmpty( tree_desc ) ) {
334 for( int i = 0; i < phylogenies.length; ++i ) {
335 phylogenies[ i ].setDescription( tree_desc );
340 if ( advanced_table ) {
341 Map<String, Map<String, String>> table = null;
343 table = PhylogenyDecorator.parseMappingTable( mapping_infile );
345 catch ( final IOException e ) {
346 ForesterUtil.fatalError( decorator.PRG_NAME,
347 "failed to read \"" + mapping_infile + "\" [" + e.getMessage() + "]" );
349 PhylogenyDecorator.decorate( phylogenies,
352 numbers_of_chars_allowed_to_remove_if_not_found_in_map );
355 PhylogenyDecorator.decorate( phylogenies,
358 extract_bracketed_scientific_name,
360 cut_name_after_space,
361 process_name_intelligently,
363 numbers_of_chars_allowed_to_remove_if_not_found_in_map,
364 move_domain_numbers_at_end_to_middle );
367 catch ( final NullPointerException e ) {
368 ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
370 catch ( final Exception e ) {
371 ForesterUtil.fatalError( decorator.PRG_NAME, "failed to map [" + e + "]" );
374 final PhylogenyWriter w = new PhylogenyWriter();
375 w.toPhyloXML( phylogenies, 0, phylogenies_outfile, ForesterUtil.getLineSeparator() );
377 catch ( final IOException e ) {
378 ForesterUtil.fatalError( decorator.PRG_NAME, "failed to write output [" + e.getMessage() + "]" );
380 System.out.println();
381 ForesterUtil.programMessage( PRG_NAME, "wrote: " + phylogenies_outfile );
382 ForesterUtil.programMessage( PRG_NAME, "OK." );