// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import java.util.Map;
import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.data.Identifier;
public final class decorator {
- private static final String SEQUENCE_NAME_FIELD = "s";
- private static final String TAXONOMY_CODE_FIELD = "c";
- private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD = "sn";
- private static final String DS_FILED = "d";
- private static final String SEQUENCE_ANNOTATION_DESC = "a";
- private static final String NODE_NAME_FIELD = "n";
- final static private String PICKY_OPTION = "p";
- final static private String FIELD_OPTION = "f";
- final static private String MOVE_DOMAIN_NUMBER_OPTION = "mdn"; // Hidden expert option.
- final static private String TREE_NAME_OPTION = "pn";
- final static private String TREE_ID_OPTION = "pi";
- final static private String TREE_DESC_OPTION = "pd";
- final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
- final static private String PROCESS_NAME_INTELLIGENTLY_OPTION = "x";
- final static private String PROCESS_SIMILAR_TO_OPTION = "xs";
- final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION = "c";
- final static private String ALLOW_REMOVAL_OF_CHARS_OPTION = "r";
- final static private String ADVANCED_TABLE_OPTION = "table";
- final static private String KEY_COLUMN = "k";
- final static private String VALUE_COLUMN = "v";
- final static private String MAPPING_FILE_SEPARATOR_OPTION = "s";
- final static private String MAPPING_FILE_SEPARATOR_DEFAULT = ":";
- final static private boolean USE_FIRST_SEPARATOR_ONLY = true;
- final static private String PRG_NAME = "decorator";
- final static private String PRG_VERSION = "1.10";
- final static private String PRG_DATE = "2009.10.08";
+ private static final String SEQUENCE_NAME_FIELD = "s";
+ private static final String TAXONOMY_CODE_FIELD = "c";
+ private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD = "sn";
+ private static final String DS_FILED = "d";
+ private static final String SEQUENCE_ANNOTATION_DESC = "a";
+ private static final String NODE_NAME_FIELD = "n";
+ final static private String PICKY_OPTION = "p";
+ final static private String FIELD_OPTION = "f";
+ final static private String TRIM_AFTER_TILDE_OPTION = "t";
+ final static private String MOVE_DOMAIN_NUMBER_OPTION = "mdn"; // Hidden expert option.
+ final static private String TREE_NAME_OPTION = "pn";
+ final static private String TREE_ID_OPTION = "pi";
+ final static private String TREE_DESC_OPTION = "pd";
+ final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
+ final static private String PROCESS_NAME_INTELLIGENTLY_OPTION = "x";
+ final static private String PROCESS_SIMILAR_TO_OPTION = "xs";
+ final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION = "c";
+ final static private String ALLOW_REMOVAL_OF_CHARS_OPTION = "r";
+ final static private String ADVANCED_TABLE_OPTION = "table";
+ final static private String KEY_COLUMN = "k";
+ final static private String VALUE_COLUMN = "v";
+ final static private String MAPPING_FILE_SEPARATOR_OPTION = "s";
+ final static private String MAPPING_FILE_SEPARATOR_DEFAULT = ": ";
+ final static private String PRG_NAME = "decorator";
+ final static private String PRG_VERSION = "1.11";
+ final static private String PRG_DATE = "2012.09.15";
private static void argumentsError() {
System.out.println();
System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=<c>)" );
System.out.println( " -r=<n> : allow to remove up to n characters from the end of the names" );
System.out.println( " in phylogenies infile if not found (in map) otherwise" );
- System.out.println( " -p : for picky, fails if node name not found in mapping table, default is off" );
+ System.out.println( " -p : picky, fails if node name not found in mapping table" );
System.out.println( " -" + TREE_NAME_OPTION + "=<s>: name for the phylogeny" );
System.out.println( " -" + TREE_ID_OPTION + "=<s>: identifier for the phylogeny (in the form provider:value)" );
System.out.println( " -" + TREE_DESC_OPTION + "=<s>: description for phylogenies" );
System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION
+ " : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" );
System.out.println( " -c : cut name after first space (only for -f=n)" );
+ System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
+ + " : trim node name to be replaced after tilde" );
System.out.println();
System.exit( -1 );
}
allowed_options.add( decorator.TREE_ID_OPTION );
allowed_options.add( decorator.TREE_DESC_OPTION );
allowed_options.add( decorator.MOVE_DOMAIN_NUMBER_OPTION );
+ allowed_options.add( decorator.TRIM_AFTER_TILDE_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options );
boolean process_similar_to = false;
boolean extract_bracketed_scientific_name = false;
boolean move_domain_numbers_at_end_to_middle = false;
+ boolean trim_after_tilde = false;
String tree_name = "";
String tree_id = "";
String tree_desc = "";
}
process_similar_to = true;
}
+ if ( cla.isOptionSet( decorator.TRIM_AFTER_TILDE_OPTION ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ trim_after_tilde = true;
+ }
if ( cla.isOptionSet( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ) ) {
numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla
.getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
Phylogeny[] phylogenies = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogenies_infile, true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogenies_infile, true );
phylogenies = factory.create( phylogenies_infile, pp );
}
catch ( final Exception e ) {
if ( !advanced_table ) {
BasicTable<String> mapping_table = null;
try {
- mapping_table = BasicTableParser.parse( mapping_infile, separator, decorator.USE_FIRST_SEPARATOR_ONLY );
+ mapping_table = BasicTableParser.parse( mapping_infile, separator, false, true );
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read [" + mapping_infile + "] ["
- + e.getMessage() + "]" );
+ ForesterUtil.fatalError( decorator.PRG_NAME,
+ "failed to read [" + mapping_infile + "] [" + e.getMessage() + "]" );
}
if ( ( key_column < 0 ) || ( key_column >= mapping_table.getNumberOfColumns() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for key column" );
table = PhylogenyDecorator.parseMappingTable( mapping_infile );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read \"" + mapping_infile + "\" ["
- + e.getMessage() + "]" );
+ ForesterUtil.fatalError( decorator.PRG_NAME,
+ "failed to read \"" + mapping_infile + "\" [" + e.getMessage() + "]" );
}
PhylogenyDecorator.decorate( phylogenies,
table,
process_name_intelligently,
process_similar_to,
numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- move_domain_numbers_at_end_to_middle );
+ move_domain_numbers_at_end_to_middle,
+ trim_after_tilde );
}
}
catch ( final NullPointerException e ) {
ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( decorator.PRG_NAME, "failed to map [" + e + "]" );
+ ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() );
}
try {
final PhylogenyWriter w = new PhylogenyWriter();
git://source.jalview.org / jalview.git / blobdiff