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 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 EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION = "tc";
+ 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( " -v=<n> : value column in mapping table (0 based)," );
System.out.println( " data which with to decorate - default is 1" );
System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
- + " : to extract bracketed scientific names" );
+ + " : to extract bracketed scientific names, e.g. [Nematostella vectensis]" );
+ System.out.println( " -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION
+ + " : to extract bracketed taxonomic codes, e.g. [NEMVE]" );
System.out.println( " -s=<c> : column separator in mapping file, default is \""
+ decorator.MAPPING_FILE_SEPARATOR_DEFAULT + "\"" );
System.out.println( " -x : process name \"intelligently\" (only for -f=n)" );
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_NAME_OPTION );
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_name_intelligently = false;
boolean process_similar_to = false;
boolean extract_bracketed_scientific_name = false;
- boolean move_domain_numbers_at_end_to_middle = false;
+ boolean extract_bracketed_tax_code = false;
+ boolean trim_after_tilde = false;
String tree_name = "";
String tree_id = "";
String tree_desc = "";
}
extract_bracketed_scientific_name = true;
}
+ if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ extract_bracketed_tax_code = true;
+ }
if ( cla.isOptionSet( decorator.KEY_COLUMN ) ) {
if ( advanced_table ) {
argumentsError();
}
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 );
}
- if ( cla.isOptionSet( decorator.MOVE_DOMAIN_NUMBER_OPTION ) ) {
- move_domain_numbers_at_end_to_middle = true;
- }
if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) {
field_str = cla.getOptionValue( decorator.FIELD_OPTION );
if ( field_str.equals( NODE_NAME_FIELD ) ) {
else if ( field_str.equals( DS_FILED ) ) {
field = FIELD.DOMAIN_STRUCTURE;
extract_bracketed_scientific_name = false;
+ extract_bracketed_tax_code = false;
}
else if ( field_str.equals( TAXONOMY_CODE_FIELD ) ) {
field = FIELD.TAXONOMY_CODE;
else if ( field_str.equals( TAXONOMY_SCIENTIFIC_NAME_FIELD ) ) {
field = FIELD.TAXONOMY_SCIENTIFIC_NAME;
extract_bracketed_scientific_name = false;
+ extract_bracketed_tax_code = false;
}
else {
ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
+ " and -c option together" );
}
+ if ( extract_bracketed_scientific_name && extract_bracketed_tax_code ) {
+ argumentsError();
+ }
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,
map,
field,
extract_bracketed_scientific_name,
+ extract_bracketed_tax_code,
picky,
cut_name_after_space,
process_name_intelligently,
process_similar_to,
numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- 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