if ( extract_bracketed_scientific_name && ( field == FIELD.TAXONOMY_SCIENTIFIC_NAME ) ) {
throw new IllegalArgumentException( "attempt to extract bracketed scientific name together with data field pointing to scientific name" );
}
+ if ( map.isEmpty() ) {
+ throw new IllegalArgumentException( "map is empty" );
+ }
for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
String name = node.getName();
if ( extract_bracketed_scientific_name && new_value.endsWith( "]" ) ) {
new_value = extractBracketedScientificNames( node, new_value );
}
- else if ( extract_bracketed_tax_code
- && ParserUtils.TAXOMONY_CODE_PATTERN_4.matcher( new_value ).matches() ) {
- new_value = extractBracketedTaxCodes( node, new_value );
+ else if ( extract_bracketed_tax_code ) {
+ if ( ParserUtils.TAXOMONY_CODE_PATTERN_4.matcher( new_value ).find() ) {
+ new_value = extractBracketedTaxCodes( node, new_value );
+ }
+ else if ( picky ) {
+ throw new IllegalArgumentException( " could not get taxonomy from \"" + new_value
+ + "\"" );
+ }
}
switch ( field ) {
case SEQUENCE_ANNOTATION_DESC:
throws IOException {
final Map<String, Map<String, String>> map = new HashMap<String, Map<String, String>>();
BasicTable<String> mapping_table = null;
- mapping_table = BasicTableParser.parse( mapping_table_file, "\t", false, false );
+ mapping_table = BasicTableParser.parse( mapping_table_file, '\t', false, false );
for( int row = 0; row < mapping_table.getNumberOfRows(); ++row ) {
final Map<String, String> row_map = new HashMap<String, String>();
String name = null;
private static String extractBracketedTaxCodes( final PhylogenyNode node, final String new_value ) {
final Matcher m = ParserUtils.TAXOMONY_CODE_PATTERN_4.matcher( new_value );
- String tc = null;
- if ( m.matches() ) {
+ String tc = "?";
+ if ( m.find() ) {
tc = m.group( 1 );
}
ForesterUtil.ensurePresenceOfTaxonomy( node );