- private static String moveDomainNumbersAtEnd( final String node_name ) {
- final Matcher m = NODENAME_SEQNUMBER_TAXDOMAINNUMBER.matcher( node_name );
- if ( m.matches() ) {
- final String seq_number = m.group( 1 );
- final String tax = m.group( 2 );
- final String domain_number = m.group( 3 );
- return seq_number + "_[" + domain_number + "]_" + tax;
- }
- else {
- return node_name;
- }
- }
-
- public static Map<String, Map<String, String>> parseMappingTable( final File mapping_table_file )
- 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 );
- for( int row = 0; row < mapping_table.getNumberOfRows(); ++row ) {
- final Map<String, String> row_map = new HashMap<String, String>();
- String name = null;
- for( int col = 0; col < mapping_table.getNumberOfColumns(); ++col ) {
- final String table_cell = mapping_table.getValue( col, row );
- if ( col == 0 ) {
- name = table_cell;
- }
- else if ( table_cell != null ) {
- final String key = table_cell.substring( 0, table_cell.indexOf( ':' ) );
- final String val = table_cell.substring( table_cell.indexOf( ':' ) + 1, table_cell.length() );
- row_map.put( key, val );
- }
- }
- map.put( name, row_map );
- }
- return map;
- }
-
- private static String processNameIntelligently( final String name ) {
- final String[] s = name.split( " " );
- if ( s.length < 2 ) {
- return name;
- }
- else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "|" ) > 0 ) ) {
- return s[ 0 ];
- }
- else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "|" ) > 0 ) ) {
- return s[ 1 ];
- }
- else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "." ) > 0 ) ) {
- return s[ 0 ];
- }
- else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "." ) > 0 ) ) {
- return s[ 1 ];
- }
- else if ( s[ 0 ].indexOf( "_" ) > 0 ) {
- return s[ 0 ];
- }
- else if ( s[ 1 ].indexOf( "_" ) > 0 ) {
- return s[ 1 ];
- }
- else {
- return s[ 0 ];
- }
- }
-
- private static String processSimilarTo( final String name ) {
- final int i = name.toLowerCase().indexOf( "similar to" );
- String similar_to = "";
- if ( i >= 0 ) {
- similar_to = " similarity=" + name.substring( i + 10 ).trim();
- }
- final String pi = processNameIntelligently( name );
- return pi + similar_to;
- }
-
- private static String sanitize( String s ) {
- s = s.replace( ' ', '_' );
- s = s.replace( '(', '{' );
- s = s.replace( ')', '}' );
- s = s.replace( '[', '{' );
- s = s.replace( ']', '}' );
- s = s.replace( ',', '_' );
- return s;
- }
-