- //
- if ( true ) { //TODO
- try {
- MinimalDomainomeCalculator.calcOme( false,
- intrees[ 0 ],
- protein_lists_per_species,
- "---",
- 1000,
- out_dir.toString() + "/" + output_file );
- }
- catch ( IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
+ final int LEVEL = 0;
+ try {
+ MinimalDomainomeCalculator.calc( false,
+ intrees[ 0 ],
+ LEVEL,
+ protein_lists_per_species,
+ SEPARATOR_FOR_DA,
+ -1,
+ out_dir.toString() + "/" + output_file,
+ true );
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );