@Override
public Msa infer( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
- InterruptedException {
+ InterruptedException {
final File file = File.createTempFile( "__clustalo_input_", ".fasta" );
file.deleteOnExit();
final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
_error = stderr.toString();
if ( _exit_code != 0 ) {
throw new IOException( "Clustal Omega program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts
- + "\nError:\n" + stderr );
+ + "\nError:\n" + stderr );
}
final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {
throw new IOException( "Clustal Omega program did not produce any output\nCommand:\n" + my_opts
- + "\nError:\n" + stderr );
+ + "\nError:\n" + stderr );
}
final Msa msa = FastaParser.parseMsa( stdout.toString() );
return msa;