- private Msa inferMsa() throws IOException, InterruptedException {
- final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
- System.out.println();
- System.out.println( "temp file: " + temp_seqs_file );
- System.out.println();
- //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
- final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
- SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
- writer.close();
- final List<String> opts = processMafftOptions();
- return runMAFFT( temp_seqs_file, opts );
+ private Msa inferMsa( final MSA_PRG msa_prg ) throws IOException, InterruptedException {
+ // final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
+ // if ( DEBUG ) {
+ // System.out.println();
+ // System.out.println( "temp file: " + temp_seqs_file );
+ // System.out.println();
+ // }
+ // //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
+ // final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
+ // SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
+ // writer.close();
+ switch ( msa_prg ) {
+ case MAFFT:
+ return runMAFFT( _seqs, processMafftOptions() );
+ case CLUSTAL_O:
+ return runClustalOmega( _seqs, processMafftOptions() );
+ default:
+ return null;
+ }