- case "Number of Results to Return":
- numberOfSequences = Integer.parseInt(arg.getValue());
- break;
- case "Automatically Align Fetched Sequences":
- if ("Automatically Align Fetched Sequences"
- .equals(arg.getValue()))
- {
- realign = true;
- }
- break;
- case "Return Accessions":
- if ("Return Accessions".equals(arg.getValue()))
- {
- command += "--acc ";
- }
- break;
- case "Sequence E-value Cutoff":
- command += "--incE " + arg.getValue() + SPACE;
- break;
- case "Sequence Score Threshold":
- command += "-incT " + arg.getValue() + SPACE;
- break;
- case "Domain E-value Threshold":
- command += "--incdomE " + arg.getValue() + SPACE;
- break;
- case "Domain Score Threshold":
- command += "--incdomT " + arg.getValue() + SPACE;
- break;
- case "Trim Non-Matching Termini":