- } catch (IOException | InterruptedException e)
- {
- e.printStackTrace();
- }
- try
- {
- importData(job);
- } catch (IOException | InterruptedException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ try
+ {
+ cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
+ hmmTemp.getAbsoluteFile());
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ try
+ {
+ boolean ran = runCommand();
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmalign_failed"));
+ return;
+ }
+ } catch (IOException | InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ try
+ {
+ importData(job);
+ } catch (IOException | InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ job++;