+ AlignmentI fullAlignment = null;
+ try
+ {
+ // locate full alignment
+ // http://www.compbio.dundee.ac.uk/jpred/results/jp_GuygEzV/jp_GuygEzV.full_MSA.fasta
+ String jobid = getJobId().substring(
+ getJobId().lastIndexOf("/") + 1);
+ String job_alignment = "http://www.compbio.dundee.ac.uk/jpred/results/"
+ + jobid + "/" + jobid + ".full_MSA.fasta";
+ fullAlignment = new FormatAdapter().readFile(job_alignment,
+ FormatAdapter.URL, "FASTA");
+ } catch (Exception q)
+ {
+
+ } finally
+ {
+ if (fullAlignment != null)
+ {
+ al = fullAlignment;
+ FirstSeq = 0;
+ }
+ else
+ {
+ al = new Alignment(preds);
+ FirstSeq = prediction.getQuerySeqPosition();
+ }
+ }
+