- Annotation[] annotations = new Annotation[al.getWidth()];
- for (int j = 0; j < values.size(); j++)
- {
- float value = Float.parseFloat(values.get(j).toString());
- annotations[gapmap[j]] = new Annotation("", value+"",' ',value);
- }
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));
- }
- private jalview.datamodel.Sequence[] getVamsasAlignment(vamsas.objects.simple.Alignment valign) {
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
- for (int i=0, j=seqs.length; i<j;i++)
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());
- return msa;
- }
- void parseResult()
- {
- SequenceI[] seqs=null;
- try {
- // OutputHeader = output.getText();
- if (result.isFailed()) {
- OutputHeader +="Job failed.\n";
- }
- if (result.getStatus()!=null) {
- OutputHeader += "\n"+result.getStatus();
- }
- if (result.getMsa()!=null) {
- OutputHeader += "\nAlignment Object Method Notes\n";
- String lines[] = result.getMsa().getMethod();
- for (int line=0;line<lines.length; line++)
- OutputHeader+=lines[line]+"\n";