- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
-
- List<SequenceI> seqList = new ArrayList<>();
- seqList.add(selectedSequence);
- SequenceI[] seqArray = new SequenceI[] { selectedSequence };
- StructureFile sf = ssm.computeMapping(true, seqArray, null,
- selectedPdbFileName, DataSourceType.FILE, null);
- // EBIAlfaFold.addAlphaFoldPAEToStructure(pdbAlignment, pae, index,
- // structIdOrFile, isStructId);
- StructureMapping[] sm = ssm.getMapping(fileEntry.getFile());
- // DO SOMETHING WITH
- String paeFilename = StructureChooser.this.localPdbPaeMatrixFileName;
- File paeFile = paeFilename == null ? null : new File(paeFilename);
- if (paeFilename != null && paeFile.exists())
- {
- AlignmentI al = StructureChooser.this.ap.getAlignment();
- try
- {
- EBIAlfaFold.importPaeJSONAsContactMatrixToSequence(al,
- paeFile, -1, selectedSequence.getName());
- } catch (IOException | ParseException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }