+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+ : tbl_local_pdb;
+
+ if (currentView == VIEWS_FILTER)
+ {
+ int[] selectedRows = restable.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
+ pdbEntriesToView = data.collectSelectedRows(restable,
+ selectedRows, selectedSeqsToView);
+
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
+ .getModelIndex();
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
+ .getModel()).getPDBEntryAt(row).getPdbEntry();
+
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ if (pdbIdStr.split(":").length > 1)
+ {
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
+ }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
+ }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
+
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ new SequenceI[]
+ { selectedSequence }, superimpose, theViewer,
+ progressBar);
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true);
+
+ sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
+ new SequenceI[] { selectedSequence }, superimpose, theViewer,
+ progressBar);
+ }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ closeAction(preferredHeight);
+ mainFrame.dispose();
+ }
+ });