+ /**
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ static String sanitizeSeqName(String seqName)
+ {
+ Objects.requireNonNull(seqName);
+ return seqName.replaceAll("\\[\\d*\\]", "")
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
+ }
+
+ /**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ static boolean isValidSeqName(String seqName)
+ {
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase();
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ /**
+ * Filters a given list of discovered structures based on supplied argument
+ *
+ * @param fieldToFilterBy
+ * the field to filter by
+ */
+ void filterResultSet(final String fieldToFilterBy)
+ {
+ Thread filterThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ long startTime = System.currentTimeMillis();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ lbl_loading.setVisible(true);
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
+ Collection<FTSData> filteredResponse = new HashSet<>();
+ HashSet<String> errors = new HashSet<>();
+
+ for (SequenceI seq : selectedSequences)
+ {
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ pdbRequest.setFacet(true);
+ pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
+ pdbRequest.setFacetPivotMinCount(1);
+ }
+ else
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ }
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ errors.add(e.getMessage());
+ continue;
+ }
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
+
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, reorderedStructuresSet));
+
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields, tempUserPrefs);
+ getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
+ getResultTable().getColumn("Ref Sequence").setMinWidth(100);
+ getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
+ // Update table selection model here
+ getResultTable().addRowSelectionInterval(0,
+ filterResponseCount - 1);
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_filter_time", totalTime));
+ }
+ else
+ {
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_filter_time", totalTime));
+ if (errors.size() > 0)
+ {
+ StringBuilder errorMsg = new StringBuilder();
+ for (String error : errors)
+ {
+ errorMsg.append(error).append("\n");
+ }
+ JvOptionPane.showMessageDialog(null, errorMsg.toString(),
+ MessageManager.getString("label.pdb_web-service_error"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ lbl_loading.setVisible(false);
+
+ validateSelections();
+ }
+ });
+ filterThread.start();
+ }
+
+ /**
+ * Handles action event for btn_pdbFromFile
+ */