X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=2d9028a4620f695bd8ee0225d446aa77e519e79d;hb=64dd25185d2caf389946bb7e70053183d5aa31a6;hp=34c9b79b778dcced73a40fd53c72a8f434724f83;hpb=756e5256d99bbeab177b1a2a8a2296aeb128866b;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 34c9b79..2d9028a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -26,16 +26,17 @@ import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.fts.api.FTSData; +import jalview.fts.api.FTSDataColumnI; +import jalview.fts.api.FTSRestClientI; +import jalview.fts.core.FTSDataColumnPreferences; +import jalview.fts.core.FTSRestRequest; +import jalview.fts.core.FTSRestResponse; +import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.jbgui.GStructureChooser; -import jalview.jbgui.PDBDocFieldPreferences; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; -import jalview.ws.dbsources.PDBRestClient; -import jalview.ws.dbsources.PDBRestClient.PDBDocField; import jalview.ws.sifts.SiftsSettings; -import jalview.ws.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; import java.awt.event.ItemEvent; import java.util.ArrayList; @@ -43,6 +44,8 @@ import java.util.Collection; import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; +import java.util.Objects; +import java.util.Vector; import javax.swing.JCheckBox; import javax.swing.JComboBox; @@ -68,11 +71,11 @@ public class StructureChooser extends GStructureChooser implements private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet; + private Collection discoveredStructuresSet; - private PDBRestRequest lastPdbRequest; + private FTSRestRequest lastPdbRequest; - private PDBRestClient pdbRestCleint; + private FTSRestClientI pdbRestCleint; private String selectedPdbFileName; @@ -144,22 +147,22 @@ public class StructureChooser extends GStructureChooser implements public void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = FTSDataColumnPreferences .getStructureSummaryFields(); - discoveredStructuresSet = new LinkedHashSet(); + discoveredStructuresSet = new LinkedHashSet(); HashSet errors = new HashSet(); for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); + FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(500); pdbRequest.setFieldToSearchBy("("); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setAssociatedSequence(seq); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -183,7 +186,7 @@ public class StructureChooser extends GStructureChooser implements if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest, + tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest, discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); @@ -253,7 +256,7 @@ public class StructureChooser extends GStructureChooser implements { if (isValidSeqName(entry.getId())) { - queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) + queryBuilder.append("pdb_id") .append(":") .append(entry.getId().toLowerCase()) .append(" OR "); @@ -272,12 +275,11 @@ public class StructureChooser extends GStructureChooser implements if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ACCESSION - .getCode()).append(":") +.append("uniprot_accession").append(":") .append(getDBRefId(dbRef)) .append(" OR "); queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode()) +.append("uniprot_id") .append(":") .append(getDBRefId(dbRef)).append(" OR "); isUniProtRefsFound = true; @@ -285,7 +287,7 @@ public class StructureChooser extends GStructureChooser implements else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) { - queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) + queryBuilder.append("pdb_id") .append(":").append(getDBRefId(dbRef).toLowerCase()) .append(" OR "); isPDBRefsFound = true; @@ -301,6 +303,7 @@ public class StructureChooser extends GStructureChooser implements if (!isPDBRefsFound && !isUniProtRefsFound) { String seqName = seq.getName(); + seqName = sanitizeSeqName(seqName); String[] names = seqName.toLowerCase().split("\\|"); for (String name : names) { @@ -328,6 +331,21 @@ public class StructureChooser extends GStructureChooser implements } /** + * Remove the following special characters from input string +, -, &, |, !, (, + * ), {, }, [, ], ^, ", ~, *, ?, :, \ + * + * @param seqName + * @return + */ + private 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 * @@ -378,26 +396,14 @@ public class StructureChooser extends GStructureChooser implements { long startTime = System.currentTimeMillis(); lbl_loading.setVisible(true); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = FTSDataColumnPreferences .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); + Collection filteredResponse = new HashSet(); HashSet errors = new HashSet(); - // try - // { - // PDBDocField fiterField = PDBRestClient - // .getPDBDocFieldByCode(fieldToFilterBy); - // if (!wantedFields.contains(fiterField)) - // { - // wantedFields.add(fiterField); - // } - // } catch (Exception e) - // { - // e.printStackTrace(); - // } for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); + FTSRestRequest pdbRequest = new FTSRestRequest(); if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) { System.out.println(">>>>>> Filtering with uniprot coverate"); @@ -422,8 +428,8 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setWantedFields(wantedFields); pdbRequest.setAssociatedSequence(seq); } - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -446,12 +452,16 @@ public class StructureChooser extends GStructureChooser implements if (!filteredResponse.isEmpty()) { final int filterResponseCount = filteredResponse.size(); - Collection reorderedStructuresSet = new LinkedHashSet(); + Collection reorderedStructuresSet = new LinkedHashSet(); reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); - tbl_summary.setModel(PDBRestResponse.getTableModel( + tbl_summary.setModel(FTSRestResponse.getTableModel( lastPdbRequest, reorderedStructuresSet)); + FTSRestResponse.configureTableColumn(tbl_summary, wantedFields); + tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120); + tbl_summary.getColumn("Ref Sequence").setMinWidth(100); + tbl_summary.getColumn("Ref Sequence").setMaxWidth(200); // Update table selection model here tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); mainFrame.setTitle(MessageManager.formatMessage( @@ -519,17 +529,17 @@ public class StructureChooser extends GStructureChooser implements if (isStructuresDiscovered()) { cmb_filterOption.addItem(new FilterOption("Best Quality", - PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER)); + "overall_quality", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage", - PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER)); + "uniprot_coverage", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Best Resolution", - PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER)); + "resolution", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Protein Chain", - PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER)); + "number_of_protein_chains", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", - PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER)); + "number_of_bound_molecules", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", - PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER)); + "number_of_polymer_residues", VIEWS_FILTER)); } cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID)); @@ -720,8 +730,8 @@ public class StructureChooser extends GStructureChooser implements String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - int pdbIdColIndex = tbl_summary.getColumn( - PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); + int pdbIdColIndex = tbl_summary.getColumn("PDB Id") + .getModelIndex(); int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") .getModelIndex(); int[] selectedRows = tbl_summary.getSelectedRows(); @@ -735,7 +745,12 @@ public class StructureChooser extends GStructureChooser implements SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); - PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); + PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = getFindEntry(pdbIdStr, + selectedSeq.getAllPDBEntries()); + } if (pdbEntry == null) { pdbEntry = new PDBEntry(); @@ -754,8 +769,8 @@ public class StructureChooser extends GStructureChooser implements int[] selectedRows = tbl_local_pdb.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; - int pdbIdColIndex = tbl_local_pdb.getColumn( - PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); + int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") + .getModelIndex(); int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") .getModelIndex(); ArrayList selectedSeqsToView = new ArrayList(); @@ -816,6 +831,21 @@ public class StructureChooser extends GStructureChooser implements }).start(); } + private PDBEntry getFindEntry(String id, Vector pdbEntries) + { + Objects.requireNonNull(id); + Objects.requireNonNull(pdbEntries); + PDBEntry foundEntry = null; + for (PDBEntry entry : pdbEntries) + { + if (entry.getId().equalsIgnoreCase(id)) + { + return entry; + } + } + return foundEntry; + } + private void launchStructureViewer(StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) @@ -897,7 +927,7 @@ public class StructureChooser extends GStructureChooser implements this.structuresDiscovered = structuresDiscovered; } - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } @@ -914,9 +944,8 @@ public class StructureChooser extends GStructureChooser implements isValidPBDEntry = false; if (txt_search.getText().length() > 0) { - List wantedFields = new ArrayList(); - wantedFields.add(PDBDocField.PDB_ID); - PDBRestRequest pdbRequest = new PDBRestRequest(); + List wantedFields = new ArrayList(); + FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); pdbRequest.setFieldToSearchBy("(pdb_id:"); @@ -924,8 +953,9 @@ public class StructureChooser extends GStructureChooser implements pdbRequest .setSearchTerm(txt_search.getText().toLowerCase() + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest);