X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=64717958d08a3d1edf90dc0fd3413be7ef8b7a4c;hb=f4c55ce8e067fc6ae84a6ae614cebed6c88a81f0;hp=2e396aa271e9e3426383a32f4b05c381dd5352f3;hpb=3fd32306db772b6d6756ca20d33519edeb353c2d;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 2e396aa..6471795 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.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.DBRefFetcher; 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; @@ -44,6 +45,7 @@ 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; @@ -69,11 +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; @@ -145,22 +147,22 @@ public class StructureChooser extends GStructureChooser implements public void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - Collection wantedFields = PDBDocFieldPreferences - .getStructureSummaryFields(); + pdbRestCleint = PDBFTSRestClient.getInstance(); + Collection wantedFields = pdbRestCleint + .getAllDefaulDisplayedDataColumns(); - 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; + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -184,7 +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(); @@ -254,7 +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 "); @@ -273,12 +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; @@ -286,7 +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; @@ -330,8 +331,8 @@ public class StructureChooser extends GStructureChooser implements } /** - * Remove the following special characters from input string +, -, &, |, !, (, - * ), {, }, [, ], ^, ", ~, *, ?, :, \ + * Remove the following special characters from input string +, -, &, !, (, ), + * {, }, [, ], ^, ", ~, *, ?, :, \ * * @param seqName * @return @@ -340,7 +341,7 @@ public class StructureChooser extends GStructureChooser implements { Objects.requireNonNull(seqName); return seqName.replaceAll("\\[\\d*\\]", "") - .replaceAll("[^\\dA-Za-z ]", "").replaceAll("\\s+", "+"); + .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+"); } @@ -394,15 +395,16 @@ public class StructureChooser extends GStructureChooser implements public void run() { long startTime = System.currentTimeMillis(); + pdbRestCleint = PDBFTSRestClient.getInstance(); lbl_loading.setVisible(true); - Collection wantedFields = PDBDocFieldPreferences - .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); + Collection wantedFields = pdbRestCleint + .getAllDefaulDisplayedDataColumns(); + Collection filteredResponse = new HashSet(); HashSet errors = new HashSet(); for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); + FTSRestRequest pdbRequest = new FTSRestRequest(); if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) { System.out.println(">>>>>> Filtering with uniprot coverate"); @@ -427,8 +429,7 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setWantedFields(wantedFields); pdbRequest.setAssociatedSequence(seq); } - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -451,12 +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( @@ -524,17 +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)); @@ -725,22 +730,27 @@ 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 refSeqColIndex = tbl_summary.getColumn("Ref Sequence") + int pdbIdColIndex = tbl_summary.getColumn("PDB Id") + .getModelIndex(); + int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") .getModelIndex(); - int[] selectedRows = tbl_summary.getSelectedRows(); + int[] selectedRows = tbl_summary.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; ArrayList selectedSeqsToView = new ArrayList(); for (int row : selectedRows) { - String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex) + String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex) .toString(); - SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, + 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(); @@ -759,8 +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(); @@ -791,6 +801,10 @@ public class StructureChooser extends GStructureChooser implements if (pdbEntry == null) { pdbEntry = new PDBEntry(); + if (pdbIdStr.split(":").length > 1) + { + pdbEntry.setChainCode(pdbIdStr.split(":")[1]); + } pdbEntry.setId(pdbIdStr); pdbEntry.setType(PDBEntry.Type.PDB); selectedSequence.getDatasetSequence().addPDBId(pdbEntry); @@ -821,6 +835,21 @@ 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) @@ -830,37 +859,76 @@ public class StructureChooser extends GStructureChooser implements if (SiftsSettings.isMapWithSifts()) { + ArrayList seqsWithoutSourceDBRef = new ArrayList(); for (SequenceI seq : sequences) { if (seq.getSourceDBRef() == null) { - ssm.setProgressBar(null); - ssm.setProgressBar("Fetching Database refs.."); - new jalview.ws.DBRefFetcher(sequences, null, null, null, false) - .fetchDBRefs(true); - break; + if (seq.getDBRefs() == null) + { + seqsWithoutSourceDBRef.add(seq); + continue; + } + for (DBRefEntry dbRef : seq.getDBRefs()) + { + if (dbRef.getSource().equalsIgnoreCase("uniprot")) + { + seq.setSourceDBRef(dbRef); + break; + } + } + for (DBRefEntry dbRef : seq.getDBRefs()) + { + if (dbRef.getSource().equalsIgnoreCase("pdb")) + { + seq.setSourceDBRef(dbRef); + break; + } + } + if (seq.getSourceDBRef() == null) + { + seqsWithoutSourceDBRef.add(seq); + } } } - } - if (pdbEntriesToView.length > 1) + if (!seqsWithoutSourceDBRef.isEmpty()) + { + int y = seqsWithoutSourceDBRef.size(); + ssm.setProgressBar(null); + ssm.setProgressBar(">>>>> Fetching Database refs for " + y + + " sequence" + (y > 1 ? "s" : "") + + " with no valid uniprot or pdb ref for SIFTS mapping"); + System.out.println(">>>>> Fetching Database refs for " + y + + " sequence" + (y > 1 ? "s" : "") + + " with no valid uniprot or pdb ref for SIFTS mapping"); + SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; + int x = 0; + for (SequenceI fSeq : seqsWithoutSourceDBRef) { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) - { - seqsMap.add(new SequenceI[] { seq }); - } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); + seqWithoutSrcDBRef[x++] = fSeq; + } + new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true); + } + } + if (pdbEntriesToView.length > 1) + { + ArrayList seqsMap = new ArrayList(); + for (SequenceI seq : sequences) + { + seqsMap.add(new SequenceI[] { seq }); + } + SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); ssm.setProgressBar(null); ssm.setProgressBar("Fetching PDB Structures for selected entries.."); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); - } - else - { + sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + } + else + { ssm.setProgressBar(null); ssm.setProgressBar("Fetching PDB Structure for " + pdbEntriesToView[0].getId()); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); - } + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } } /** @@ -902,7 +970,7 @@ public class StructureChooser extends GStructureChooser implements this.structuresDiscovered = structuresDiscovered; } - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } @@ -919,18 +987,21 @@ 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(); + String searchTerm = txt_search.getText().toLowerCase(); + searchTerm = searchTerm.split(":")[0]; + System.out.println(">>>>> search term : " + searchTerm); + List wantedFields = new ArrayList(); + FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); pdbRequest.setFieldToSearchBy("(pdb_id:"); pdbRequest.setWantedFields(wantedFields); pdbRequest - .setSearchTerm(txt_search.getText().toLowerCase() + ")"); +.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest);