X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=3581cf93c085c2abbd0f002a859b57f4a6695716;hb=781218e12641a89d5dd99906369d5b9807c1d203;hp=720dc9e0ab743ae03d89e02e3c5f8820c4045260;hpb=26a8bcef19885071a20e238d06c514404ecbc573;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 720dc9e..3581cf9 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,19 +21,23 @@ package jalview.gui; +import jalview.bin.Jalview; 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.io.DataSourceType; 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.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; +import jalview.ws.DBRefFetcher; +import jalview.ws.sifts.SiftsSettings; import java.awt.event.ItemEvent; import java.util.ArrayList; @@ -41,6 +45,9 @@ import java.util.Collection; import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; +import java.util.Objects; +import java.util.Set; +import java.util.Vector; import javax.swing.JCheckBox; import javax.swing.JComboBox; @@ -55,7 +62,8 @@ import javax.swing.table.AbstractTableModel; * */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser +public class StructureChooser extends GStructureChooser implements + IProgressIndicator { private boolean structuresDiscovered = false; @@ -65,11 +73,11 @@ public class StructureChooser extends GStructureChooser private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet; + private Collection discoveredStructuresSet; - private PDBRestRequest lastPdbRequest; + private FTSRestRequest lastPdbRequest; - private PDBRestClient pdbRestCleint; + private FTSRestClientI pdbRestCleint; private String selectedPdbFileName; @@ -90,6 +98,11 @@ public class StructureChooser extends GStructureChooser */ public void init() { + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + Thread discoverPDBStructuresThread = new Thread(new Runnable() { @Override @@ -136,22 +149,22 @@ public class StructureChooser extends GStructureChooser public void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - Collection wantedFields = PDBDocFieldPreferences + pdbRestCleint = PDBFTSRestClient.getInstance(); + Collection wantedFields = pdbDocFieldPrefs .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; + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -175,7 +188,8 @@ public class StructureChooser extends GStructureChooser if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest, + getResultTable().setModel( + FTSRestResponse.getTableModel(lastPdbRequest, discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); @@ -237,7 +251,7 @@ public class StructureChooser extends GStructureChooser boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - HashSet seqRefs = new LinkedHashSet(); + Set seqRefs = new LinkedHashSet(); if (seq.getAllPDBEntries() != null) { @@ -245,9 +259,8 @@ public class StructureChooser extends GStructureChooser { if (isValidSeqName(entry.getId())) { - queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) - .append(":") -.append(entry.getId().toLowerCase()) + queryBuilder.append("pdb_id:") + .append(entry.getId().toLowerCase()) .append(" OR "); isPDBRefsFound = true; // seqRefs.add(entry.getId()); @@ -263,22 +276,18 @@ public class StructureChooser extends GStructureChooser { if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { - queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ACCESSION - .getCode()).append(":") + queryBuilder.append("uniprot_accession:") .append(getDBRefId(dbRef)) .append(" OR "); - queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode()) - .append(":") - .append(getDBRefId(dbRef)).append(" OR "); + queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef)) + .append(" OR "); isUniProtRefsFound = true; } else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) { - queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) - .append(":").append(getDBRefId(dbRef).toLowerCase()) + queryBuilder.append("pdb_id:") + .append(getDBRefId(dbRef).toLowerCase()) .append(" OR "); isPDBRefsFound = true; } @@ -293,6 +302,7 @@ public class StructureChooser extends GStructureChooser if (!isPDBRefsFound && !isUniProtRefsFound) { String seqName = seq.getName(); + seqName = sanitizeSeqName(seqName); String[] names = seqName.toLowerCase().split("\\|"); for (String name : names) { @@ -320,6 +330,21 @@ public class StructureChooser extends GStructureChooser } /** + * 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 * @@ -369,24 +394,40 @@ public class StructureChooser extends GStructureChooser public void run() { long startTime = System.currentTimeMillis(); + pdbRestCleint = PDBFTSRestClient.getInstance(); lbl_loading.setVisible(true); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); + Collection filteredResponse = new HashSet(); HashSet errors = new HashSet(); + for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("("); - pdbRequest.setFieldToSortBy(fieldToFilterBy, - !chk_invertFilter.isSelected()); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setAssociatedSequence(seq); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + 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); @@ -409,14 +450,21 @@ public class StructureChooser extends GStructureChooser 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( + 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 - tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); + getResultTable().addRowSelectionInterval(0, + filterResponseCount - 1); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_filter_time", totalTime)); } @@ -482,17 +530,15 @@ public class StructureChooser extends GStructureChooser if (isStructuresDiscovered()) { cmb_filterOption.addItem(new FilterOption("Best Quality", - PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage", - PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Resolution", - PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Protein Chain", - PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules", - PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues", - PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER)); + "overall_quality", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Best Resolution", + "resolution", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Most Protein Chain", + "number_of_protein_chains", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", + "number_of_bound_molecules", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", + "number_of_polymer_residues", VIEWS_FILTER)); } cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID)); @@ -545,7 +591,7 @@ public class StructureChooser extends GStructureChooser String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - if (tbl_summary.getSelectedRows().length > 0) + if (getResultTable().getSelectedRows().length > 0) { btn_view.setEnabled(true); } @@ -669,27 +715,43 @@ public class StructureChooser extends GStructureChooser @Override public void ok_ActionPerformed() { + final long progressSessionId = System.currentTimeMillis(); + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + ssm.setProgressIndicator(this); + ssm.setProgressSessionId(progressSessionId); + new Thread(new Runnable() + { + @Override + public void run() + { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); 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 = getResultTable().getColumn("PDB Id") + .getModelIndex(); + int refSeqColIndex = getResultTable().getColumn("Ref Sequence") .getModelIndex(); - int[] selectedRows = tbl_summary.getSelectedRows(); + int[] selectedRows = getResultTable().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 = getResultTable().getValueAt(row, + pdbIdColIndex) .toString(); - SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, + SequenceI selectedSeq = (SequenceI) getResultTable() + .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(); @@ -701,16 +763,15 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, selectedSeqs); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); } 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( - 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(); @@ -725,8 +786,7 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, selectedSeqs); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) { @@ -742,14 +802,22 @@ public class StructureChooser extends GStructureChooser if (pdbEntry == null) { pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); + if (pdbIdStr.split(":").length > 1) + { + pdbEntry.setId(pdbIdStr.split(":")[0]); + pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase()); + } + else + { + pdbEntry.setId(pdbIdStr); + } pdbEntry.setType(PDBEntry.Type.PDB); selectedSequence.getDatasetSequence().addPDBId(pdbEntry); } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); + launchStructureViewer(ssm, pdbEntriesToView, ap, + new SequenceI[] { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -761,45 +829,88 @@ public class StructureChooser extends GStructureChooser } PDBEntry fileEntry = new AssociatePdbFileWithSeq() .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, + DataSourceType.FILE, selectedSequence, true, Desktop.instance); - launchStructureViewer(ap.getStructureSelectionManager(), - new PDBEntry[] { fileEntry }, ap, - new SequenceI[] { selectedSequence }); + launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + new SequenceI[] { selectedSequence }); } - mainFrame.dispose(); + closeAction(); + } + }).start(); } - private void launchStructureViewer(final StructureSelectionManager ssm, + 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, final SequenceI[] sequences) + final AlignmentPanel alignPanel, SequenceI[] sequences) { + ssm.setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer")); final StructureViewer sViewer = new StructureViewer(ssm); - new jalview.ws.DBRefFetcher(sequences, null, null, null, false) - .fetchDBRefs(true); - new Thread(new Runnable() + if (SiftsSettings.isMapWithSifts()) { - @Override - public void run() + ArrayList seqsWithoutSourceDBRef = new ArrayList(); + for (SequenceI seq : sequences) { - if (pdbEntriesToView.length > 1) + if (seq.getSourceDBRef() == null && seq.getDBRefs() == null) { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) - { - seqsMap.add(new SequenceI[] { seq }); + seqsWithoutSourceDBRef.add(seq); + continue; } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); - } - else + } + if (!seqsWithoutSourceDBRef.isEmpty()) + { + int y = seqsWithoutSourceDBRef.size(); + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y)); + SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; + int x = 0; + for (SequenceI fSeq : seqsWithoutSourceDBRef) { - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + seqWithoutSrcDBRef[x++] = fSeq; } + new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true); } - }).start(); + } + 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(MessageManager + .getString("status.fetching_3d_structures_for_selected_entries")); + sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + } + else + { + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId())); + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } } /** @@ -841,7 +952,7 @@ public class StructureChooser extends GStructureChooser this.structuresDiscovered = structuresDiscovered; } - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } @@ -858,17 +969,21 @@ public class StructureChooser extends GStructureChooser 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() + ")"); + pdbRequest +.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -1008,4 +1123,24 @@ public class StructureChooser extends GStructureChooser } } + + private IProgressIndicator progressBar; + + @Override + public void setProgressBar(String message, long id) + { + progressBar.setProgressBar(message, id); + } + + @Override + public void registerHandler(long id, IProgressIndicatorHandler handler) + { + progressBar.registerHandler(id, handler); + } + + @Override + public boolean operationInProgress() + { + return progressBar.operationInProgress(); + } }