X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=d924e735e916834f9144c4f1d96160893f7b014c;hb=721eacfd0eb9bfb415c60448b8ec8f24774b196b;hp=63a8654e3a76cc723e9379ba125e9822fe2fe726;hpb=abcfb92b105fb0bac6648c863c4141d691635e2a;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 63a8654..d924e73 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,18 +21,21 @@ 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.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.sifts.SiftsSettings; import java.awt.event.ItemEvent; import java.util.ArrayList; @@ -40,6 +43,8 @@ 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; @@ -54,7 +59,8 @@ import javax.swing.table.AbstractTableModel; * */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser +public class StructureChooser extends GStructureChooser implements + IProgressIndicator { private boolean structuresDiscovered = false; @@ -64,11 +70,11 @@ 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; @@ -89,6 +95,11 @@ 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 @@ -135,22 +146,22 @@ public class StructureChooser extends GStructureChooser 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("(text:"); + pdbRequest.setFieldToSearchBy("("); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setAssociatedSequence(seq); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -174,7 +185,7 @@ public class StructureChooser extends GStructureChooser if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest, + tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest, discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); @@ -233,18 +244,10 @@ public class StructureChooser extends GStructureChooser public static String buildQuery(SequenceI seq) { + boolean isPDBRefsFound = false; + boolean isUniProtRefsFound = false; + StringBuilder queryBuilder = new StringBuilder(); HashSet seqRefs = new LinkedHashSet(); - String seqName = seq.getName(); - String[] names = seqName.toLowerCase().split("\\|"); - for (String name : names) - { - // System.out.println("Found name : " + name); - name.trim(); - if (isValidSeqName(name)) - { - seqRefs.add(name); - } - } if (seq.getAllPDBEntries() != null) { @@ -252,44 +255,96 @@ public class StructureChooser extends GStructureChooser { if (isValidSeqName(entry.getId())) { - seqRefs.add(entry.getId()); + queryBuilder.append("pdb_id") + .append(":") +.append(entry.getId().toLowerCase()) + .append(" OR "); + isPDBRefsFound = true; + // seqRefs.add(entry.getId()); } } } - if (seq.getDBRef() != null && seq.getDBRef().length != 0) + if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) { - int count = 0; - for (DBRefEntry dbRef : seq.getDBRef()) + for (DBRefEntry dbRef : seq.getDBRefs()) { if (isValidSeqName(getDBRefId(dbRef))) { - seqRefs.add(getDBRefId(dbRef)); - } - ++count; - if (count > 10) - { - break; + if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) + { + queryBuilder +.append("uniprot_accession").append(":") + .append(getDBRefId(dbRef)) + .append(" OR "); + queryBuilder +.append("uniprot_id") + .append(":") + .append(getDBRefId(dbRef)).append(" OR "); + isUniProtRefsFound = true; + } + else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) + { + + queryBuilder.append("pdb_id") + .append(":").append(getDBRefId(dbRef).toLowerCase()) + .append(" OR "); + isPDBRefsFound = true; + } + else + { + seqRefs.add(getDBRefId(dbRef)); + } } } } - StringBuilder queryBuilder = new StringBuilder(); - for (String seqRef : seqRefs) + if (!isPDBRefsFound && !isUniProtRefsFound) { - queryBuilder.append("text:").append(seqRef).append(" OR "); + String seqName = seq.getName(); + seqName = sanitizeSeqName(seqName); + String[] names = seqName.toLowerCase().split("\\|"); + for (String name : names) + { + // System.out.println("Found name : " + name); + name.trim(); + if (isValidSeqName(name)) + { + seqRefs.add(name); + } + } + + for (String seqRef : seqRefs) + { + queryBuilder.append("text:").append(seqRef).append(" OR "); + } } - int endIndex = queryBuilder.lastIndexOf(" OR "); + int endIndex = queryBuilder.lastIndexOf(" OR "); if (queryBuilder.toString().length() < 6) { return null; } - String query = queryBuilder.toString().substring(5, endIndex); + String query = queryBuilder.toString().substring(0, endIndex); return query; } /** + * 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 * @@ -339,24 +394,41 @@ public class StructureChooser extends GStructureChooser 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(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(text:"); - 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")) + { + System.out.println(">>>>>> Filtering with uniprot coverate"); + 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); @@ -379,12 +451,16 @@ 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( + 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( @@ -420,6 +496,7 @@ public class StructureChooser extends GStructureChooser /** * Handles action event for btn_pdbFromFile */ + @Override public void pdbFromFile_actionPerformed() { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( @@ -445,22 +522,23 @@ public class StructureChooser extends GStructureChooser * Populates the filter combo-box options dynamically depending on discovered * structures */ + @Override protected void populateFilterComboBox() { 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("Most UniProt Coverage", + "uniprot_coverage", 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)); @@ -473,6 +551,7 @@ public class StructureChooser extends GStructureChooser /** * Updates the displayed view based on the selected filter option */ + @Override protected void updateCurrentView() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -503,6 +582,7 @@ public class StructureChooser extends GStructureChooser * Validates user selection and activates the view button if all parameters * are correct */ + @Override public void validateSelections() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -635,13 +715,22 @@ 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 pdbIdColIndex = tbl_summary.getColumn("PDB Id") + .getModelIndex(); int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") .getModelIndex(); int[] selectedRows = tbl_summary.getSelectedRows(); @@ -655,7 +744,12 @@ public class StructureChooser extends GStructureChooser 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(); @@ -667,16 +761,15 @@ 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(); @@ -691,8 +784,7 @@ 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) { @@ -714,8 +806,8 @@ public class StructureChooser extends GStructureChooser } 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) { @@ -730,22 +822,50 @@ public class StructureChooser extends GStructureChooser jalview.io.AppletFormatAdapter.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(); + } + }).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("Launching PDB structure viewer.."); final StructureViewer sViewer = new StructureViewer(ssm); - new Thread(new Runnable() + + if (SiftsSettings.isMapWithSifts()) { - public void run() + 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 (pdbEntriesToView.length > 1) { ArrayList seqsMap = new ArrayList(); @@ -754,20 +874,24 @@ public class StructureChooser extends GStructureChooser 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 { + ssm.setProgressBar(null); + ssm.setProgressBar("Fetching PDB Structure for " + + pdbEntriesToView[0].getId()); sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } - } - }).start(); } /** * Populates the combo-box used in associating manually fetched structures to * a unique sequence when more than one sequence selection is made. */ + @Override public void populateCmbAssociateSeqOptions( JComboBox cmb_assSeq, JLabel lbl_associateSeq) { @@ -802,7 +926,7 @@ public class StructureChooser extends GStructureChooser this.structuresDiscovered = structuresDiscovered; } - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } @@ -812,23 +936,25 @@ public class StructureChooser extends GStructureChooser { new Thread() { + @Override public void run() { errorWarning.setLength(0); 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:"); pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(txt_search.getText() + ")"); + 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); @@ -968,4 +1094,24 @@ 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(); + } }