X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=a8ce65971d1cef0164e2555711857ddbfa8566ac;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=c30d8c74ece16176b1f8b9d367ae0b3e9eaf000c;hpb=be8b1d254f658181eec3c29dc696114e3ffdd4df;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index c30d8c7..a8ce659 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,40 +21,52 @@ package jalview.gui; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Locale; +import java.util.concurrent.Executors; + +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; +import javax.swing.JTable; +import javax.swing.SwingUtilities; +import javax.swing.table.AbstractTableModel; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; 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.FTSDataColumnPreferences; import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; +import jalview.fts.service.threedbeacons.TDB_FTSData; +import jalview.gui.structurechooser.PDBStructureChooserQuerySource; +import jalview.gui.structurechooser.StructureChooserQuerySource; +import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; import jalview.io.DataSourceType; +import jalview.jbgui.FilterOption; import jalview.jbgui.GStructureChooser; +import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; - -import java.awt.event.ItemEvent; -import java.util.ArrayList; -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; -import javax.swing.JLabel; -import javax.swing.JTable; -import javax.swing.SwingUtilities; -import javax.swing.table.AbstractTableModel; +import jalview.ws.DBRefFetcher; +import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.sifts.SiftsSettings; /** * Provides the behaviors for the Structure chooser Panel @@ -66,9 +78,7 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { - static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; - - private static int MAX_QLENGTH = 7820; + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; private SequenceI selectedSequence; @@ -78,9 +88,13 @@ public class StructureChooser extends GStructureChooser private Collection discoveredStructuresSet; - private FTSRestRequest lastPdbRequest; + private StructureChooserQuerySource data; - private FTSRestClientI pdbRestClient; + @Override + protected FTSDataColumnPreferences getFTSDocFieldPrefs() + { + return data.getDocFieldPrefs(); + } private String selectedPdbFileName; @@ -88,11 +102,22 @@ public class StructureChooser extends GStructureChooser private boolean cachedPDBExists; - static StructureViewer lastTargetedView = null; + private Collection lastDiscoveredStructuresSet; + + private boolean canQueryTDB = false; + + private boolean notQueriedTDBYet = true; + + List seqsWithoutSourceDBRef = null; + + private static StructureViewer lastTargetedView = null; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { + // which FTS engine to use + data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs); + initDialog(); this.ap = ap; this.selectedSequence = selectedSeq; this.selectedSequences = selectedSeqs; @@ -101,6 +126,52 @@ public class StructureChooser extends GStructureChooser } /** + * sets canQueryTDB if protein sequences without a canonical uniprot ref or at + * least one structure are discovered. + */ + private void populateSeqsWithoutSourceDBRef() + { + seqsWithoutSourceDBRef = new ArrayList(); + boolean needCanonical = false; + for (SequenceI seq : selectedSequences) + { + if (seq.isProtein()) + { + int dbRef = ThreeDBStructureChooserQuerySource + .checkUniprotRefs(seq.getDBRefs()); + if (dbRef < 0) + { + if (dbRef == -1) + { + // need to retrieve canonicals + needCanonical = true; + seqsWithoutSourceDBRef.add(seq); + } + else + { + // could be a sequence with pdb ref + if (seq.getAllPDBEntries() == null + || seq.getAllPDBEntries().size() == 0) + { + seqsWithoutSourceDBRef.add(seq); + } + } + } + } + } + // retrieve database refs for protein sequences + if (!seqsWithoutSourceDBRef.isEmpty()) + { + canQueryTDB = true; + if (needCanonical) + { + // triggers display of the 'Query TDB' button + notQueriedTDBYet = true; + } + } + }; + + /** * Initializes parameters used by the Structure Chooser Panel */ protected void init() @@ -111,31 +182,173 @@ public class StructureChooser extends GStructureChooser } chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); + btn_queryTDB.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + promptForTDBFetch(false); + } + }); + + Executors.defaultThreadFactory().newThread(new Runnable() + { + public void run() + { + populateSeqsWithoutSourceDBRef(); + initialStructureDiscovery(); + } + + }).start(); + + } + + // called by init + private void initialStructureDiscovery() + { + // check which FTS engine to use + data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences); // ensure a filter option is in force for search populateFilterComboBox(true, cachedPDBExists); - Thread discoverPDBStructuresThread = new Thread(new Runnable() + // looks for any existing structures already loaded + // for the sequences (the cached ones) + // then queries the StructureChooserQuerySource to + // discover more structures. + // + // Possible optimisation is to only begin querying + // the structure chooser if there are no cached structures. + + long startTime = System.currentTimeMillis(); + updateProgressIndicator( + MessageManager.getString("status.loading_cached_pdb_entries"), + startTime); + loadLocalCachedPDBEntries(); + updateProgressIndicator(null, startTime); + updateProgressIndicator( + MessageManager.getString("status.searching_for_pdb_structures"), + startTime); + fetchStructuresMetaData(); + // revise filter options if no results were found + populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); + discoverStructureViews(); + updateProgressIndicator(null, startTime); + mainFrame.setVisible(true); + updateCurrentView(); + } + + /** + * raises dialog for Uniprot fetch followed by 3D beacons search + * @param ignoreGui - when true, don't ask, just fetch + */ + public void promptForTDBFetch(boolean ignoreGui) + { + final long progressId = System.currentTimeMillis(); + + // final action after prompting and discovering db refs + final Runnable strucDiscovery = new Runnable() { @Override public void run() { - long startTime = System.currentTimeMillis(); - updateProgressIndicator(MessageManager - .getString("status.loading_cached_pdb_entries"), startTime); - loadLocalCachedPDBEntries(); - updateProgressIndicator(null, startTime); - updateProgressIndicator(MessageManager.getString( - "status.searching_for_pdb_structures"), startTime); - fetchStructuresMetaData(); - // revise filter options if no results were found - populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); - discoverStructureViews(); - updateProgressIndicator(null, startTime); - mainFrame.setVisible(true); - updateCurrentView(); + mainFrame.setEnabled(false); + cmb_filterOption.setEnabled(false); + progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId); + // TODO: warn if no accessions discovered + populateSeqsWithoutSourceDBRef(); + // redo initial discovery - this time with 3d beacons + // Executors. + previousWantedFields=null; + lastSelected=(FilterOption) cmb_filterOption.getSelectedItem(); + cmb_filterOption.setSelectedItem(null); + cachedPDBExists=false; // reset to initial + initialStructureDiscovery(); + if (!isStructuresDiscovered()) + { + progressBar.setProgressBar(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"), progressId); + btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons")); + btn_queryTDB.setEnabled(false); + } else { + cmb_filterOption.setSelectedIndex(0); // select 'best' + btn_queryTDB.setVisible(false); + progressBar.setProgressBar(null, progressId); + } + mainFrame.setEnabled(true); + cmb_filterOption.setEnabled(true); } - }); - discoverPDBStructuresThread.start(); + }; + + final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI() + { + + @Override + public void finished() + { + // filter has been selected, so we set flag to remove ourselves + notQueriedTDBYet = false; + // new thread to discover structures - via 3d beacons + Executors.defaultThreadFactory().newThread(strucDiscovery).start(); + + } + }; + + // fetch db refs if OK pressed + final Runnable discoverCanonicalDBrefs = new Runnable() + { + @Override + public void run() + { + populateSeqsWithoutSourceDBRef(); + + final int y = seqsWithoutSourceDBRef.size(); + if (y > 0) + { + final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef, + progressBar, new DbSourceProxy[] + { new jalview.ws.dbsources.Uniprot() }, null, false); + dbRefFetcher.addListener(afterDbRefFetch); + // ideally this would also gracefully run with callbacks + dbRefFetcher.fetchDBRefs(true); + } else { + // call finished action directly + afterDbRefFetch.finished(); + } + } + + }; + final Runnable revertview = new Runnable() { + public void run() { + if (lastSelected!=null) { + cmb_filterOption.setSelectedItem(lastSelected); + } + }; + }; + if (ignoreGui) + { + Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start(); + return; + } + // need cancel and no to result in the discoverPDB action - mocked is + // 'cancel' TODO: mock should be OK + JvOptionPane.newOptionDialog(this) + .setResponseHandler(JvOptionPane.OK_OPTION, + discoverCanonicalDBrefs) + .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) + .setResponseHandler(JvOptionPane.NO_OPTION, revertview) + .showDialog( + MessageManager.formatMessage( + "label.fetch_references_for_3dbeacons", + seqsWithoutSourceDBRef.size()), + MessageManager + .getString("label.3dbeacons"), + JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE, + null, new Object[] + { MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }, + MessageManager.getString("action.ok")); } /** @@ -213,36 +426,33 @@ public class StructureChooser extends GStructureChooser void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - pdbRestClient = PDBFTSRestClient.getInstance(); - Collection wantedFields = pdbDocFieldPrefs + Collection wantedFields = data.getDocFieldPrefs() .getStructureSummaryFields(); discoveredStructuresSet = new LinkedHashSet<>(); HashSet errors = new HashSet<>(); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); for (SequenceI seq : selectedSequences) { - FTSRestRequest pdbRequest = new FTSRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(500); - pdbRequest.setFieldToSearchBy("("); - FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption - .getSelectedItem()); - pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), - !chk_invertFilter.isSelected()); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setAssociatedSequence(seq); FTSRestResponse resultList; try { - resultList = pdbRestClient.executeRequest(pdbRequest); + resultList = data.fetchStructuresMetaData(seq, wantedFields, + selectedFilterOpt, !chk_invertFilter.isSelected()); + // null response means the FTSengine didn't yield a query for this + // consider designing a special exception if we really wanted to be + // OOCrazy + if (resultList == null) + { + continue; + } } catch (Exception e) { e.printStackTrace(); errors.add(e.getMessage()); continue; } - lastPdbRequest = pdbRequest; if (resultList.getSearchSummary() != null && !resultList.getSearchSummary().isEmpty()) { @@ -256,9 +466,10 @@ public class StructureChooser extends GStructureChooser if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - getResultTable().setModel(FTSRestResponse - .getTableModel(lastPdbRequest, discoveredStructuresSet)); + getResultTable() + .setModel(data.getTableModel(discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); + lastDiscoveredStructuresSet = discoveredStructuresSet; mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", noOfStructuresFound, totalTime)); @@ -305,157 +516,6 @@ public class StructureChooser extends GStructureChooser } /** - * Builds a query string for a given sequences using its DBRef entries - * - * @param seq - * the sequences to build a query for - * @return the built query string - */ - - static String buildQuery(SequenceI seq) - { - boolean isPDBRefsFound = false; - boolean isUniProtRefsFound = false; - StringBuilder queryBuilder = new StringBuilder(); - Set seqRefs = new LinkedHashSet<>(); - - /* - * note PDBs as DBRefEntry so they are not duplicated in query - */ - Set pdbids = new HashSet<>(); - - if (seq.getAllPDBEntries() != null - && queryBuilder.length() < MAX_QLENGTH) - { - for (PDBEntry entry : seq.getAllPDBEntries()) - { - if (isValidSeqName(entry.getId())) - { - String id = entry.getId().toLowerCase(); - queryBuilder.append("pdb_id:").append(id).append(" OR "); - isPDBRefsFound = true; - pdbids.add(id); - } - } - } - - List refs = seq.getDBRefs(); - if (refs != null && refs.size() != 0) - { - for (int ib = 0, nb = refs.size(); ib < nb; ib++) - { - DBRefEntry dbRef = refs.get(ib); - if (isValidSeqName(getDBRefId(dbRef)) - && queryBuilder.length() < MAX_QLENGTH) - { - if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) - { - queryBuilder.append("uniprot_accession:") - .append(getDBRefId(dbRef)).append(" OR "); - queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef)) - .append(" OR "); - isUniProtRefsFound = true; - } - else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) - { - - String id = getDBRefId(dbRef).toLowerCase(); - if (!pdbids.contains(id)) - { - queryBuilder.append("pdb_id:").append(id).append(" OR "); - isPDBRefsFound = true; - pdbids.add(id); - } - } - else - { - seqRefs.add(getDBRefId(dbRef)); - } - } - } - } - - if (!isPDBRefsFound && !isUniProtRefsFound) - { - 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 "); - if (queryBuilder.toString().length() < 6) - { - return null; - } - String query = queryBuilder.toString().substring(0, endIndex); - return query; - } - - /** - * 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 @@ -469,50 +529,26 @@ public class StructureChooser extends GStructureChooser public void run() { long startTime = System.currentTimeMillis(); - pdbRestClient = PDBFTSRestClient.getInstance(); lbl_loading.setVisible(true); - Collection wantedFields = pdbDocFieldPrefs + Collection wantedFields = data.getDocFieldPrefs() .getStructureSummaryFields(); Collection filteredResponse = new HashSet<>(); HashSet 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 = pdbRestClient.executeRequest(pdbRequest); + resultList = data.selectFirstRankedQuery(seq, + discoveredStructuresSet, wantedFields, fieldToFilterBy, + !chk_invertFilter.isSelected()); } catch (Exception e) { e.printStackTrace(); errors.add(e.getMessage()); continue; } - lastPdbRequest = pdbRequest; if (resultList.getSearchSummary() != null && !resultList.getSearchSummary().isEmpty()) { @@ -528,8 +564,8 @@ public class StructureChooser extends GStructureChooser Collection reorderedStructuresSet = new LinkedHashSet<>(); reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); - getResultTable().setModel(FTSRestResponse - .getTableModel(lastPdbRequest, reorderedStructuresSet)); + getResultTable() + .setModel(data.getTableModel(reorderedStructuresSet)); FTSRestResponse.configureTableColumn(getResultTable(), wantedFields, tempUserPrefs); @@ -602,46 +638,67 @@ public class StructureChooser extends GStructureChooser protected void populateFilterComboBox(boolean haveData, boolean cachedPDBExist) { + populateFilterComboBox(haveData, cachedPDBExist, null); + } + + /** + * Populates the filter combo-box options dynamically depending on discovered + * structures + */ + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExist, FilterOption lastSel) + { /* * temporarily suspend the change listener behaviour */ cmb_filterOption.removeItemListener(this); + int selSet = -1; cmb_filterOption.removeAllItems(); if (haveData) { - cmb_filterOption.addItem(new FilterOption( - MessageManager.getString("label.best_quality"), - "overall_quality", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption( - MessageManager.getString("label.best_resolution"), - "resolution", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption( - MessageManager.getString("label.most_protein_chain"), - "number_of_protein_chains", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption( - MessageManager.getString("label.most_bound_molecules"), - "number_of_bound_molecules", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption( - MessageManager.getString("label.most_polymer_residues"), - "number_of_polymer_residues", VIEWS_FILTER, true)); + List filters = data + .getAvailableFilterOptions(VIEWS_FILTER); + data.updateAvailableFilterOptions(VIEWS_FILTER, filters, + lastDiscoveredStructuresSet); + int p = 0; + for (FilterOption filter : filters) + { + if (lastSel != null && filter.equals(lastSel)) + { + selSet = p; + } + p++; + cmb_filterOption.addItem(filter); + } } cmb_filterOption.addItem( new FilterOption(MessageManager.getString("label.enter_pdb_id"), - "-", VIEWS_ENTER_ID, false)); + "-", VIEWS_ENTER_ID, false, null)); cmb_filterOption.addItem( new FilterOption(MessageManager.getString("label.from_file"), - "-", VIEWS_FROM_FILE, false)); + "-", VIEWS_FROM_FILE, false, null)); + if (canQueryTDB && notQueriedTDBYet) + { + btn_queryTDB.setVisible(true); + } if (cachedPDBExist) { FilterOption cachedOption = new FilterOption( MessageManager.getString("label.cached_structures"), "-", - VIEWS_LOCAL_PDB, false); + VIEWS_LOCAL_PDB, false, null); cmb_filterOption.addItem(cachedOption); - cmb_filterOption.setSelectedItem(cachedOption); + if (selSet == -1) + { + cmb_filterOption.setSelectedItem(cachedOption); + } } + if (selSet > -1) + { + cmb_filterOption.setSelectedIndex(selSet); + } cmb_filterOption.addItemListener(this); } @@ -652,16 +709,40 @@ public class StructureChooser extends GStructureChooser { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); + + if (lastSelected == selectedFilterOpt) + { + // don't need to do anything, probably + return; + } + // otherwise, record selection + // and update the layout and dialog accordingly + lastSelected = selectedFilterOpt; layout_switchableViews.show(pnl_switchableViews, selectedFilterOpt.getView()); String filterTitle = mainFrame.getTitle(); mainFrame.setTitle(frameTitle); chk_invertFilter.setVisible(false); + if (selectedFilterOpt.getView() == VIEWS_FILTER) { mainFrame.setTitle(filterTitle); - chk_invertFilter.setVisible(true); - filterResultSet(selectedFilterOpt.getValue()); + // TDB Query has no invert as yet + chk_invertFilter.setVisible(selectedFilterOpt + .getQuerySource() instanceof PDBStructureChooserQuerySource); + + if (data != selectedFilterOpt.getQuerySource() + || data.needsRefetch(selectedFilterOpt)) + { + data = selectedFilterOpt.getQuerySource(); + // rebuild the views completely, since prefs will also change + tabRefresh(); + return; + } + else + { + filterResultSet(selectedFilterOpt.getValue()); + } } else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID || selectedFilterOpt.getView() == VIEWS_FROM_FILE) @@ -727,6 +808,38 @@ public class StructureChooser extends GStructureChooser .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); } + @Override + protected boolean showPopupFor(int selectedRow, int x, int y) + { + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + + if (currentView == VIEWS_FILTER && data instanceof ThreeDBStructureChooserQuerySource) + { + + TDB_FTSData row=((ThreeDBStructureChooserQuerySource)data).getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet); + String pageUrl = row.getModelViewUrl(); + JPopupMenu popup = new JPopupMenu("3D Beacons"); + JMenuItem viewUrl = new JMenuItem("View model web page"); + viewUrl.addActionListener( + new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) + { + Desktop.showUrl(pageUrl); + } + } + ); + popup.add(viewUrl); + SwingUtilities.invokeLater(new Runnable() { + public void run() { popup.show(getResultTable(), x, y); } + }); + return true; + } + // event not handled by us + return false; + } /** * Validates inputs from the Manual PDB entry panel */ @@ -799,6 +912,7 @@ public class StructureChooser extends GStructureChooser validateSelections(); } + private FilterOption lastSelected=null; /** * Handles the state change event for the 'filter' combo-box and 'invert' * check-box @@ -858,7 +972,6 @@ public class StructureChooser extends GStructureChooser } return found; } - /** * Handles the 'New View' action */ @@ -886,10 +999,9 @@ public class StructureChooser extends GStructureChooser public void showStructures(boolean waitUntilFinished) { - final int preferredHeight = pnl_filter.getHeight(); + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - final StructureViewer theViewer = getTargetedStructureViewer(); - boolean superimpose = chk_superpose.isSelected(); + final int preferredHeight = pnl_filter.getHeight(); Runnable viewStruc = new Runnable() { @@ -904,38 +1016,16 @@ public class StructureChooser extends GStructureChooser if (currentView == VIEWS_FILTER) { - int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex(); - int refSeqColIndex = restable.getColumn("Ref Sequence") - .getModelIndex(); int[] selectedRows = restable.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; List selectedSeqsToView = new ArrayList<>(); - for (int row : selectedRows) - { - String pdbIdStr = restable.getValueAt(row, pdbIdColIndex) - .toString(); - SequenceI selectedSeq = (SequenceI) restable.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); - if (pdbEntry == null) - { - pdbEntry = getFindEntry(pdbIdStr, - selectedSeq.getAllPDBEntries()); - } + pdbEntriesToView = data.collectSelectedRows(restable, + selectedRows, selectedSeqsToView); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(pdbIdStr, null, "pdb"); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); - } - pdbEntriesToView[count++] = pdbEntry; - } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, - selectedSeqs, superimpose, theViewer, progressBar); + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + selectedSeqs); } else if (currentView == VIEWS_LOCAL_PDB) { @@ -949,8 +1039,8 @@ public class StructureChooser extends GStructureChooser List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { - PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, - pdbIdColIndex); + PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb + .getModel()).getPDBEntryAt(row).getPdbEntry(); pdbEntriesToView[count++] = pdbEntry; SequenceI selectedSeq = (SequenceI) tbl_local_pdb .getValueAt(row, refSeqColIndex); @@ -958,8 +1048,8 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, - selectedSeqs, superimpose, theViewer, progressBar); + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) { @@ -977,7 +1067,7 @@ public class StructureChooser extends GStructureChooser if (pdbIdStr.split(":").length > 1) { pdbEntry.setId(pdbIdStr.split(":")[0]); - pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase()); + pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); } else { @@ -988,10 +1078,9 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] - { selectedSequence }, superimpose, theViewer, - progressBar); + { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -1001,12 +1090,14 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true); - sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry }, - new SequenceI[] - { selectedSequence }, superimpose, theViewer, - progressBar); + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true, + Desktop.getInstance()); + + sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, + ap, new SequenceI[] + { selectedSequence }); } SwingUtilities.invokeLater(new Runnable() { @@ -1038,31 +1129,110 @@ public class StructureChooser extends GStructureChooser } } - private PDBEntry getFindEntry(String id, Vector pdbEntries) + /** + * Answers a structure viewer (new or existing) configured to superimpose + * added structures or not according to the user's choice + * + * @param ssm + * @return + */ + StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm) { - Objects.requireNonNull(id); - Objects.requireNonNull(pdbEntries); - PDBEntry foundEntry = null; - for (PDBEntry entry : pdbEntries) - { - if (entry.getId().equalsIgnoreCase(id)) - { - return entry; - } - } - return foundEntry; + Object sv = targetView.getSelectedItem(); + + return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; } /** - * Answers a structure viewer (new or existing) configured to superimpose - * added structures or not according to the user's choice + * Adds PDB structures to a new or existing structure viewer * * @param ssm + * @param pdbEntriesToView + * @param alignPanel + * @param sequences * @return */ - StructureViewer getTargetedStructureViewer() + private StructureViewer launchStructureViewer( + StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, + final AlignmentPanel alignPanel, SequenceI[] sequences) { - return (StructureViewer) targetView.getSelectedItem(); + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); + final StructureViewer theViewer = getTargetedStructureViewer(ssm); + boolean superimpose = chk_superpose.isSelected(); + theViewer.setSuperpose(superimpose); + + /* + * remember user's choice of superimpose or not + */ + Cache.setProperty(AUTOSUPERIMPOSE, + Boolean.valueOf(superimpose).toString()); + + setProgressBar(null, progressId); + if (SiftsSettings.isMapWithSifts()) + { + List seqsWithoutSourceDBRef = new ArrayList<>(); + int p = 0; + // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a + // real PDB ID. For moment, we can also safely do this if there is already + // a known mapping between the PDBEntry and the sequence. + for (SequenceI seq : sequences) + { + PDBEntry pdbe = pdbEntriesToView[p++]; + if (pdbe != null && pdbe.getFile() != null) + { + StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); + if (smm != null && smm.length > 0) + { + for (StructureMapping sm : smm) + { + if (sm.getSequence() == seq) + { + continue; + } + } + } + } + if (seq.getPrimaryDBRefs().isEmpty()) + { + seqsWithoutSourceDBRef.add(seq); + continue; + } + } + if (!seqsWithoutSourceDBRef.isEmpty()) + { + int y = seqsWithoutSourceDBRef.size(); + setProgressBar(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y), progressId); + SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); + dbRefFetcher.fetchDBRefs(true); + + setProgressBar("Fetch complete.", progressId); // todo i18n + } + } + if (pdbEntriesToView.length > 1) + { + setProgressBar( + MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); + theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + } + else + { + setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId()), progressId); + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } + setProgressBar(null, progressId); + // remember the last viewer we used... + lastTargetedView = theViewer; + return theViewer; } /** @@ -1121,7 +1291,10 @@ public class StructureChooser extends GStructureChooser isValidPBDEntry = false; if (text.length() > 0) { - String searchTerm = text.toLowerCase(); + // TODO move this pdb id search into the PDB specific + // FTSSearchEngine + // for moment, it will work fine as is because it is self-contained + String searchTerm = text.toLowerCase(Locale.ROOT); searchTerm = searchTerm.split(":")[0]; // System.out.println(">>>>> search term : " + searchTerm); List wantedFields = new ArrayList<>(); @@ -1132,7 +1305,7 @@ public class StructureChooser extends GStructureChooser pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestClient = PDBFTSRestClient.getInstance(); + FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance(); wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); FTSRestResponse resultList; try @@ -1168,6 +1341,7 @@ public class StructureChooser extends GStructureChooser public void run() { fetchStructuresMetaData(); + // populateFilterComboBox(true, cachedPDBExists); filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); @@ -1224,7 +1398,7 @@ public class StructureChooser extends GStructureChooser value = entry.getSequence(); break; case 1: - value = entry.getPdbEntry(); + value = entry.getQualifiedId(); break; case 2: value = entry.getPdbEntry().getChainCode() == null ? "_" @@ -1265,6 +1439,15 @@ public class StructureChooser extends GStructureChooser this.pdbEntry = pdbEntry; } + public String getQualifiedId() + { + if (pdbEntry.hasProvider()) + { + return pdbEntry.getProvider() + ":" + pdbEntry.getId(); + } + return pdbEntry.toString(); + } + public SequenceI getSequence() { return sequence; @@ -1284,6 +1467,12 @@ public class StructureChooser extends GStructureChooser { progressBar.setProgressBar(message, id); } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(long id, IProgressIndicatorHandler handler) @@ -1302,4 +1491,34 @@ public class StructureChooser extends GStructureChooser return sViewer == null ? null : sViewer.sview; } + @Override + protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs) + { + data.setDocFieldPrefs(newPrefs); + + } + + /** + * + * @return true when all initialisation threads have finished and dialog is + * visible + */ + public boolean isDialogVisible() + { + return mainFrame != null && data != null && cmb_filterOption != null + && mainFrame.isVisible() + && cmb_filterOption.getSelectedItem() != null; + } + /** + * + * @return true if the 3D-Beacons query button will/has been displayed + */ + public boolean isCanQueryTDB() { + return canQueryTDB; + } + + public boolean isNotQueriedTDBYet() + { + return notQueriedTDBYet; + } }