X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5ea68fb5e2f825d838b7dc0233fc008eb08ca0ba;hp=1c99f029819fbc1be390273481827841fe40e007;hb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;hpb=5a3e8375831cd87fb3668e0945f907ddce0ab82a diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 1c99f02..5ea68fb 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,43 +21,54 @@ 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 jalview.ws.DBRefFetcher; +import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.seqfetcher.DbSourceProxy; import jalview.ws.sifts.SiftsSettings; -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; - /** * Provides the behaviors for the Structure chooser Panel * @@ -68,7 +79,7 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { - private static int MAX_QLENGTH = 7820; + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; private SequenceI selectedSequence; @@ -78,9 +89,13 @@ public class StructureChooser extends GStructureChooser private Collection discoveredStructuresSet; - private FTSRestRequest lastPdbRequest; + private StructureChooserQuerySource data; - private FTSRestClientI pdbRestCleint; + @Override + protected FTSDataColumnPreferences getFTSDocFieldPrefs() + { + return data.getDocFieldPrefs(); + } private String selectedPdbFileName; @@ -88,64 +103,290 @@ public class StructureChooser extends GStructureChooser private boolean cachedPDBExists; + 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; this.progressIndicator = (ap == null) ? null : ap.alignFrame; init(); + } /** + * 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 */ - public void init() + protected void init() { if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + 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); + btn_queryTDB.setEnabled(false); + // 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); + pnl_queryTDB.setVisible(false); + } + else + { + cmb_filterOption.setSelectedIndex(0); // select 'best' + btn_queryTDB.setVisible(false); + pnl_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")); } + /** + * Builds a drop-down choice list of existing structure viewers to which new + * structures may be added. If this list is empty then it, and the 'Add' + * button, are hidden. + */ private void discoverStructureViews() { if (Desktop.instance != null) { targetView.removeAllItems(); - targetView.addItem( - new StructureViewer(ap.getStructureSelectionManager())); if (lastTargetedView != null && !lastTargetedView.isVisible()) { lastTargetedView = null; } - int linkedViewsAt = 1; + int linkedViewsAt = 0; for (StructureViewerBase view : Desktop.instance .getStructureViewers(null, null)) { @@ -155,26 +396,34 @@ public class StructureChooser extends GStructureChooser if (view.isLinkedWith(ap)) { - targetView.insertItemAt(viewHandler, - linkedViewsAt++); + targetView.insertItemAt(viewHandler, linkedViewsAt++); } else { targetView.addItem(viewHandler); } } - targetView.setVisible(targetView.getItemCount() > 1); - // finally, restore last targeted view by default. - if (lastTargetedView != null) + /* + * show option to Add to viewer if at least 1 viewer found + */ + targetView.setVisible(false); + if (targetView.getItemCount() > 0) { - targetView.setSelectedItem(lastTargetedView); + targetView.setVisible(true); + if (lastTargetedView != null) + { + targetView.setSelectedItem(lastTargetedView); + } + else + { + targetView.setSelectedIndex(0); + } } + btn_add.setVisible(targetView.isVisible()); } } - private static StructureViewer lastTargetedView = null; - /** * Updates the progress indicator with the specified message * @@ -183,7 +432,7 @@ public class StructureChooser extends GStructureChooser * @param id * unique handle for this indicator */ - public void updateProgressIndicator(String message, long id) + protected void updateProgressIndicator(String message, long id) { if (progressIndicator != null) { @@ -195,39 +444,39 @@ public class StructureChooser extends GStructureChooser * Retrieve meta-data for all the structure(s) for a given sequence(s) in a * selection group */ - public void fetchStructuresMetaData() + void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - pdbRestCleint = 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 = pdbRestCleint.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()) { @@ -241,9 +490,11 @@ 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)); @@ -266,7 +517,7 @@ public class StructureChooser extends GStructureChooser } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) @@ -290,202 +541,42 @@ 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 - */ - - public static String buildQuery(SequenceI seq) - { - boolean isPDBRefsFound = false; - boolean isUniProtRefsFound = false; - StringBuilder queryBuilder = new StringBuilder(); - Set seqRefs = new LinkedHashSet<>(); - - if (seq.getAllPDBEntries() != null - && queryBuilder.length() < MAX_QLENGTH) - { - for (PDBEntry entry : seq.getAllPDBEntries()) - { - if (isValidSeqName(entry.getId())) - { - queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase()) - .append(" OR "); - isPDBRefsFound = true; - } - } - } - - if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) - { - for (DBRefEntry dbRef : seq.getDBRefs()) - { - 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)) - { - - queryBuilder.append("pdb_id:") - .append(getDBRefId(dbRef).toLowerCase()).append(" OR "); - isPDBRefsFound = true; - } - 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 - */ - public 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; - } - - public 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 * the field to filter by */ - public void filterResultSet(final String fieldToFilterBy) + void filterResultSet(final String fieldToFilterBy) { Thread filterThread = new Thread(new Runnable() { + @Override public void run() { long startTime = System.currentTimeMillis(); - pdbRestCleint = 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 = pdbRestCleint.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()) { @@ -501,8 +592,8 @@ 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); @@ -544,10 +635,13 @@ public class StructureChooser extends GStructureChooser * Handles action event for btn_pdbFromFile */ @Override - public void pdbFromFile_actionPerformed() + protected void pdbFromFile_actionPerformed() { + // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and + // StructureChooser + // works jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle( MessageManager.formatMessage("label.select_pdb_file_for", @@ -560,7 +654,7 @@ public class StructureChooser extends GStructureChooser if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { selectedPdbFileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); validateSelections(); } } @@ -572,46 +666,68 @@ 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); + pnl_queryTDB.setVisible(true); + } if (cachedPDBExist) { FilterOption cachedOption = new FilterOption( - MessageManager.getString("label.cached_structures"), - "-", VIEWS_LOCAL_PDB, false); + MessageManager.getString("label.cached_structures"), "-", + 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); } @@ -622,16 +738,41 @@ 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) @@ -645,28 +786,37 @@ public class StructureChooser extends GStructureChooser } /** - * Validates user selection and activates the view button if all parameters - * are correct + * Validates user selection and enables the 'Add' and 'New View' buttons if + * all parameters are correct (the Add button will only be visible if there is + * at least one existing structure viewer open). This basically means at least + * one structure selected and no error messages. + *

+ * The 'Superpose Structures' option is enabled if either more than one + * structure is selected, or the 'Add' to existing view option is enabled, and + * disabled if the only option is to open a new view of a single structure. */ @Override - public void validateSelections() + protected void validateSelections() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); - btn_view.setEnabled(false); + btn_add.setEnabled(false); String currentView = selectedFilterOpt.getView(); + int selectedCount = 0; if (currentView == VIEWS_FILTER) { - if (getResultTable().getSelectedRows().length > 0) + selectedCount = getResultTable().getSelectedRows().length; + if (selectedCount > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); } } else if (currentView == VIEWS_LOCAL_PDB) { - if (tbl_local_pdb.getSelectedRows().length > 0) + selectedCount = tbl_local_pdb.getSelectedRows().length; + if (selectedCount > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); } } else if (currentView == VIEWS_ENTER_ID) @@ -677,12 +827,60 @@ public class StructureChooser extends GStructureChooser { validateAssociationFromFile(); } + + btn_newView.setEnabled(btn_add.isEnabled()); + + /* + * enable 'Superpose' option if more than one structure is selected, + * or there are view(s) available to add structure(s) to + */ + chk_superpose + .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 */ - public void validateAssociationEnterPdb() + protected void validateAssociationEnterPdb() { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel .getCmb_assSeq().getSelectedItem(); @@ -708,7 +906,7 @@ public class StructureChooser extends GStructureChooser txt_search.setEnabled(true); if (isValidPBDEntry) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } @@ -723,7 +921,7 @@ public class StructureChooser extends GStructureChooser /** * Validates inputs for the manual PDB file selection options */ - public void validateAssociationFromFile() + protected void validateAssociationFromFile() { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); @@ -734,7 +932,7 @@ public class StructureChooser extends GStructureChooser btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_fromFileStatus.setIcon(goodImage); } } @@ -746,11 +944,13 @@ public class StructureChooser extends GStructureChooser } @Override - public void cmbAssSeqStateChanged() + protected void cmbAssSeqStateChanged() { validateSelections(); } + private FilterOption lastSelected = null; + /** * Handles the state change event for the 'filter' combo-box and 'invert' * check-box @@ -810,11 +1010,22 @@ public class StructureChooser extends GStructureChooser } return found; } + /** - * Handles action event for btn_ok + * Handles the 'New View' action */ @Override - public void ok_ActionPerformed() + protected void newView_ActionPerformed() + { + targetView.setSelectedItem(null); + showStructures(false); + } + + /** + * Handles the 'Add to existing viewer' action + */ + @Override + protected void add_ActionPerformed() { showStructures(false); } @@ -844,37 +1055,12 @@ 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(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); - } - pdbEntriesToView[count++] = pdbEntry; - } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, @@ -892,8 +1078,9 @@ 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); @@ -920,7 +1107,8 @@ 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 { @@ -948,10 +1136,8 @@ public class StructureChooser extends GStructureChooser DataSourceType.FILE, selectedSequence, true, Desktop.instance); - sViewer = launchStructureViewer( - ssm, new PDBEntry[] - { fileEntry }, ap, - new SequenceI[] + sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, + ap, new SequenceI[] { selectedSequence }); } SwingUtilities.invokeLater(new Runnable() @@ -984,42 +1170,45 @@ public class StructureChooser extends GStructureChooser } } - 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; - } - - public StructureViewer getTargetedStructureViewer( - StructureSelectionManager ssm) + /** + * 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) { - Object _sv = targetView.getSelectedItem(); + Object sv = targetView.getSelectedItem(); - if (_sv == null) - { - return new StructureViewer(ssm); - } else { - return (StructureViewer) _sv; - } + return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; } + + /** + * Adds PDB structures to a new or existing structure viewer + * + * @param ssm + * @param pdbEntriesToView + * @param alignPanel + * @param sequences + * @return + */ private StructureViewer launchStructureViewer( - StructureSelectionManager ssm, - final PDBEntry[] pdbEntriesToView, + StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { long progressId = sequences.hashCode(); setProgressBar(MessageManager .getString("status.launching_3d_structure_viewer"), progressId); - final StructureViewer sViewer = getTargetedStructureViewer(ssm); + 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()) @@ -1046,7 +1235,7 @@ public class StructureChooser extends GStructureChooser } } } - if (seq.getPrimaryDBRefs().size() == 0) + if (seq.getPrimaryDBRefs().isEmpty()) { seqsWithoutSourceDBRef.add(seq); continue; @@ -1058,13 +1247,8 @@ public class StructureChooser extends GStructureChooser setProgressBar(MessageManager.formatMessage( "status.fetching_dbrefs_for_sequences_without_valid_refs", y), progressId); - SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; - int x = 0; - for (SequenceI fSeq : seqsWithoutSourceDBRef) - { - seqWithoutSrcDBRef[x++] = fSeq; - } - + SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); dbRefFetcher.fetchDBRefs(true); @@ -1073,22 +1257,23 @@ public class StructureChooser extends GStructureChooser } if (pdbEntriesToView.length > 1) { - setProgressBar(MessageManager.getString( - "status.fetching_3d_structures_for_selected_entries"), + setProgressBar( + MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), progressId); - sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); } else { setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId()),progressId); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + pdbEntriesToView[0].getId()), progressId); + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } setProgressBar(null, progressId); // remember the last viewer we used... - lastTargetedView = sViewer; - return sViewer; + lastTargetedView = theViewer; + return theViewer; } /** @@ -1096,7 +1281,7 @@ public class StructureChooser extends GStructureChooser * a unique sequence when more than one sequence selection is made. */ @Override - public void populateCmbAssociateSeqOptions( + protected void populateCmbAssociateSeqOptions( JComboBox cmb_assSeq, JLabel lbl_associateSeq) { @@ -1121,67 +1306,73 @@ public class StructureChooser extends GStructureChooser } } - public boolean isStructuresDiscovered() + protected boolean isStructuresDiscovered() { return discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty(); } - public Collection getDiscoveredStructuresSet() - { - return discoveredStructuresSet; - } + protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes + // this. + // Doing a search for "1" or "1c" is valuable? + // Those work but are enormously slow. @Override protected void txt_search_ActionPerformed() { - new Thread() - { - @Override - public void run() + String text = txt_search.getText().trim(); + if (text.length() >= PDB_ID_MIN) + new Thread() { - errorWarning.setLength(0); - isValidPBDEntry = false; - if (txt_search.getText().length() > 0) + + @Override + public void run() { - 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(searchTerm + ")"); - pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = PDBFTSRestClient.getInstance(); - wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); - FTSRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - errorWarning.append(e.getMessage()); - return; - } finally - { - validateSelections(); - } - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) + errorWarning.setLength(0); + isValidPBDEntry = false; + if (text.length() > 0) { - isValidPBDEntry = true; + // 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<>(); + FTSRestRequest pdbRequest = new FTSRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("(pdb_id:"); + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setSearchTerm(searchTerm + ")"); + pdbRequest.setAssociatedSequence(selectedSequence); + FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); + FTSRestResponse resultList; + try + { + resultList = pdbRestClient.executeRequest(pdbRequest); + } catch (Exception e) + { + errorWarning.append(e.getMessage()); + return; + } finally + { + validateSelections(); + } + if (resultList.getSearchSummary() != null + && resultList.getSearchSummary().size() > 0) + { + isValidPBDEntry = true; + } } + validateSelections(); } - validateSelections(); - } - }.start(); + }.start(); } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) { @@ -1191,6 +1382,8 @@ public class StructureChooser extends GStructureChooser public void run() { fetchStructuresMetaData(); + // populateFilterComboBox(true, cachedPDBExists); + filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); @@ -1247,7 +1440,7 @@ 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 ? "_" @@ -1288,6 +1481,15 @@ 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; @@ -1324,4 +1526,37 @@ 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; + } }