X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5ea68fb5e2f825d838b7dc0233fc008eb08ca0ba;hb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;hp=976b77b9c89227e3995c2a4cd095e2802729cfef;hpb=7a1a7eea9501cd9e3841e996f4926cf1686be76a;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 976b77b..5ea68fb 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,7 +1,6 @@ /* - - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -22,33 +21,53 @@ package jalview.gui; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -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 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.Hashtable; 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.JOptionPane; -import javax.swing.table.DefaultTableModel; - +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.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; /** * Provides the behaviors for the Structure chooser Panel @@ -58,8 +77,9 @@ import javax.swing.table.DefaultTableModel; */ @SuppressWarnings("serial") public class StructureChooser extends GStructureChooser + implements IProgressIndicator { - private boolean structuresDiscovered = false; + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; private SequenceI selectedSequence; @@ -67,54 +87,341 @@ public class StructureChooser extends GStructureChooser private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet; + private Collection discoveredStructuresSet; - private PDBRestRequest lastPdbRequest; + private StructureChooserQuerySource data; - private PDBRestClient pdbRestCleint; + @Override + protected FTSDataColumnPreferences getFTSDocFieldPrefs() + { + return data.getDocFieldPrefs(); + } private String selectedPdbFileName; private boolean isValidPBDEntry; - private static Hashtable cachedEntryMap; + 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() { - Thread discoverPDBStructuresThread = new Thread(new Runnable() + 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 run() + public void actionPerformed(ActionEvent e) { - 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(); - populateFilterComboBox(); - updateProgressIndicator(null, startTime); - mainFrame.setVisible(true); - updateCurrentView(); + promptForTDBFetch(false); } }); - discoverPDBStructuresThread.start(); + + 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); + + // 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() + { + 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); + } + }; + + 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(); + if (lastTargetedView != null && !lastTargetedView.isVisible()) + { + lastTargetedView = null; + } + int linkedViewsAt = 0; + for (StructureViewerBase view : Desktop.instance + .getStructureViewers(null, null)) + { + StructureViewer viewHandler = (lastTargetedView != null + && lastTargetedView.sview == view) ? lastTargetedView + : StructureViewer.reconfigure(view); + + if (view.isLinkedWith(ap)) + { + targetView.insertItemAt(viewHandler, linkedViewsAt++); + } + else + { + targetView.addItem(viewHandler); + } + } + + /* + * show option to Add to viewer if at least 1 viewer found + */ + targetView.setVisible(false); + if (targetView.getItemCount() > 0) + { + targetView.setVisible(true); + if (lastTargetedView != null) + { + targetView.setSelectedItem(lastTargetedView); + } + else + { + targetView.setSelectedIndex(0); + } + } + btn_add.setVisible(targetView.isVisible()); + } } /** @@ -125,7 +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) { @@ -137,40 +444,43 @@ 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(); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = data.getDocFieldPrefs() .getStructureSummaryFields(); - discoveredStructuresSet = new LinkedHashSet(); - HashSet errors = new HashSet(); + discoveredStructuresSet = new LinkedHashSet<>(); + HashSet errors = new HashSet<>(); + + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(500); - pdbRequest.setFieldToSearchBy("(text:"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setAssociatedSequence(seq); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + + 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()) { discoveredStructuresSet.addAll(resultList.getSearchSummary()); - updateSequencePDBEntries(seq, resultList.getSearchSummary()); } } @@ -180,195 +490,54 @@ public class StructureChooser extends GStructureChooser if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); - structuresDiscovered = true; + getResultTable() + .setModel(data.getTableModel(discoveredStructuresSet)); + noOfStructuresFound = discoveredStructuresSet.size(); - mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound - + " Found (" + totalTime + ")"); + lastDiscoveredStructuresSet = discoveredStructuresSet; + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_no_of_structures", + noOfStructuresFound, totalTime)); } else { - mainFrame -.setTitle("Structure Chooser - Manual association"); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); if (errors.size() > 0) { StringBuilder errorMsg = new StringBuilder(); - // "Operation was unsuccessful due to the following: \n"); for (String error : errors) { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(this, errorMsg.toString(), - "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(this, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JvOptionPane.ERROR_MESSAGE); } } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { - DefaultTableModel tableModel = new DefaultTableModel() - { - @Override - public boolean isCellEditable(int row, int column) - { - return false; - } - }; - tableModel.addColumn("Ref Sequence"); - tableModel.addColumn("PDB Id"); - tableModel.addColumn("Chain"); - tableModel.addColumn("Type"); - tableModel.addColumn("File"); - cachedEntryMap = new Hashtable(); + ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null - && seq.getDatasetSequence().getPDBId() != null) + && seq.getDatasetSequence().getAllPDBEntries() != null) { - for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId()) + for (PDBEntry pdbEntry : seq.getDatasetSequence() + .getAllPDBEntries()) { - - String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry - .getChainCode(); - Object[] pdbEntryRowData = new Object[] - { seq, pdbEntry.getId(), - chain, - pdbEntry.getType(), - pdbEntry.getFile() }; if (pdbEntry.getFile() != null) { - tableModel.addRow(pdbEntryRowData); + entries.add(new CachedPDB(seq, pdbEntry)); } - cachedEntryMap.put(pdbEntry.getId().toLowerCase(), - pdbEntry); } } } - tbl_local_pdb.setModel(tableModel); - } - - /** - * Update the PDBEntry for a given sequence with values retrieved from - * PDBResponseSummary - * - * @param seq - * the Sequence to update its DBRef entry - * @param responseSummaries - * a collection of PDBResponseSummary - */ - public void updateSequencePDBEntries(SequenceI seq, - Collection responseSummaries) - { - for (PDBResponseSummary response : responseSummaries) - { - String pdbIdStr = response.getPdbId(); - PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - } - seq.getDatasetSequence().addPDBId(pdbEntry); - } - } - - /** - * 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) - { - 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.getPDBId() != null) - { - for (PDBEntry entry : seq.getPDBId()) - { - if (isValidSeqName(entry.getId())) - { - seqRefs.add(entry.getId()); - } - } - } - - if (seq.getDBRef() != null && seq.getDBRef().length != 0) - { - int count = 0; - for (DBRefEntry dbRef : seq.getDBRef()) - { - if (isValidSeqName(getDBRefId(dbRef))) - { - seqRefs.add(getDBRefId(dbRef)); - } - ++count; - if (count > 10) - { - break; - } - } - } - - StringBuilder queryBuilder = new StringBuilder(); - for (String seqRef : seqRefs) - { - queryBuilder.append("text:").append(seqRef).append(" OR "); - } - int endIndex = queryBuilder.lastIndexOf(" OR "); - String query = queryBuilder.toString().substring(5, endIndex); - return query; - } - - /** - * 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; + cachedPDBExists = !entries.isEmpty(); + PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); + tbl_local_pdb.setModel(tableModelx); } /** @@ -377,42 +546,37 @@ public class StructureChooser extends GStructureChooser * @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(); lbl_loading.setVisible(true); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = data.getDocFieldPrefs() .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); - HashSet errors = new HashSet(); + Collection filteredResponse = new HashSet<>(); + HashSet errors = new HashSet<>(); + for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(text:"); - pdbRequest.setFieldToSortBy(fieldToFilterBy, - !chk_invertFilter.isSelected()); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setAssociatedSequence(seq); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + + 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()) { @@ -425,22 +589,27 @@ 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( - lastPdbRequest, reorderedStructuresSet)); - + getResultTable() + .setModel(data.getTableModel(reorderedStructuresSet)); + + FTSRestResponse.configureTableColumn(getResultTable(), + wantedFields, tempUserPrefs); + getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); + getResultTable().getColumn("Ref Sequence").setMinWidth(100); + getResultTable().getColumn("Ref Sequence").setMaxWidth(200); // Update table selection model here - tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); - - mainFrame.setTitle("Structure Chooser - Filter time (" - + totalTime + ")"); + getResultTable().addRowSelectionInterval(0, + filterResponseCount - 1); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); } else { - mainFrame.setTitle("Structure Chooser - Filter time (" - + totalTime + ")"); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); if (errors.size() > 0) { StringBuilder errorMsg = new StringBuilder(); @@ -448,8 +617,9 @@ public class StructureChooser extends GStructureChooser { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(null, errorMsg.toString(), - "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(null, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JvOptionPane.ERROR_MESSAGE); } } @@ -461,27 +631,30 @@ public class StructureChooser extends GStructureChooser filterThread.start(); } - /** * Handles action event for btn_pdbFromFile */ - public void pdbFromFile_actionPerformed() + @Override + 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", new String[] - { selectedSequence.getDisplayId(false) })); + chooser.setDialogTitle( + MessageManager.formatMessage("label.select_pdb_file_for", + selectedSequence.getDisplayId(false))); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { selectedSequence.getDisplayId(false) })); + "label.load_pdb_file_associate_with_sequence", + selectedSequence.getDisplayId(false))); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { selectedPdbFileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); validateSelections(); } } @@ -490,29 +663,72 @@ public class StructureChooser extends GStructureChooser * Populates the filter combo-box options dynamically depending on discovered * structures */ - 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)); - } - cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB)); + 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) + { + 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, null)); + cmb_filterOption.addItem( + new FilterOption(MessageManager.getString("label.from_file"), + "-", 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, null); + cmb_filterOption.addItem(cachedOption); + if (selSet == -1) + { + cmb_filterOption.setSelectedItem(cachedOption); + } + } + if (selSet > -1) + { + cmb_filterOption.setSelectedIndex(selSet); + } + cmb_filterOption.addItemListener(this); } /** @@ -522,21 +738,47 @@ 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) { - mainFrame.setTitle(filterTitle); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); idInputAssSeqPanel.loadCmbAssSeq(); fileChooserAssSeqPanel.loadCmbAssSeq(); } @@ -544,27 +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. */ - public void validateSelections() + @Override + 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 (tbl_summary.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) @@ -575,12 +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(); @@ -588,26 +888,25 @@ public class StructureChooser extends GStructureChooser lbl_pdbManualFetchStatus.setToolTipText(""); if (txt_search.getText().length() > 0) { - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, "No PDB entry found for \'" + txt_search.getText() - + "\'")); + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); } if (errorWarning.length() > 0) { lbl_pdbManualFetchStatus.setIcon(warningImage); - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, errorWarning.toString())); + lbl_pdbManualFetchStatus.setToolTipText( + JvSwingUtils.wrapTooltip(true, errorWarning.toString())); } - if (selectedSequences.length == 1 - || !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-")) + if (selectedSequences.length == 1 || !assSeqOpt.getName() + .equalsIgnoreCase("-Select Associated Seq-")) { txt_search.setEnabled(true); if (isValidPBDEntry) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } @@ -622,20 +921,18 @@ 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(); lbl_fromFileStatus.setIcon(errorImage); - if (selectedSequences.length == 1 - || (assSeqOpt != null - && !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-"))) + if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt + .getName().equalsIgnoreCase("-Select Associated Seq-"))) { btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_fromFileStatus.setIcon(goodImage); } } @@ -647,11 +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 @@ -674,154 +973,321 @@ public class StructureChooser extends GStructureChooser } /** - * Handles action event for btn_ok + * select structures for viewing by their PDB IDs + * + * @param pdbids + * @return true if structures were found and marked as selected */ - @Override - public void ok_ActionPerformed() + public boolean selectStructure(String... pdbids) { + boolean found = false; + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); String currentView = selectedFilterOpt.getView(); - if (currentView == VIEWS_FILTER) + JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() + : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null; + + if (restable == null) { - int pdbIdColIndex = tbl_summary.getColumn( - PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); - int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") - .getModelIndex(); - int[] selectedRows = tbl_summary.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); - for (int summaryRow : selectedRows) - { - String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex) - .toString(); - SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt( - summaryRow, refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - } - pdbEntriesToView[count++] = pdbEntry; - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ap.getStructureSelectionManager(), - 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 refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") - .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { - String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex) - .toString() - .toLowerCase(); - pdbEntriesToView[count++] = cachedEntryMap.get(entryKey); - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, selectedSeqs); + // can't select (enter PDB ID, or load file - need to also select which + // sequence to associate with) + return false; } - else if (currentView == VIEWS_ENTER_ID) + + int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex(); + for (int r = 0; r < restable.getRowCount(); r++) { - SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) + for (int p = 0; p < pdbids.length; p++) { - selectedSequence = userSelectedSeq; + if (String.valueOf(restable.getValueAt(r, pdbIdColIndex)) + .equalsIgnoreCase(pdbids[p])) + { + restable.setRowSelectionInterval(r, r); + found = true; + } } + } + return found; + } - String pdbIdStr = txt_search.getText(); - PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(txt_search.getText()); - pdbEntry.setType(PDBEntry.Type.PDB); - } + /** + * Handles the 'New View' action + */ + @Override + protected void newView_ActionPerformed() + { + targetView.setSelectedItem(null); + showStructures(false); + } - selectedSequence.getDatasetSequence().addPDBId(pdbEntry); - PDBEntry[] pdbEntriesToView = new PDBEntry[] - { pdbEntry }; - launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, new SequenceI[] - { selectedSequence }); - } - else if (currentView == VIEWS_FROM_FILE) + /** + * Handles the 'Add to existing viewer' action + */ + @Override + protected void add_ActionPerformed() + { + showStructures(false); + } + + /** + * structure viewer opened by this dialog, or null + */ + private StructureViewer sViewer = null; + + public void showStructures(boolean waitUntilFinished) + { + + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + + final int preferredHeight = pnl_filter.getHeight(); + + Runnable viewStruc = new Runnable() { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) + @Override + public void run() { - selectedSequence = userSelectedSeq; + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() + : tbl_local_pdb; + + if (currentView == VIEWS_FILTER) + { + int[] selectedRows = restable.getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + List selectedSeqsToView = new ArrayList<>(); + pdbEntriesToView = data.collectSelectedRows(restable, + selectedRows, selectedSeqsToView); + + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + sViewer = 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("PDB Id") + .getModelIndex(); + int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") + .getModelIndex(); + List selectedSeqsToView = new ArrayList<>(); + for (int row : selectedRows) + { + PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb + .getModel()).getPDBEntryAt(row).getPdbEntry(); + + pdbEntriesToView[count++] = pdbEntry; + SequenceI selectedSeq = (SequenceI) tbl_local_pdb + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + selectedSeqs); + } + else if (currentView == VIEWS_ENTER_ID) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + String pdbIdStr = txt_search.getText(); + PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + if (pdbIdStr.split(":").length > 1) + { + pdbEntry.setId(pdbIdStr.split(":")[0]); + pdbEntry.setChainCode( + pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); + } + else + { + pdbEntry.setId(pdbIdStr); + } + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); + } + + PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + new SequenceI[] + { selectedSequence }); + } + else if (currentView == VIEWS_FROM_FILE) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true, + Desktop.instance); + + sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, + ap, new SequenceI[] + { selectedSequence }); + } + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + closeAction(preferredHeight); + mainFrame.dispose(); + } + }); } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq( - selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + }; + Thread runner = new Thread(viewStruc); + runner.start(); + if (waitUntilFinished) + { + while (sViewer == null ? runner.isAlive() + : (sViewer.sview == null ? true + : !sViewer.sview.hasMapping())) + { + try + { + Thread.sleep(300); + } catch (InterruptedException ie) + { - launchStructureViewer(ap.getStructureSelectionManager(), - new PDBEntry[] - { fileEntry }, ap, new SequenceI[] - { selectedSequence }); + } + } } - mainFrame.dispose(); } - private void launchStructureViewer(StructureSelectionManager ssm, - PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel, - SequenceI[] sequences) + /** + * 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) { - StructureViewer sViewer = new StructureViewer(ssm); - if (pdbEntriesToView.length > 1) + Object sv = targetView.getSelectedItem(); + + 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, + final AlignmentPanel alignPanel, SequenceI[] sequences) + { + 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()) { - ArrayList seqsMap = new ArrayList(); + 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) { - seqsMap.add(new SequenceI[] - { seq }); + 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; + } } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, - alignPanel); - // sViewer.viewStructures(pdbEntriesToView, - // alignPanel.av.collateForPDB(pdbEntriesToView), - // alignPanel); + 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 { - sViewer.viewStructures(pdbEntriesToView[0], sequences, - alignPanel); + 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; } /** * Populates the combo-box used in associating manually fetched structures to * a unique sequence when more than one sequence selection is made. */ - public void populateCmbAssociateSeqOptions( - JComboBox cmb_assSeq, JLabel lbl_associateSeq) + @Override + protected void populateCmbAssociateSeqOptions( + JComboBox cmb_assSeq, + JLabel lbl_associateSeq) { cmb_assSeq.removeAllItems(); - cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-", - null)); - // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null)); + cmb_assSeq.addItem( + new AssociateSeqOptions("-Select Associated Seq-", null)); lbl_associateSeq.setVisible(false); if (selectedSequences.length > 1) { @@ -840,61 +1306,73 @@ public class StructureChooser extends GStructureChooser } } - public boolean isStructuresDiscovered() - { - return structuresDiscovered; - } - - public void setStructuresDiscovered(boolean structuresDiscovered) + protected boolean isStructuresDiscovered() { - this.structuresDiscovered = structuresDiscovered; + 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() { - errorWarning.setLength(0); - isValidPBDEntry = false; - if (txt_search.getText().length() > 0) - { - List wantedFields = new ArrayList(); - wantedFields.add(PDBDocField.PDB_ID); - PDBRestRequest pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(pdb_id:"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(txt_search.getText() + ")"); - pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) + String text = txt_search.getText().trim(); + if (text.length() >= PDB_ID_MIN) + new Thread() { - errorWarning.append(e.getMessage()); - return; - } finally - { - validateSelections(); - } - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) - { - isValidPBDEntry = true; - } - } - validateSelections(); + + @Override + public void run() + { + errorWarning.setLength(0); + isValidPBDEntry = false; + if (text.length() > 0) + { + // 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(); + } + }.start(); } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) { @@ -904,12 +1382,181 @@ public class StructureChooser extends GStructureChooser public void run() { fetchStructuresMetaData(); - filterResultSet(((FilterOption) cmb_filterOption - .getSelectedItem()).getValue()); + // populateFilterComboBox(true, cachedPDBExists); + + filterResultSet( + ((FilterOption) cmb_filterOption.getSelectedItem()) + .getValue()); } }); refreshThread.start(); } } + public class PDBEntryTableModel extends AbstractTableModel + { + String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", + "File" }; + + private List pdbEntries; + + public PDBEntryTableModel(List pdbEntries) + { + this.pdbEntries = new ArrayList<>(pdbEntries); + } + + @Override + public String getColumnName(int columnIndex) + { + return columns[columnIndex]; + } + + @Override + public int getRowCount() + { + return pdbEntries.size(); + } + + @Override + public int getColumnCount() + { + return columns.length; + } + + @Override + public boolean isCellEditable(int row, int column) + { + return false; + } + + @Override + public Object getValueAt(int rowIndex, int columnIndex) + { + Object value = "??"; + CachedPDB entry = pdbEntries.get(rowIndex); + switch (columnIndex) + { + case 0: + value = entry.getSequence(); + break; + case 1: + value = entry.getQualifiedId(); + break; + case 2: + value = entry.getPdbEntry().getChainCode() == null ? "_" + : entry.getPdbEntry().getChainCode(); + break; + case 3: + value = entry.getPdbEntry().getType(); + break; + case 4: + value = entry.getPdbEntry().getFile(); + break; + } + return value; + } + + @Override + public Class getColumnClass(int columnIndex) + { + return columnIndex == 0 ? SequenceI.class : PDBEntry.class; + } + + public CachedPDB getPDBEntryAt(int row) + { + return pdbEntries.get(row); + } + + } + + private class CachedPDB + { + private SequenceI sequence; + + private PDBEntry pdbEntry; + + public CachedPDB(SequenceI sequence, PDBEntry pdbEntry) + { + this.sequence = sequence; + this.pdbEntry = pdbEntry; + } + + public String getQualifiedId() + { + if (pdbEntry.hasProvider()) + { + return pdbEntry.getProvider() + ":" + pdbEntry.getId(); + } + return pdbEntry.toString(); + } + + public SequenceI getSequence() + { + return sequence; + } + + public PDBEntry getPdbEntry() + { + return pdbEntry; + } + + } + + 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(); + } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + 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; + } }