From aa96618cbd41b40e2377f3f1f105aea90a5a86e0 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 21 Sep 2021 11:36:27 +0100 Subject: [PATCH] JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched --- resources/lang/Messages.properties | 3 + src/jalview/gui/StructureChooser.java | 367 +++++++++++++------- .../StructureChooserQuerySource.java | 57 +-- 3 files changed, 281 insertions(+), 146 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 92a6ab8..fabd577 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -513,7 +513,10 @@ label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = label.standard_databases = Standard Databases label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources label.fetch_uniprot_references = Fetch Uniprot references +label.search_3dbeacons = Find models with 3D-Beacons +label.3dbeacons = 3D-Beacons label.fetch_references_for = Fetch database references for {0} sequences ? +label.fetch_references_for_3dbeacons = 3D Beacons needs Uniprot References. Fetch database references for {0} sequences ? label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences. label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s) label.threshold_feature_display_by_score = Threshold the feature display by score. diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 82ad03b..ae7971c 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -73,6 +73,11 @@ public class StructureChooser extends GStructureChooser { private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + /** + * transient combo box choice for initiating 3db fetch + */ + private static final String VIEWS_QUERYING_TDB = "QUERY_3DB"; + private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -97,25 +102,75 @@ public class StructureChooser extends GStructureChooser 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); + 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) + { + notQueriedTDBYet = false; + } + } + }; + + /** * Initializes parameters used by the Structure Chooser Panel */ protected void init() @@ -127,115 +182,146 @@ public class StructureChooser extends GStructureChooser chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); - final Runnable discoverPDBStructures = new Runnable() + Executors.defaultThreadFactory().newThread(new Runnable() { - @Override public void run() { - // check which FTS engine to use - data = StructureChooserQuerySource - .getQuerySourceFor(selectedSequences); + populateSeqsWithoutSourceDBRef(); + initialStructureDiscovery(); + } + + }).start(); - // 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. + // called by init + private void initialStructureDiscovery() + { + // check which FTS engine to use + data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences); - 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(); - } - }; - final List seqsWithoutSourceDBRef = new ArrayList(); + // ensure a filter option is in force for search + populateFilterComboBox(true, cachedPDBExists); - final Runnable discoverCanonicalDBrefs = 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(); + } + + private void promptForTDBFetch() + { + final long progressId = System.currentTimeMillis(); + + // final action after prompting and discovering db refs + final Runnable strucDiscovery = new Runnable() { @Override public void run() { - long progressId = System.currentTimeMillis(); - - int y = seqsWithoutSourceDBRef.size(); - - setProgressBar(MessageManager.formatMessage( - "status.fetching_dbrefs_for_sequences_without_valid_refs", - y), progressId); - SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef - .toArray(new SequenceI[y]); + // TODO: warn if no accessions discovered + populateSeqsWithoutSourceDBRef(); + // redo initial discovery - this time with 3d beacons + // Executors. + previousWantedFields=null; - DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef, - progressBar, new DbSourceProxy[] - { new jalview.ws.dbsources.Uniprot() }, - null, false); - - dbRefFetcher.fetchDBRefs(true); - - setProgressBar("Fetch complete.", progressId); // todo i18n - - Executors.defaultThreadFactory().newThread(discoverPDBStructures).start(); + initialStructureDiscovery(); } }; - Executors.defaultThreadFactory().newThread(new Runnable() + // fetch db refs if OK pressed + final Runnable discoverCanonicalDBrefs = new Runnable() { + @Override public void run() { + populateSeqsWithoutSourceDBRef(); - for (SequenceI seq : selectedSequences) + final int y = seqsWithoutSourceDBRef.size(); + if (y > 0) { - if (seq.isProtein()) - { - int dbRef = ThreeDBStructureChooserQuerySource - .checkUniprotRefs(seq.getDBRefs()); - if (dbRef < 0) + SwingUtilities.invokeLater(new Runnable() { + @Override + public void run() { - if (seq.getAllPDBEntries()==null && seq.getAllPDBEntries().size()==0) - { - seqsWithoutSourceDBRef.add(seq); - } + updateProgressIndicator(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y), progressId); + } - } + }); + + final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef, + progressBar, new DbSourceProxy[] + { new jalview.ws.dbsources.Uniprot() }, null, false); + + // ideally this would also gracefully run with callbacks + dbRefFetcher.fetchDBRefs(true); } - // retrieve database refs for protein sequences - if (!seqsWithoutSourceDBRef.isEmpty()) - { - // need cancel and no to result in the discoverPDB action - mocked is 'cancel' - JvOptionPane.newOptionDialog(Desktop.getDesktop()) - .setResponseHandler(JvOptionPane.OK_OPTION, discoverCanonicalDBrefs) - .setResponseHandler(JvOptionPane.CANCEL_OPTION, discoverPDBStructures) - .setResponseHandler(JvOptionPane.NO_OPTION, discoverPDBStructures) - .showDialog(MessageManager.formatMessage("label.fetch_references_for", - seqsWithoutSourceDBRef.size()), MessageManager.getString( - "label.fetch_uniprot_references"), - JvOptionPane.YES_NO_OPTION, - JvOptionPane.PLAIN_MESSAGE, null, new Object[] - { MessageManager.getString("action.ok"), - MessageManager.getString("action.cancel") }, - MessageManager.getString("action.ok")); - } else { - // get structures directly - Executors.defaultThreadFactory().newThread(discoverPDBStructures).start(); + SwingUtilities.invokeLater(new Runnable() { + @Override + public void run() + { + if (y>0) { + updateProgressIndicator("Fetch complete.", progressId); // todo i18n + } + // filter has been selected, so we set flag to remove ourselves + notQueriedTDBYet = false; + + Executors.defaultThreadFactory().newThread(strucDiscovery).start(); + + } + }); + + } + }; + final Runnable revertview = new Runnable() { + public void run() { + if (lastSelected!=null) { + cmb_filterOption.setSelectedItem(lastSelected); } }; - }).start();; - + }; + // need cancel and no to result in the discoverPDB action - mocked is + // 'cancel' + 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")); } /** @@ -331,8 +417,9 @@ public class StructureChooser extends GStructureChooser 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) + // consider designing a special exception if we really wanted to be + // OOCrazy + if (resultList == null) { continue; } @@ -357,9 +444,9 @@ public class StructureChooser extends GStructureChooser { getResultTable() .setModel(data.getTableModel(discoveredStructuresSet)); - + noOfStructuresFound = discoveredStructuresSet.size(); - lastDiscoveredStructuresSet=discoveredStructuresSet; + lastDiscoveredStructuresSet = discoveredStructuresSet; mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", noOfStructuresFound, totalTime)); @@ -432,8 +519,9 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = data.selectFirstRankedQuery(seq, discoveredStructuresSet,wantedFields, - fieldToFilterBy, !chk_invertFilter.isSelected()); + resultList = data.selectFirstRankedQuery(seq, + discoveredStructuresSet, wantedFields, fieldToFilterBy, + !chk_invertFilter.isSelected()); } catch (Exception e) { @@ -458,7 +546,7 @@ public class StructureChooser extends GStructureChooser reorderedStructuresSet.addAll(discoveredStructuresSet); getResultTable() .setModel(data.getTableModel(reorderedStructuresSet)); - + FTSRestResponse.configureTableColumn(getResultTable(), wantedFields, tempUserPrefs); getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); @@ -532,6 +620,7 @@ public class StructureChooser extends GStructureChooser { populateFilterComboBox(haveData, cachedPDBExist, null); } + /** * Populates the filter combo-box options dynamically depending on discovered * structures @@ -539,45 +628,57 @@ public class StructureChooser extends GStructureChooser protected void populateFilterComboBox(boolean haveData, boolean cachedPDBExist, FilterOption lastSel) { - + /* * temporarily suspend the change listener behaviour */ cmb_filterOption.removeItemListener(this); - int selSet=-1; + 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) + 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; + 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)); + "-", VIEWS_ENTER_ID, false, null)); cmb_filterOption.addItem( new FilterOption(MessageManager.getString("label.from_file"), - "-", VIEWS_FROM_FILE, false,null)); + "-", VIEWS_FROM_FILE, false, null)); + if (canQueryTDB && notQueriedTDBYet) + { + FilterOption queryTDBOption = new FilterOption( + MessageManager.getString("label.search_3dbeacons"), "-", + VIEWS_QUERYING_TDB, false, null); + cmb_filterOption.addItem(queryTDBOption); + } if (cachedPDBExist) { FilterOption cachedOption = new FilterOption( MessageManager.getString("label.cached_structures"), "-", - VIEWS_LOCAL_PDB, false,null); + VIEWS_LOCAL_PDB, false, null); cmb_filterOption.addItem(cachedOption); - if (selSet==-1) { + if (selSet == -1) + { cmb_filterOption.setSelectedItem(cachedOption); } } - if (selSet>-1) + if (selSet > -1) { cmb_filterOption.setSelectedIndex(selSet); } @@ -591,24 +692,45 @@ public class StructureChooser extends GStructureChooser { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); + + // first check if we need to rebuild dialog + if (selectedFilterOpt.getView() == VIEWS_QUERYING_TDB) + { + promptForTDBFetch(); + return; + } + 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); // TDB Query has no invert as yet - chk_invertFilter.setVisible(selectedFilterOpt.getQuerySource() instanceof PDBStructureChooserQuerySource); - - if (data!=selectedFilterOpt.getQuerySource() || data.needsRefetch(selectedFilterOpt)) + 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 { + } + else + { filterResultSet(selectedFilterOpt.getValue()); } } @@ -747,7 +869,7 @@ public class StructureChooser extends GStructureChooser { validateSelections(); } - + private FilterOption lastSelected=null; /** * Handles the state change event for the 'filter' combo-box and 'invert' * check-box @@ -855,7 +977,8 @@ public class StructureChooser extends GStructureChooser int[] selectedRows = restable.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; List selectedSeqsToView = new ArrayList<>(); - pdbEntriesToView = data.collectSelectedRows(restable,selectedRows,selectedSeqsToView); + pdbEntriesToView = data.collectSelectedRows(restable, + selectedRows, selectedSeqsToView); SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); @@ -874,8 +997,9 @@ public class StructureChooser extends GStructureChooser List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { - PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb.getModel()).getPDBEntryAt(row).getPdbEntry(); - + PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb + .getModel()).getPDBEntryAt(row).getPdbEntry(); + pdbEntriesToView[count++] = pdbEntry; SequenceI selectedSeq = (SequenceI) tbl_local_pdb .getValueAt(row, refSeqColIndex); @@ -1176,7 +1300,7 @@ public class StructureChooser extends GStructureChooser public void run() { fetchStructuresMetaData(); - //populateFilterComboBox(true, cachedPDBExists); + // populateFilterComboBox(true, cachedPDBExists); filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) @@ -1279,8 +1403,8 @@ public class StructureChooser extends GStructureChooser { if (pdbEntry.hasProvider()) { - return pdbEntry.getProvider()+":"+pdbEntry.getId(); - } + return pdbEntry.getProvider() + ":" + pdbEntry.getId(); + } return pdbEntry.toString(); } @@ -1325,12 +1449,13 @@ public class StructureChooser extends GStructureChooser protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs) { data.setDocFieldPrefs(newPrefs); - + } /** * - * @return true when all initialisation threads have finished and dialog is visible + * @return true when all initialisation threads have finished and dialog is + * visible */ public boolean isDialogVisible() { diff --git a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java index 45c58cf..a4ae2c8 100644 --- a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java +++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java @@ -42,7 +42,7 @@ public abstract class StructureChooserQuerySource public static StructureChooserQuerySource getPDBfts() { - return new PDBStructureChooserQuerySource(); + return new PDBStructureChooserQuerySource(); } public static StructureChooserQuerySource getTDBfts() @@ -65,7 +65,6 @@ public abstract class StructureChooserQuerySource return docFieldPrefs; } - /** * Builds a query string for a given sequences using its DBRef entries * @@ -75,7 +74,6 @@ public abstract class StructureChooserQuerySource */ public abstract String buildQuery(SequenceI seq); - /** * Remove the following special characters from input string +, -, &, !, (, ), @@ -167,7 +165,8 @@ public abstract class StructureChooserQuerySource * * @param seq * - seq to generate a query for - * @param discoveredStructuresSet - existing set of entries - allows client side selection + * @param discoveredStructuresSet + * - existing set of entries - allows client side selection * @param wantedFields * - fields to retrieve * @param selectedFilterOpt @@ -178,7 +177,8 @@ public abstract class StructureChooserQuerySource * @throws Exception */ public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq, - Collection discoveredStructuresSet, Collection wantedFields, String fieldToFilterBy, + Collection discoveredStructuresSet, + Collection wantedFields, String fieldToFilterBy, boolean b) throws Exception; /** @@ -200,15 +200,17 @@ public abstract class StructureChooserQuerySource /** * @param VIEWS_FILTER - * - a String key that can be used by the caller to tag the returned filter - * options to distinguish them in a collection + * - a String key that can be used by the caller to tag the returned + * filter options to distinguish them in a collection * @return list of FilterOption - convention is that the last one in the list * will be constructed with 'addSeparator==true' */ - public abstract List getAvailableFilterOptions(String VIEWS_FILTER); + public abstract List getAvailableFilterOptions( + String VIEWS_FILTER); /** * construct a structure chooser query source for the given set of sequences + * * @param selectedSeqs * @return PDBe or 3DB query source */ @@ -216,34 +218,39 @@ public abstract class StructureChooserQuerySource SequenceI[] selectedSeqs) { ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource(); - boolean hasUniprot=false,hasCanonical=false; - boolean hasNA=false,hasProtein=false; - int protWithoutUni=0; + boolean hasUniprot = false, hasCanonical = false; + boolean hasNA = false, hasProtein = false; + int protWithoutUni = 0; + int protWithoutCanon = 0; for (SequenceI seq : selectedSeqs) { hasNA |= !seq.isProtein(); hasProtein |= seq.isProtein(); if (seq.isProtein()) { - int refsAvailable = ThreeDBStructureChooserQuerySource.checkUniprotRefs(seq.getDBRefs()); + int refsAvailable = ThreeDBStructureChooserQuerySource + .checkUniprotRefs(seq.getDBRefs()); if (refsAvailable > -2) { if (refsAvailable > -1) + { hasCanonical = true; + } else { + protWithoutCanon++; + } + hasUniprot = true; + } else { + protWithoutUni++; + } - hasUniprot = true; - } - else - { - protWithoutUni++; } } // // logic: all canonicals - no fetchdb - // some uniprot no canonicals: prompt do fetchDb for remaining - // no uniprot but protein: offer 3d-beacons search + // some uniprot no canonicals: defer to PDB, user can optionally fetch // - if (hasProtein && hasCanonical && !hasNA) + if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 && protWithoutUni == 0) + { return tdbSource; } @@ -251,17 +258,17 @@ public abstract class StructureChooserQuerySource } /** - * some filter options may mean the original query needs to be executed again. + * some filter options may mean the original query needs to be executed again. + * * @param selectedFilterOpt * @return true if the fetchStructuresMetadata method needs to be called again */ public abstract boolean needsRefetch(FilterOption selectedFilterOpt); - - public void updateAvailableFilterOptions(String VIEWS_FILTER, List xtantOptions, Collection lastFTSData) { // TODO Auto-generated method stub - - }} \ No newline at end of file + + } +} \ No newline at end of file -- 1.7.10.2