X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=9f9de6ea386372cea19dc89eb1f90b301c2c7250;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=ea2d50dcd2bf5636b56d061d60f74a3506cd0ed9;hpb=55ea4d59b2f4ce51f8310047dd1f8898697dde0c;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index ea2d50d..9f9de6e 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,11 +21,26 @@ package jalview.gui; +import java.util.Locale; + +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.concurrent.Executors; + +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JTable; +import javax.swing.SwingUtilities; +import javax.swing.table.AbstractTableModel; + import jalview.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; @@ -37,32 +52,18 @@ import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; 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.jbgui.GStructureChooser.FilterOption; 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 * @@ -75,6 +76,11 @@ 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 +103,77 @@ 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 - .getTDBfts(); + 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() @@ -127,30 +185,138 @@ public class StructureChooser extends GStructureChooser chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); + 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(); + } + + 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 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(); + // TODO: warn if no accessions discovered + populateSeqsWithoutSourceDBRef(); + // redo initial discovery - this time with 3d beacons + // Executors. + previousWantedFields=null; + + initialStructureDiscovery(); } - }); - 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); + } + }; + }; + // 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")); } /** @@ -246,8 +412,9 @@ 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; } @@ -272,7 +439,9 @@ public class StructureChooser extends GStructureChooser { getResultTable() .setModel(data.getTableModel(discoveredStructuresSet)); + noOfStructuresFound = discoveredStructuresSet.size(); + lastDiscoveredStructuresSet = discoveredStructuresSet; mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", noOfStructuresFound, totalTime)); @@ -328,6 +497,7 @@ public class StructureChooser extends GStructureChooser { Thread filterThread = new Thread(new Runnable() { + @Override public void run() { @@ -344,8 +514,9 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = data.selectFirstRankedQuery(seq, wantedFields, - fieldToFilterBy, !chk_invertFilter.isSelected()); + resultList = data.selectFirstRankedQuery(seq, + discoveredStructuresSet, wantedFields, fieldToFilterBy, + !chk_invertFilter.isSelected()); } catch (Exception e) { @@ -442,46 +613,70 @@ 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) + { + 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); + 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); } @@ -492,16 +687,47 @@ 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); - 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) @@ -638,7 +864,7 @@ public class StructureChooser extends GStructureChooser { validateSelections(); } - + private FilterOption lastSelected=null; /** * Handles the state change event for the 'filter' combo-box and 'invert' * check-box @@ -746,7 +972,8 @@ 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()]); @@ -765,8 +992,9 @@ 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); @@ -793,7 +1021,7 @@ public class StructureChooser extends GStructureChooser if (pdbIdStr.split(":").length > 1) { pdbEntry.setId(pdbIdStr.split(":")[0]); - pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase()); + pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); } else { @@ -1020,7 +1248,7 @@ public class StructureChooser extends GStructureChooser // 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(); + String searchTerm = text.toLowerCase(Locale.ROOT); searchTerm = searchTerm.split(":")[0]; // System.out.println(">>>>> search term : " + searchTerm); List wantedFields = new ArrayList<>(); @@ -1067,6 +1295,8 @@ public class StructureChooser extends GStructureChooser public void run() { fetchStructuresMetaData(); + // populateFilterComboBox(true, cachedPDBExists); + filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); @@ -1123,7 +1353,7 @@ 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 ? "_" @@ -1164,6 +1394,15 @@ 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; @@ -1205,6 +1444,18 @@ 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 + */ + public boolean isDialogVisible() + { + return mainFrame != null && data != null && cmb_filterOption != null + && mainFrame.isVisible() + && cmb_filterOption.getSelectedItem() != null; } }