X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5e4226ad816c90aa90be64debe734b92e31a1347;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=7a9da92716b54267b45bb93bafa5e95c4f228220;hpb=bf5bc203579d7a291844f3b34d5e8431984ee8e2;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 7a9da92..5e4226a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,11 +21,31 @@ package jalview.gui; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Locale; +import java.util.concurrent.Executors; + +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; +import javax.swing.JTable; +import javax.swing.SwingUtilities; +import javax.swing.table.AbstractTableModel; + import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; +import jalview.bin.Console; 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; @@ -35,8 +55,10 @@ 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; @@ -44,25 +66,10 @@ 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 * @@ -73,8 +80,12 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { - private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + protected static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + /** + * warn user if need to fetch more than this many uniprot records at once + */ + private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20; private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -97,25 +108,78 @@ public class StructureChooser extends GStructureChooser private boolean cachedPDBExists; - private static StructureViewer lastTargetedView = null; + private Collection lastDiscoveredStructuresSet; + + private boolean canQueryTDB = false; + + private boolean notQueriedTDBYet = true; + + List seqsWithoutSourceDBRef = null; + + protected 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) + { + // triggers display of the 'Query TDB' button + notQueriedTDBYet = true; + } + } + }; + + /** * Initializes parameters used by the Structure Chooser Panel */ protected void init() @@ -126,31 +190,198 @@ public class StructureChooser extends GStructureChooser } chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); + btn_queryTDB.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + promptForTDBFetch(false); + } + }); + + Executors.defaultThreadFactory().newThread(new Runnable() + { + @Override + public void run() + { + populateSeqsWithoutSourceDBRef(); + initialStructureDiscovery(); + } + + }).start(); + + } + + // called by init + private void initialStructureDiscovery() + { + // check which FTS engine to use + data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences); // ensure a filter option is in force for search populateFilterComboBox(true, cachedPDBExists); - Thread discoverPDBStructuresThread = new Thread(new Runnable() + + // looks for any existing structures already loaded + // for the sequences (the cached ones) + // then queries the StructureChooserQuerySource to + // discover more structures. + // + // Possible optimisation is to only begin querying + // the structure chooser if there are no cached structures. + + long startTime = System.currentTimeMillis(); + updateProgressIndicator( + MessageManager.getString("status.loading_cached_pdb_entries"), + startTime); + loadLocalCachedPDBEntries(); + updateProgressIndicator(null, startTime); + updateProgressIndicator( + MessageManager.getString("status.searching_for_pdb_structures"), + startTime); + fetchStructuresMetaData(); + // revise filter options if no results were found + populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); + discoverStructureViews(); + updateProgressIndicator(null, startTime); + mainFrame.setVisible(true); + updateCurrentView(); + } + + /** + * raises dialog for Uniprot fetch followed by 3D beacons search + * + * @param ignoreGui + * - when true, don't ask, just fetch + */ + public void promptForTDBFetch(boolean ignoreGui) + { + final long progressId = System.currentTimeMillis(); + + // final action after prompting and discovering db refs + final Runnable strucDiscovery = new Runnable() { @Override public void run() { - long startTime = System.currentTimeMillis(); - updateProgressIndicator(MessageManager - .getString("status.loading_cached_pdb_entries"), startTime); - loadLocalCachedPDBEntries(); - updateProgressIndicator(null, startTime); - updateProgressIndicator(MessageManager.getString( - "status.searching_for_pdb_structures"), startTime); - fetchStructuresMetaData(); - // revise filter options if no results were found - populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); - discoverStructureViews(); - updateProgressIndicator(null, startTime); - mainFrame.setVisible(true); - updateCurrentView(); + mainFrame.setEnabled(false); + cmb_filterOption.setEnabled(false); + progressBar.setProgressBar( + MessageManager.getString("status.searching_3d_beacons"), + progressId); + btn_queryTDB.setEnabled(false); + // TODO: warn if no accessions discovered + populateSeqsWithoutSourceDBRef(); + // redo initial discovery - this time with 3d beacons + // Executors. + previousWantedFields = null; + lastSelected = (FilterOption) cmb_filterOption.getSelectedItem(); + cmb_filterOption.setSelectedItem(null); + cachedPDBExists=false; // reset to initial + initialStructureDiscovery(); + if (!isStructuresDiscovered()) + { + progressBar.setProgressBar(MessageManager.getString( + "status.no_structures_discovered_from_3d_beacons"), + progressId); + btn_queryTDB.setToolTipText(MessageManager.getString( + "status.no_structures_discovered_from_3d_beacons")); + btn_queryTDB.setEnabled(false); + pnl_queryTDB.setVisible(false); + } + else + { + cmb_filterOption.setSelectedIndex(0); // select 'best' + btn_queryTDB.setVisible(false); + pnl_queryTDB.setVisible(false); + progressBar.setProgressBar(null, progressId); + } + mainFrame.setEnabled(true); + cmb_filterOption.setEnabled(true); } - }); - discoverPDBStructuresThread.start(); + }; + + final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI() + { + + @Override + public void finished() + { + // filter has been selected, so we set flag to remove ourselves + notQueriedTDBYet = false; + // new thread to discover structures - via 3d beacons + Executors.defaultThreadFactory().newThread(strucDiscovery).start(); + + } + }; + + // fetch db refs if OK pressed + final Runnable discoverCanonicalDBrefs = new Runnable() + { + @Override + public void run() + { + btn_queryTDB.setEnabled(false); + 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() + { + @Override + public void run() + { + if (lastSelected != null) + { + cmb_filterOption.setSelectedItem(lastSelected); + } + }; + }; + int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD", + THRESHOLD_WARN_UNIPROT_FETCH_NEEDED); + Console.debug("Using Uniprot fetch threshold of " + threshold); + if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold) + { + Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start(); + return; + } + // need cancel and no to result in the discoverPDB action - mocked is + // 'cancel' TODO: mock should be OK + StructureChooser thisSC = this; + JvOptionPane.newOptionDialog(thisSC.getFrame()) + .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"), false); } /** @@ -160,7 +391,7 @@ public class StructureChooser extends GStructureChooser */ private void discoverStructureViews() { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { targetView.removeAllItems(); if (lastTargetedView != null && !lastTargetedView.isVisible()) @@ -168,7 +399,7 @@ public class StructureChooser extends GStructureChooser lastTargetedView = null; } int linkedViewsAt = 0; - for (StructureViewerBase view : Desktop.instance + for (StructureViewerBase view : Desktop.getInstance() .getStructureViewers(null, null)) { StructureViewer viewHandler = (lastTargetedView != null @@ -246,8 +477,9 @@ 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 +504,9 @@ 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 +562,7 @@ public class StructureChooser extends GStructureChooser { Thread filterThread = new Thread(new Runnable() { + @Override public void run() { @@ -344,8 +579,9 @@ 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) { @@ -417,7 +653,7 @@ public class StructureChooser extends GStructureChooser // 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", @@ -430,7 +666,7 @@ public class StructureChooser extends GStructureChooser if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { selectedPdbFileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); validateSelections(); } } @@ -442,36 +678,68 @@ public class StructureChooser extends GStructureChooser protected void populateFilterComboBox(boolean haveData, boolean cachedPDBExist) { + populateFilterComboBox(haveData, cachedPDBExist, null); + } + + /** + * Populates the filter combo-box options dynamically depending on discovered + * structures + */ + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExist, FilterOption lastSel) + { + /* * temporarily suspend the change listener behaviour */ cmb_filterOption.removeItemListener(this); - + int selSet = -1; cmb_filterOption.removeAllItems(); if (haveData) { - List filters = data.getAvailableFilterOptions(VIEWS_FILTER); - 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; + } + p++; cmb_filterOption.addItem(filter); } } + cmb_filterOption.addItem( new FilterOption(MessageManager.getString("label.enter_pdb_id"), - "-", VIEWS_ENTER_ID, false)); + "-", VIEWS_ENTER_ID, false, null)); cmb_filterOption.addItem( new FilterOption(MessageManager.getString("label.from_file"), - "-", VIEWS_FROM_FILE, false)); + "-", VIEWS_FROM_FILE, false, null)); + if (canQueryTDB && notQueriedTDBYet) + { + btn_queryTDB.setVisible(true); + pnl_queryTDB.setVisible(true); + } if (cachedPDBExist) { FilterOption cachedOption = new FilterOption( MessageManager.getString("label.cached_structures"), "-", - VIEWS_LOCAL_PDB, false); + 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); } @@ -482,16 +750,41 @@ public class StructureChooser extends GStructureChooser { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); + + if (lastSelected == selectedFilterOpt) + { + // don't need to do anything, probably + return; + } + // otherwise, record selection + // and update the layout and dialog accordingly + lastSelected = selectedFilterOpt; + layout_switchableViews.show(pnl_switchableViews, selectedFilterOpt.getView()); String filterTitle = mainFrame.getTitle(); mainFrame.setTitle(frameTitle); chk_invertFilter.setVisible(false); + if (selectedFilterOpt.getView() == VIEWS_FILTER) { mainFrame.setTitle(filterTitle); - chk_invertFilter.setVisible(true); - filterResultSet(selectedFilterOpt.getValue()); + // TDB Query has no invert as yet + chk_invertFilter.setVisible(selectedFilterOpt + .getQuerySource() instanceof PDBStructureChooserQuerySource); + + if (data != selectedFilterOpt.getQuerySource() + || data.needsRefetch(selectedFilterOpt)) + { + data = selectedFilterOpt.getQuerySource(); + // rebuild the views completely, since prefs will also change + tabRefresh(); + return; + } + else + { + filterResultSet(selectedFilterOpt.getValue()); + } } else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID || selectedFilterOpt.getView() == VIEWS_FROM_FILE) @@ -557,6 +850,43 @@ public class StructureChooser extends GStructureChooser .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); } + @Override + protected boolean showPopupFor(int selectedRow, int x, int y) + { + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + if (currentView == VIEWS_FILTER + && data instanceof ThreeDBStructureChooserQuerySource) + { + TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data) + .getFTSDataFor(getResultTable(), selectedRow, + discoveredStructuresSet); + String pageUrl = row.getModelViewUrl(); + JPopupMenu popup = new JPopupMenu("3D Beacons"); + JMenuItem viewUrl = new JMenuItem("View model web page"); + viewUrl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + Desktop.showUrl(pageUrl); + } + }); + popup.add(viewUrl); + SwingUtilities.invokeLater(new Runnable() + { + @Override + 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 */ @@ -628,7 +958,7 @@ public class StructureChooser extends GStructureChooser { validateSelections(); } - + private FilterOption lastSelected=null; /** * Handles the state change event for the 'filter' combo-box and 'invert' * check-box @@ -717,7 +1047,8 @@ public class StructureChooser extends GStructureChooser { final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - + final StructureViewer theViewer = getTargetedStructureViewer(ssm); + boolean superimpose = chk_superpose.isSelected(); final int preferredHeight = pnl_filter.getHeight(); Runnable viewStruc = new Runnable() @@ -736,12 +1067,13 @@ 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()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + selectedSeqs, superimpose, theViewer, progressBar); } else if (currentView == VIEWS_LOCAL_PDB) { @@ -755,8 +1087,9 @@ 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); @@ -764,8 +1097,8 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + selectedSeqs, superimpose, theViewer, progressBar); } else if (currentView == VIEWS_ENTER_ID) { @@ -783,7 +1116,7 @@ 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 { @@ -794,9 +1127,10 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, - new SequenceI[] - { selectedSequence }); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + new SequenceI[] + { selectedSequence }, superimpose, theViewer, + progressBar); } else if (currentView == VIEWS_FROM_FILE) { @@ -806,14 +1140,12 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.instance); - - sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, - ap, new SequenceI[] - { selectedSequence }); + PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true); + + sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry }, + new SequenceI[] { selectedSequence }, superimpose, theViewer, + progressBar); } SwingUtilities.invokeLater(new Runnable() { @@ -860,98 +1192,6 @@ public class StructureChooser extends GStructureChooser } /** - * 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()) - { - List seqsWithoutSourceDBRef = new ArrayList<>(); - int p = 0; - // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a - // real PDB ID. For moment, we can also safely do this if there is already - // a known mapping between the PDBEntry and the sequence. - for (SequenceI seq : sequences) - { - PDBEntry pdbe = pdbEntriesToView[p++]; - if (pdbe != null && pdbe.getFile() != null) - { - StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); - if (smm != null && smm.length > 0) - { - for (StructureMapping sm : smm) - { - if (sm.getSequence() == seq) - { - continue; - } - } - } - } - if (seq.getPrimaryDBRefs().isEmpty()) - { - seqsWithoutSourceDBRef.add(seq); - continue; - } - } - if (!seqsWithoutSourceDBRef.isEmpty()) - { - int y = seqsWithoutSourceDBRef.size(); - setProgressBar(MessageManager.formatMessage( - "status.fetching_dbrefs_for_sequences_without_valid_refs", - y), progressId); - SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef - .toArray(new SequenceI[y]); - DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); - dbRefFetcher.fetchDBRefs(true); - - setProgressBar("Fetch complete.", progressId); // todo i18n - } - } - if (pdbEntriesToView.length > 1) - { - setProgressBar( - MessageManager.getString( - "status.fetching_3d_structures_for_selected_entries"), - progressId); - theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); - } - else - { - setProgressBar(MessageManager.formatMessage( - "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId()), progressId); - theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); - } - setProgressBar(null, progressId); - // remember the last viewer we used... - lastTargetedView = theViewer; - return theViewer; - } - - /** * Populates the combo-box used in associating manually fetched structures to * a unique sequence when more than one sequence selection is made. */ @@ -1010,7 +1250,7 @@ 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<>(); @@ -1051,15 +1291,19 @@ public class StructureChooser extends GStructureChooser { if (selectedSequences != null) { + lbl_loading.setVisible(true); Thread refreshThread = new Thread(new Runnable() { @Override public void run() { fetchStructuresMetaData(); + // populateFilterComboBox(true, cachedPDBExists); + filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); + lbl_loading.setVisible(false); } }); refreshThread.start(); @@ -1113,7 +1357,7 @@ 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 ? "_" @@ -1154,6 +1398,15 @@ 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; @@ -1173,6 +1426,18 @@ public class StructureChooser extends GStructureChooser { progressBar.setProgressBar(message, id); } + + @Override + public void addProgressBar(long id, String message) + { + progressBar.addProgressBar(id, message); + } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(long id, IProgressIndicatorHandler handler) @@ -1195,6 +1460,31 @@ 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; + } + /** + * + * @return true if the 3D-Beacons query button will/has been displayed + */ + public boolean isCanQueryTDB() + { + return canQueryTDB; + } + + public boolean isNotQueriedTDBYet() + { + return notQueriedTDBYet; } }