X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=29551b88b98878d39abc7950832100231a346b25;hb=0fbfbe484308a0a6d9663f69f287cc61cfba958a;hp=9f9de6ea386372cea19dc89eb1f90b301c2c7250;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 9f9de6e..29551b8 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,28 +21,37 @@ package jalview.gui; -import java.util.Locale; - +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; import java.awt.event.ItemEvent; +import java.io.File; 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.Callable; import java.util.concurrent.Executors; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; import javax.swing.JTable; import javax.swing.SwingUtilities; import javax.swing.table.AbstractTableModel; +import com.stevesoft.pat.Regex; + import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.bin.Jalview; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; import jalview.fts.api.FTSData; import jalview.fts.api.FTSDataColumnI; import jalview.fts.api.FTSRestClientI; @@ -50,15 +59,21 @@ 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.io.JalviewFileChooser; +import jalview.io.JalviewFileView; import jalview.jbgui.FilterOption; import jalview.jbgui.GStructureChooser; +import jalview.structure.StructureImportSettings.TFType; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.StringUtils; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.seqfetcher.DbSourceProxy; @@ -77,9 +92,9 @@ public class StructureChooser extends GStructureChooser private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; /** - * transient combo box choice for initiating 3db fetch + * warn user if need to fetch more than this many uniprot records at once */ - private static final String VIEWS_QUERYING_TDB = "QUERY_3DB"; + private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20; private SequenceI selectedSequence; @@ -99,6 +114,10 @@ public class StructureChooser extends GStructureChooser private String selectedPdbFileName; + private TFType localPdbTempfacType; + + private String localPdbPaeMatrixFileName; + private boolean isValidPBDEntry; private boolean cachedPDBExists; @@ -111,11 +130,19 @@ public class StructureChooser extends GStructureChooser List seqsWithoutSourceDBRef = null; + private boolean showChooserGUI = true; + private static StructureViewer lastTargetedView = null; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { + this(selectedSeqs, selectedSeq, ap, true); + } + + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, + AlignmentPanel ap, boolean showGUI) + { // which FTS engine to use data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs); initDialog(); @@ -124,6 +151,7 @@ public class StructureChooser extends GStructureChooser this.selectedSequence = selectedSeq; this.selectedSequences = selectedSeqs; this.progressIndicator = (ap == null) ? null : ap.alignFrame; + this.showChooserGUI = showGUI; init(); } @@ -168,7 +196,8 @@ public class StructureChooser extends GStructureChooser canQueryTDB = true; if (needCanonical) { - notQueriedTDBYet = false; + // triggers display of the 'Query TDB' button + notQueriedTDBYet = true; } } }; @@ -184,9 +213,19 @@ 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(); @@ -228,11 +267,17 @@ public class StructureChooser extends GStructureChooser populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); discoverStructureViews(); updateProgressIndicator(null, startTime); - mainFrame.setVisible(true); + mainFrame.setVisible(showChooserGUI); updateCurrentView(); } - private void promptForTDBFetch() + /** + * 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(); @@ -242,19 +287,46 @@ public class StructureChooser extends GStructureChooser @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; - + 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() { @@ -262,46 +334,55 @@ public class StructureChooser extends GStructureChooser 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() + final Callable discoverCanonicalDBrefs = () -> { + btn_queryTDB.setEnabled(false); + populateSeqsWithoutSourceDBRef(); + + final int y = seqsWithoutSourceDBRef.size(); + if (y > 0) { - populateSeqsWithoutSourceDBRef(); + 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 - 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(); - } + dbRefFetcher.fetchDBRefs(true); } - + else + { + // call finished action directly + afterDbRefFetch.finished(); + } + return null; }; - final Runnable revertview = new Runnable() { - public void run() { - if (lastSelected!=null) { - cmb_filterOption.setSelectedItem(lastSelected); - } - }; + final Callable revertview = () -> { + if (lastSelected != null) + { + cmb_filterOption.setSelectedItem(lastSelected); + } + return null; }; + 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.newSingleThreadExecutor().submit(discoverCanonicalDBrefs); + return; + } // need cancel and no to result in the discoverPDB action - mocked is - // 'cancel' - JvOptionPane.newOptionDialog(this) + // 'cancel' TODO: mock should be OK + + StructureChooser thisSC = this; + JvOptionPane.newOptionDialog(thisSC.getFrame()) .setResponseHandler(JvOptionPane.OK_OPTION, discoverCanonicalDBrefs) .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) @@ -310,13 +391,12 @@ public class StructureChooser extends GStructureChooser MessageManager.formatMessage( "label.fetch_references_for_3dbeacons", seqsWithoutSourceDBRef.size()), - MessageManager - .getString("label.3dbeacons"), + 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")); + MessageManager.getString("action.ok"), false); } /** @@ -587,9 +667,9 @@ public class StructureChooser extends GStructureChooser // 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")); - chooser.setFileView(new jalview.io.JalviewFileView()); + JalviewFileChooser chooser = new JalviewFileChooser( + Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.formatMessage("label.select_pdb_file_for", selectedSequence.getDisplayId(false))); @@ -598,15 +678,96 @@ public class StructureChooser extends GStructureChooser selectedSequence.getDisplayId(false))); int value = chooser.showOpenDialog(null); - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + if (value == JalviewFileChooser.APPROVE_OPTION) { selectedPdbFileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + boolean guessTFType = localPdbPaeMatrixFileName == null; + localPdbPaeMatrixFileName = guessPAEFilename(); + guessTFType |= localPdbPaeMatrixFileName != null; + Regex alphaFold = JmolParser.getNewAlphafoldValidator(); + if (guessTFType + && alphaFold.search(new File(selectedPdbFileName).getName()) + && !tempFacAsChanged) + { + // localPdbPaeMatrixFileName was null and now isn't and filename could + // well be AlphaFold and user hasn't adjusted the tempFacType + combo_tempFacAs.setSelectedItem(TFType.PLDDT); + } validateSelections(); } } /** + * Handles action event for btn_pdbFromFile + */ + @Override + protected void paeMatrixFile_actionPerformed() + { + File pdbFile = new File(selectedPdbFileName); + String setFile = Cache.getProperty("LAST_DIRECTORY"); + if (localPdbPaeMatrixFileName != null) + { + File paeFile = new File(localPdbPaeMatrixFileName); + if (paeFile.exists()) + setFile = paeFile.getAbsolutePath(); + else if (paeFile.getParentFile().exists()) + setFile = paeFile.getParentFile().getAbsolutePath(); + } + else + { + String guess = guessPAEFilename(); + if (guess != null) + setFile = guess; + } + JalviewFileChooser chooser = new JalviewFileChooser(setFile); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.formatMessage( + "label.select_pae_matrix_file_for", pdbFile.getName())); + chooser.setToolTipText(MessageManager.formatMessage( + "label.load_pae_matrix_file_associate_with_structure", + pdbFile.getName())); + + int value = chooser.showOpenDialog(null); + if (value == JalviewFileChooser.APPROVE_OPTION) + { + localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName); + } + validateAssociationFromFile(); + } + + private String guessPAEFilename() + { + if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb") + || selectedPdbFileName.toLowerCase(Locale.ROOT) + .endsWith(".cif")) + { + String jsonExt = selectedPdbFileName.substring(0, + selectedPdbFileName.length() - 4) + ".json"; + // AlphaFold naming scheme + String guessFile1 = StringUtils.replaceLast(jsonExt, "model", + "predicted_aligned_error"); + // nf-core mode naming scheme + String guessFile2 = StringUtils.replaceLast(jsonExt, ".json", + "_scores.json"); + if (new File(guessFile1).exists()) + { + return guessFile1; + } + else if (new File(jsonExt).exists()) + { + return jsonExt; + } + else if (new File(guessFile2).exists()) + { + return guessFile2; + } + } + return null; + } + + /** * Populates the filter combo-box options dynamically depending on discovered * structures */ @@ -656,10 +817,8 @@ public class StructureChooser extends GStructureChooser "-", 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); + btn_queryTDB.setVisible(true); + pnl_queryTDB.setVisible(true); } if (cachedPDBExist) @@ -687,13 +846,7 @@ 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 @@ -708,7 +861,7 @@ public class StructureChooser extends GStructureChooser String filterTitle = mainFrame.getTitle(); mainFrame.setTitle(frameTitle); chk_invertFilter.setVisible(false); - + if (selectedFilterOpt.getView() == VIEWS_FILTER) { mainFrame.setTitle(filterTitle); @@ -793,6 +946,46 @@ 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 */ @@ -841,7 +1034,9 @@ public class StructureChooser extends GStructureChooser { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); - lbl_fromFileStatus.setIcon(errorImage); + // lbl_fromFileStatus.setIcon(errorImage); + String pdbFileString = ""; + String pdbFileTooltip = ""; if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt .getName().equalsIgnoreCase("-Select Associated Seq-"))) { @@ -849,14 +1044,44 @@ public class StructureChooser extends GStructureChooser if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) { btn_add.setEnabled(true); - lbl_fromFileStatus.setIcon(goodImage); + // lbl_fromFileStatus.setIcon(goodImage); + pdbFileString = new File(selectedPdbFileName).getName(); + pdbFileTooltip = new File(selectedPdbFileName).getAbsolutePath(); + setPdbOptionsEnabled(true); + } + else + { + pdbFileString = MessageManager.getString("label.none"); + pdbFileTooltip = MessageManager.getString("label.nothing_selected"); } } else { btn_pdbFromFile.setEnabled(false); - lbl_fromFileStatus.setIcon(errorImage); + // lbl_fromFileStatus.setIcon(errorImage); + pdbFileString = MessageManager.getString("label.none"); + pdbFileTooltip = MessageManager.getString("label.nothing_selected"); + } + lbl_pdbFile.setText(pdbFileString); + lbl_pdbFile.setToolTipText(pdbFileTooltip); + + // PAE file choice + String paeFileString = ""; + String paeFileTooltip = ""; + if (localPdbPaeMatrixFileName != null + && localPdbPaeMatrixFileName.length() > 0) + { + paeFileString = new File(localPdbPaeMatrixFileName).getName(); + paeFileTooltip = new File(localPdbPaeMatrixFileName) + .getAbsolutePath(); + } + else + { + paeFileString = MessageManager.getString("label.none"); + paeFileTooltip = MessageManager.getString("label.nothing_selected"); } + lbl_paeFile.setText(paeFileString); + lbl_paeFile.setToolTipText(paeFileTooltip); } @Override @@ -864,7 +1089,9 @@ public class StructureChooser extends GStructureChooser { validateSelections(); } - private FilterOption lastSelected=null; + + private FilterOption lastSelected = null; + /** * Handles the state change event for the 'filter' combo-box and 'invert' * check-box @@ -1021,7 +1248,8 @@ public class StructureChooser extends GStructureChooser if (pdbIdStr.split(":").length > 1) { pdbEntry.setId(pdbIdStr.split(":")[0]); - pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); + pdbEntry.setChainCode( + pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); } else { @@ -1038,20 +1266,18 @@ public class StructureChooser extends GStructureChooser } else if (currentView == VIEWS_FROM_FILE) { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); + StructureChooser sc = StructureChooser.this; + TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem(); + String paeFilename = sc.localPdbPaeMatrixFileName; + AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem(); + SequenceI userSelectedSeq = assSeqOpt.getSequence(); if (userSelectedSeq != null) - { selectedSequence = userSelectedSeq; - } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.instance); + String pdbFilename = selectedPdbFileName; - sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, - ap, new SequenceI[] - { selectedSequence }); + StructureChooser.openStructureFileForSequence(ssm, sc, null, + selectedSequence, true, pdbFilename, tft, paeFilename); } SwingUtilities.invokeLater(new Runnable() { @@ -1181,6 +1407,7 @@ public class StructureChooser extends GStructureChooser setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", pdbEntriesToView[0].getId()), progressId); + // Can we pass a pre-computeMappinged pdbFile? theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } setProgressBar(null, progressId); @@ -1289,6 +1516,7 @@ public class StructureChooser extends GStructureChooser { if (selectedSequences != null) { + lbl_loading.setVisible(true); Thread refreshThread = new Thread(new Runnable() { @Override @@ -1300,6 +1528,7 @@ public class StructureChooser extends GStructureChooser filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); + lbl_loading.setVisible(false); } }); refreshThread.start(); @@ -1420,7 +1649,8 @@ public class StructureChooser extends GStructureChooser @Override public void setProgressBar(String message, long id) { - progressBar.setProgressBar(message, id); + if (!Platform.isHeadless()) + progressBar.setProgressBar(message, id); } @Override @@ -1458,4 +1688,47 @@ public class StructureChooser extends GStructureChooser && 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; + } + + /** + * Open a single structure file for a given sequence + */ + public static void openStructureFileForSequence( + StructureSelectionManager ssm, StructureChooser sc, + AlignmentPanel ap, SequenceI seq, boolean prompt, + String sFilename, TFType tft, String paeFilename) + { + boolean headless = false; + if (sc == null) + { + headless = true; + sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false); + } + if (ssm == null) + ssm = ap.getStructureSelectionManager(); + + PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq( + sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance, + tft, paeFilename); + + StructureViewer sViewer = sc.launchStructureViewer(ssm, + new PDBEntry[] + { fileEntry }, ap, new SequenceI[] { seq }); + + if (headless) + sc.mainFrame.dispose(); + } }