X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=6fce9847e02af1843fdfa933bb9e0f93a38610b3;hb=e67a74ee1dac618d941fce0fc5ef4561f76380b1;hp=89d5c6b39ba7a62f8ad16037ee9a51389de87c64;hpb=512a360277338f2aea7d8bcc6804e103f3185fcf;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 89d5c6b..6fce984 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -28,9 +28,11 @@ import java.io.File; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; +import java.util.LinkedHashMap; import java.util.LinkedHashSet; import java.util.List; import java.util.Locale; +import java.util.Map; import java.util.concurrent.Executors; import javax.swing.JCheckBox; @@ -42,12 +44,20 @@ import javax.swing.JTable; import javax.swing.SwingUtilities; import javax.swing.table.AbstractTableModel; +import com.stevesoft.pat.Regex; + +import jalview.analysis.AlignmentUtils; +import jalview.api.AlignmentViewPanel; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.bin.Console; import jalview.bin.Jalview; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; import jalview.fts.api.FTSData; import jalview.fts.api.FTSDataColumnI; import jalview.fts.api.FTSRestClientI; @@ -56,17 +66,26 @@ 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.StructureViewer.ViewerType; import jalview.gui.structurechooser.PDBStructureChooserQuerySource; import jalview.gui.structurechooser.StructureChooserQuerySource; import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; import jalview.io.DataSourceType; +import jalview.io.FileFormatException; +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.datamodel.alphafold.PAEContactMatrix; +import jalview.ws.dbsources.EBIAlfaFold; import jalview.ws.seqfetcher.DbSourceProxy; import jalview.ws.sifts.SiftsSettings; @@ -105,6 +124,10 @@ public class StructureChooser extends GStructureChooser private String selectedPdbFileName; + private TFType localPdbTempfacType; + + private String localPdbPaeMatrixFileName; + private boolean isValidPBDEntry; private boolean cachedPDBExists; @@ -117,18 +140,18 @@ public class StructureChooser extends GStructureChooser List seqsWithoutSourceDBRef = null; - private boolean noChooserGUI = false; + private boolean showChooserGUI = true; private static StructureViewer lastTargetedView = null; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { - this(selectedSeqs, selectedSeq, ap, false); + this(selectedSeqs, selectedSeq, ap, true); } public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, - AlignmentPanel ap, boolean noChooserGUI) + AlignmentPanel ap, boolean showGUI) { // which FTS engine to use data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs); @@ -138,7 +161,7 @@ public class StructureChooser extends GStructureChooser this.selectedSequence = selectedSeq; this.selectedSequences = selectedSeqs; this.progressIndicator = (ap == null) ? null : ap.alignFrame; - this.noChooserGUI = noChooserGUI; + this.showChooserGUI = showGUI; init(); } @@ -254,7 +277,7 @@ public class StructureChooser extends GStructureChooser populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); discoverStructureViews(); updateProgressIndicator(null, startTime); - mainFrame.setVisible(noChooserGUI); + mainFrame.setVisible(showChooserGUI); updateCurrentView(); } @@ -326,53 +349,41 @@ public class StructureChooser extends GStructureChooser }; // fetch db refs if OK pressed - final Runnable discoverCanonicalDBrefs = new Runnable() - { - @Override - public void run() + final Runnable discoverCanonicalDBrefs = () -> { + btn_queryTDB.setEnabled(false); + populateSeqsWithoutSourceDBRef(); + + final int y = seqsWithoutSourceDBRef.size(); + if (y > 0) { - btn_queryTDB.setEnabled(false); - 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(); } - }; - final Runnable revertview = new Runnable() - { - @Override - public void run() + final Runnable revertview = () -> { + if (lastSelected != null) { - if (lastSelected != null) - { - cmb_filterOption.setSelectedItem(lastSelected); - } - }; + 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(); + Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs); return; } // need cancel and no to result in the discoverPDB action - mocked is @@ -664,9 +675,9 @@ 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( + JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY")); - chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.formatMessage("label.select_pdb_file_for", selectedSequence.getDisplayId(false))); @@ -675,15 +686,112 @@ 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(); 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_paeMatrixFile + */ + @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())); + + // TODO convert to Callable/Promise + int value = chooser.showOpenDialog(null); + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String fileName = chooser.getSelectedFile().getPath(); + try + { + PAEContactMatrix.validateContactMatrixFile(fileName); + } catch (Exception thr) + { + JvOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_load_file", new Object[] + { fileName }) + "
" + thr.getLocalizedMessage(), + MessageManager.getString("label.error_loading_file"), + JvOptionPane.WARNING_MESSAGE); + Console.error("Couldn't import " + fileName + " as a PAE matrix", + thr); + return; + } + localPdbPaeMatrixFileName = fileName; + 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 */ @@ -950,7 +1058,9 @@ 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-"))) { @@ -958,14 +1068,46 @@ 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"); + setPdbOptionsEnabled(false); } } else { btn_pdbFromFile.setEnabled(false); - lbl_fromFileStatus.setIcon(errorImage); + setPdbOptionsEnabled(false); + // 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 @@ -1066,7 +1208,14 @@ public class StructureChooser extends GStructureChooser final StructureSelectionManager ssm = ap.getStructureSelectionManager(); final int preferredHeight = pnl_filter.getHeight(); + btn_add.setEnabled(false); + btn_newView.setEnabled(false); + btn_cancel.setEnabled(false); + actionsPanel.setEnabled(false); + final String progress = MessageManager + .getString("label.working_ellipsis"); + setProgressBar(progress, progress.hashCode()); Runnable viewStruc = new Runnable() { @Override @@ -1150,26 +1299,28 @@ 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, ap, + selectedSequence, true, pdbFilename, tft, paeFilename, + true); } SwingUtilities.invokeLater(new Runnable() { @Override public void run() { + setProgressBar("Complete.", progress.hashCode()); closeAction(preferredHeight); mainFrame.dispose(); } @@ -1222,6 +1373,15 @@ public class StructureChooser extends GStructureChooser StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { + return launchStructureViewer(ssm, pdbEntriesToView, alignPanel, + sequences, null); + } + + private StructureViewer launchStructureViewer( + StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, + final AlignmentPanel alignPanel, SequenceI[] sequences, + ViewerType viewerType) + { long progressId = sequences.hashCode(); setProgressBar(MessageManager .getString("status.launching_3d_structure_viewer"), progressId); @@ -1286,14 +1446,17 @@ public class StructureChooser extends GStructureChooser MessageManager.getString( "status.fetching_3d_structures_for_selected_entries"), progressId); - theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel, + viewerType); } else { setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", pdbEntriesToView[0].getId()), progressId); - theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + // Can we pass a pre-computeMappinged pdbFile? + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel, + viewerType); } setProgressBar(null, progressId); // remember the last viewer we used... @@ -1534,19 +1697,21 @@ public class StructureChooser extends GStructureChooser @Override public void setProgressBar(String message, long id) { - progressBar.setProgressBar(message, id); + if (!Platform.isHeadless() && progressBar != null) + progressBar.setProgressBar(message, id); } @Override public void registerHandler(long id, IProgressIndicatorHandler handler) { - progressBar.registerHandler(id, handler); + if (progressBar != null) + progressBar.registerHandler(id, handler); } @Override public boolean operationInProgress() { - return progressBar.operationInProgress(); + return progressBar == null ? false : progressBar.operationInProgress(); } public JalviewStructureDisplayI getOpenedStructureViewer() @@ -1590,29 +1755,76 @@ public class StructureChooser extends GStructureChooser /** * Open a single structure file for a given sequence */ - public static void openStructureFileForSequence(AlignmentPanel ap, - SequenceI seq, File sFile) + public static void openStructureFileForSequence( + StructureSelectionManager ssm, StructureChooser sc, + AlignmentPanel ap, SequenceI seq, boolean prompt, + String sFilename, TFType tft, String paeFilename, + boolean doXferSettings) { - StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq, - ap, true); - StructureSelectionManager ssm = ap.getStructureSelectionManager(); - PDBEntry fileEntry = null; - try - { - fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq( - sFile.getAbsolutePath(), DataSourceType.FILE, seq, true, - Desktop.instance); - } catch (Exception e) - { - Console.error("Could not open structure file '" - + sFile.getAbsolutePath() + "'"); - return; + openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft, + paeFilename, false, true, doXferSettings, null); + } + + public static StructureViewer openStructureFileForSequence( + StructureSelectionManager ssm, StructureChooser sc, + AlignmentPanel ap, SequenceI seq, boolean prompt, + String sFilename, TFType tft, String paeFilename, + boolean forceHeadless, boolean showRefAnnotations, + boolean doXferSettings, ViewerType viewerType) + { + StructureViewer sv = null; + boolean headless = forceHeadless; + if (sc == null) + { + // headless = true; + prompt = false; + sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false); + } + if (ssm == null) + { + ssm = ap.getStructureSelectionManager(); } - StructureViewer sViewer = sc.launchStructureViewer(ssm, - new PDBEntry[] - { fileEntry }, ap, new SequenceI[] { seq }); + PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq( + sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance, + tft, paeFilename, doXferSettings); + + // if headless, "false" in the sc constructor above will avoid GUI behaviour + // in sc.launchStructureViewer() + if (!headless && !(viewerType == null)) + { + sv = sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + new SequenceI[] + { seq }, viewerType); + } sc.mainFrame.dispose(); + + if (showRefAnnotations) + showReferenceAnnotationsForSequence(ap.alignFrame, seq); + + return sv; + } + + public static void showReferenceAnnotationsForSequence(AlignFrame af, + SequenceI sequence) + { + AlignViewport av = af.getCurrentView(); + AlignmentI al = av.getAlignment(); + + List forSequences = new ArrayList<>(); + forSequences.add(sequence); + final Map> candidates = new LinkedHashMap<>(); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, null, + candidates, al); + final SequenceGroup selectionGroup = av.getSelectionGroup(); + AlignmentUtils.addReferenceAnnotations(candidates, al, selectionGroup); + for (AlignmentViewPanel ap : af.getAlignPanels()) + { + // required to readjust the height and position of the PAE + // annotation + ap.adjustAnnotationHeight(); + } + } }