X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=29551b88b98878d39abc7950832100231a346b25;hb=0fbfbe484308a0a6d9663f69f287cc61cfba958a;hp=b32e43517e3d709bc58163b943c4f42fac81271f;hpb=89350c76ad3884aa1394952979998ea58902063c;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index b32e435..29551b8 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -24,12 +24,14 @@ package jalview.gui; 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; @@ -41,11 +43,15 @@ 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; @@ -58,11 +64,16 @@ 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; @@ -103,6 +114,10 @@ public class StructureChooser extends GStructureChooser private String selectedPdbFileName; + private TFType localPdbTempfacType; + + private String localPdbPaeMatrixFileName; + private boolean isValidPBDEntry; private boolean cachedPDBExists; @@ -115,11 +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(); @@ -128,6 +151,7 @@ public class StructureChooser extends GStructureChooser this.selectedSequence = selectedSeq; this.selectedSequences = selectedSeqs; this.progressIndicator = (ap == null) ? null : ap.alignFrame; + this.showChooserGUI = showGUI; init(); } @@ -243,7 +267,7 @@ public class StructureChooser extends GStructureChooser populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); discoverStructureViews(); updateProgressIndicator(null, startTime); - mainFrame.setVisible(true); + mainFrame.setVisible(showChooserGUI); updateCurrentView(); } @@ -315,54 +339,50 @@ public class StructureChooser extends GStructureChooser }; // 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() - { - @Override - public void run() + final Callable revertview = () -> { + if (lastSelected != null) { - if (lastSelected != null) - { - cmb_filterOption.setSelectedItem(lastSelected); - } - }; + cmb_filterOption.setSelectedItem(lastSelected); + } + return null; }; - if (ignoreGui || seqsWithoutSourceDBRef - .size() < THRESHOLD_WARN_UNIPROT_FETCH_NEEDED) + 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 // 'cancel' TODO: mock should be OK - JvOptionPane.newOptionDialog(this) + + StructureChooser thisSC = this; + JvOptionPane.newOptionDialog(thisSC.getFrame()) .setResponseHandler(JvOptionPane.OK_OPTION, discoverCanonicalDBrefs) .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) @@ -376,7 +396,7 @@ public class StructureChooser extends GStructureChooser null, new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }, - MessageManager.getString("action.ok")); + MessageManager.getString("action.ok"), false); } /** @@ -647,9 +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( + 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))); @@ -658,15 +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(); 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 */ @@ -933,7 +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-"))) { @@ -941,14 +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 @@ -1133,20 +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() { @@ -1276,6 +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); @@ -1384,6 +1516,7 @@ public class StructureChooser extends GStructureChooser { if (selectedSequences != null) { + lbl_loading.setVisible(true); Thread refreshThread = new Thread(new Runnable() { @Override @@ -1395,6 +1528,7 @@ public class StructureChooser extends GStructureChooser filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); + lbl_loading.setVisible(false); } }); refreshThread.start(); @@ -1515,7 +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 @@ -1567,4 +1702,33 @@ public class StructureChooser extends GStructureChooser { 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(); + } }