X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=6132908afdafaa7a1f1ff3bbc2c2e51e9c229bc2;hb=ca9a7a8387cb17ea0a4511d1ce3c4c0c45e50db4;hp=4ecde85c571a4174a187fcd8833d9ae069d8b3bc;hpb=80b889f0cca49103e1b20ed806755a0719789906;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 4ecde85..6132908 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -28,10 +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.concurrent.Callable; +import java.util.Map; import java.util.concurrent.Executors; import javax.swing.JCheckBox; @@ -45,11 +46,16 @@ 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; @@ -60,11 +66,11 @@ 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; @@ -78,7 +84,6 @@ 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; @@ -135,6 +140,12 @@ public class StructureChooser extends GStructureChooser private boolean showChooserGUI = true; + /** + * when true, queries to external services are supressed (no SIFTs, no PDBe, + * no 3D-Beacons, etc) + */ + private boolean dontQueryServices = false; + private static StructureViewer lastTargetedView = null; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, @@ -146,6 +157,13 @@ public class StructureChooser extends GStructureChooser public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap, boolean showGUI) { + this(selectedSeqs, selectedSeq, ap, showGUI, false); + } + + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, + AlignmentPanel ap, boolean showGUI, boolean dontQueryServices) + { + // which FTS engine to use data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs); initDialog(); @@ -155,6 +173,7 @@ public class StructureChooser extends GStructureChooser this.selectedSequences = selectedSeqs; this.progressIndicator = (ap == null) ? null : ap.alignFrame; this.showChooserGUI = showGUI; + this.dontQueryServices = dontQueryServices; init(); } @@ -226,17 +245,24 @@ public class StructureChooser extends GStructureChooser } }); - Executors.defaultThreadFactory().newThread(new Runnable() + if (!dontQueryServices) { - @Override - public void run() + Executors.defaultThreadFactory().newThread(new Runnable() { - populateSeqsWithoutSourceDBRef(); - initialStructureDiscovery(); - } - - }).start(); + @Override + public void run() + { + populateSeqsWithoutSourceDBRef(); + initialStructureDiscovery(); + } + }).start(); + } + else + { + Console.debug( + "Structure chooser not querying services to discover metadata."); + } } // called by init @@ -342,7 +368,7 @@ public class StructureChooser extends GStructureChooser }; // fetch db refs if OK pressed - final Callable discoverCanonicalDBrefs = () -> { + final Runnable discoverCanonicalDBrefs = () -> { btn_queryTDB.setEnabled(false); populateSeqsWithoutSourceDBRef(); @@ -364,14 +390,12 @@ public class StructureChooser extends GStructureChooser // call finished action directly afterDbRefFetch.finished(); } - return null; }; - final Callable revertview = () -> { + final Runnable revertview = () -> { if (lastSelected != null) { cmb_filterOption.setSelectedItem(lastSelected); } - return null; }; int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD", THRESHOLD_WARN_UNIPROT_FETCH_NEEDED); @@ -503,7 +527,7 @@ public class StructureChooser extends GStructureChooser } } catch (Exception e) { - e.printStackTrace(); + Console.printStackTrace(e); errors.add(e.getMessage()); continue; } @@ -540,9 +564,18 @@ public class StructureChooser extends GStructureChooser { errorMsg.append(error).append("\n"); } - JvOptionPane.showMessageDialog(this, errorMsg.toString(), - MessageManager.getString("label.pdb_web-service_error"), - JvOptionPane.ERROR_MESSAGE); + if (!Jalview.isHeadlessMode()) + { + JvOptionPane.showMessageDialog(this, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JvOptionPane.ERROR_MESSAGE); + } + else + { + Console.error( + MessageManager.getString("label.pdb_web-service_error")); + Console.debug(errorMsg.toString()); + } } } } @@ -603,7 +636,7 @@ public class StructureChooser extends GStructureChooser } catch (Exception e) { - e.printStackTrace(); + Console.debugPrintStackTrace(e); errors.add(e.getMessage()); continue; } @@ -980,8 +1013,14 @@ public class StructureChooser extends GStructureChooser .getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet); String pageUrl = row.getModelViewUrl(); + JPopupMenu popup = new JPopupMenu("3D Beacons"); JMenuItem viewUrl = new JMenuItem("View model web page"); + if (pageUrl == null || "".equals(pageUrl.trim())) + { + viewUrl.setEnabled(false); + viewUrl.setText("No model page available."); + } viewUrl.addActionListener(new ActionListener() { @Override @@ -1307,7 +1346,8 @@ public class StructureChooser extends GStructureChooser String pdbFilename = selectedPdbFileName; StructureChooser.openStructureFileForSequence(ssm, sc, ap, - selectedSequence, true, pdbFilename, tft, paeFilename); + selectedSequence, true, pdbFilename, tft, paeFilename, + true); } SwingUtilities.invokeLater(new Runnable() { @@ -1367,6 +1407,15 @@ 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); @@ -1374,6 +1423,12 @@ public class StructureChooser extends GStructureChooser boolean superimpose = chk_superpose.isSelected(); theViewer.setSuperpose(superimpose); + // if we're running in --headless mode make this viewer synchronous + if (Jalview.isHeadlessMode()) + { + theViewer.setAsync(false); + } + /* * remember user's choice of superimpose or not */ @@ -1431,7 +1486,8 @@ 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 { @@ -1439,7 +1495,8 @@ public class StructureChooser extends GStructureChooser "status.fetching_3d_structures_for", pdbEntriesToView[0].getId()), progressId); // Can we pass a pre-computeMappinged pdbFile? - theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel, + viewerType); } setProgressBar(null, progressId); // remember the last viewer we used... @@ -1508,7 +1565,8 @@ public class StructureChooser extends GStructureChooser // for moment, it will work fine as is because it is self-contained String searchTerm = text.toLowerCase(Locale.ROOT); searchTerm = searchTerm.split(":")[0]; - // System.out.println(">>>>> search term : " + searchTerm); + // jalview.bin.Console.outPrintln(">>>>> search term : " + + // searchTerm); List wantedFields = new ArrayList<>(); FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); @@ -1680,20 +1738,21 @@ public class StructureChooser extends GStructureChooser @Override public void setProgressBar(String message, long id) { - if (!Platform.isHeadless()) + 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() @@ -1740,26 +1799,78 @@ public class StructureChooser extends GStructureChooser public static void openStructureFileForSequence( StructureSelectionManager ssm, StructureChooser sc, AlignmentPanel ap, SequenceI seq, boolean prompt, - String sFilename, TFType tft, String paeFilename) + String sFilename, TFType tft, String paeFilename, + boolean doXferSettings) + { + 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) { - boolean headless = false; + StructureViewer sv = null; + boolean headless = forceHeadless; if (sc == null) { - headless = true; - sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false); + // headless = true; + prompt = false; + // suppress structure viewer's external service queries + sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false, + true); } if (ssm == null) + { ssm = ap.getStructureSelectionManager(); + StructureSelectionManager.doConfigureStructurePrefs(ssm); + } PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq( sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance, - tft, paeFilename); + 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(); - StructureViewer sViewer = sc.launchStructureViewer(ssm, - new PDBEntry[] - { fileEntry }, ap, new SequenceI[] { seq }); + 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(); + } - if (headless) - sc.mainFrame.dispose(); } }