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;
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.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.util.StringUtils;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.sifts.SiftsSettings;
List<SequenceI> seqsWithoutSourceDBRef = null;
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,
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();
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
this.showChooserGUI = showGUI;
+ this.dontQueryServices = dontQueryServices;
init();
}
}
});
- 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
};
// fetch db refs if OK pressed
- final Callable discoverCanonicalDBrefs = () -> {
+ final Runnable discoverCanonicalDBrefs = () -> {
btn_queryTDB.setEnabled(false);
populateSeqsWithoutSourceDBRef();
// 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);
}
} catch (Exception e)
{
- e.printStackTrace();
+ Console.printStackTrace(e);
errors.add(e.getMessage());
continue;
}
{
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());
+ }
}
}
}
} catch (Exception e)
{
- e.printStackTrace();
+ Console.debugPrintStackTrace(e);
errors.add(e.getMessage());
continue;
}
}
/**
- * Handles action event for btn_pdbFromFile
+ * Handles action event for btn_paeMatrixFile
*/
@Override
protected void paeMatrixFile_actionPerformed()
"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)
{
- localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
+ String fileName = chooser.getSelectedFile().getPath();
+ try
+ {
+ PAEContactMatrix.validateContactMatrixFile(fileName);
+ } catch (Exception thr)
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_load_file", new Object[]
+ { fileName }) + "<br>" + 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();
{
pdbFileString = MessageManager.getString("label.none");
pdbFileTooltip = MessageManager.getString("label.nothing_selected");
+ setPdbOptionsEnabled(false);
}
}
else
{
btn_pdbFromFile.setEnabled(false);
+ setPdbOptionsEnabled(false);
// lbl_fromFileStatus.setIcon(errorImage);
pdbFileString = MessageManager.getString("label.none");
pdbFileTooltip = MessageManager.getString("label.nothing_selected");
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
.getCmb_assSeq().getSelectedItem();
SequenceI userSelectedSeq = assSeqOpt.getSequence();
if (userSelectedSeq != null)
+ {
selectedSequence = userSelectedSeq;
+ }
String pdbFilename = selectedPdbFileName;
StructureChooser.openStructureFileForSequence(ssm, sc, ap,
- selectedSequence, true, pdbFilename, tft, paeFilename);
+ selectedSequence, true, pdbFilename, tft, paeFilename,
+ true);
}
SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
+ setProgressBar("Complete.", progress.hashCode());
closeAction(preferredHeight);
mainFrame.dispose();
}
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);
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
*/
MessageManager.getString(
"status.fetching_3d_structures_for_selected_entries"),
progressId);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel,
+ viewerType);
}
else
{
"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...
// 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<FTSDataColumnI> wantedFields = new ArrayList<>();
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
@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()
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();
+ }
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<SequenceI> forSequences = new ArrayList<>();
+ forSequences.add(sequence);
+ final Map<SequenceI, List<AlignmentAnnotation>> 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();
}
}
git://source.jalview.org / jalview.git / blobdiff