import java.util.List;
import java.util.Locale;
import java.util.Map;
-import java.util.concurrent.Callable;
import java.util.concurrent.Executors;
import javax.swing.JCheckBox;
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;
};
// 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.debugPrintStackTrace(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,
@Override
public void run()
{
+ setProgressBar("Complete.", progress.hashCode());
closeAction(preferredHeight);
mainFrame.dispose();
}
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
*/
// 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);
{ seq }, viewerType);
}
- if (headless)
- sc.mainFrame.dispose();
+ sc.mainFrame.dispose();
if (showRefAnnotations)
+ {
showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+ }
return sv;
}