X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=666ff7409b7b68a38cc66845a37ce35900493548;hb=9d465da4f21e403c20b835264929906b538c0c9b;hp=8423ed9b5b5c15020b4fc2ce9d50ee55085c0668;hpb=559683447a76180ede214c9b44f018b5c7539987;p=jalview.git
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 8423ed9..666ff74 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -83,6 +83,7 @@ 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.seqfetcher.DbSourceProxy;
import jalview.ws.sifts.SiftsSettings;
@@ -139,6 +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,
@@ -150,6 +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();
@@ -159,6 +173,7 @@ public class StructureChooser extends GStructureChooser
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
this.showChooserGUI = showGUI;
+ this.dontQueryServices = dontQueryServices;
init();
}
@@ -230,17 +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
@@ -505,7 +527,7 @@ public class StructureChooser extends GStructureChooser
}
} catch (Exception e)
{
- e.printStackTrace();
+ Console.printStackTrace(e);
errors.add(e.getMessage());
continue;
}
@@ -542,9 +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());
+ }
}
}
}
@@ -605,7 +636,7 @@ public class StructureChooser extends GStructureChooser
} catch (Exception e)
{
- e.printStackTrace();
+ Console.debugPrintStackTrace(e);
errors.add(e.getMessage());
continue;
}
@@ -704,7 +735,7 @@ public class StructureChooser extends GStructureChooser
}
/**
- * Handles action event for btn_pdbFromFile
+ * Handles action event for btn_paeMatrixFile
*/
@Override
protected void paeMatrixFile_actionPerformed()
@@ -733,10 +764,26 @@ public class StructureChooser extends GStructureChooser
"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 }) + "
" + 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();
@@ -966,8 +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
@@ -1058,11 +1111,13 @@ public class StructureChooser extends GStructureChooser
{
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");
@@ -1187,7 +1242,14 @@ 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
@@ -1278,7 +1340,9 @@ public class StructureChooser extends GStructureChooser
.getCmb_assSeq().getSelectedItem();
SequenceI userSelectedSeq = assSeqOpt.getSequence();
if (userSelectedSeq != null)
+ {
selectedSequence = userSelectedSeq;
+ }
String pdbFilename = selectedPdbFileName;
StructureChooser.openStructureFileForSequence(ssm, sc, ap,
@@ -1290,6 +1354,7 @@ public class StructureChooser extends GStructureChooser
@Override
public void run()
{
+ setProgressBar("Complete.", progress.hashCode());
closeAction(preferredHeight);
mainFrame.dispose();
}
@@ -1358,6 +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
*/
@@ -1494,7 +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);
@@ -1747,7 +1819,9 @@ public class StructureChooser extends GStructureChooser
{
// headless = true;
prompt = false;
- sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
+ // suppress structure viewer's external service queries
+ sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,
+ true);
}
if (ssm == null)
{
@@ -1770,7 +1844,9 @@ public class StructureChooser extends GStructureChooser
sc.mainFrame.dispose();
if (showRefAnnotations)
+ {
showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+ }
return sv;
}