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;
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;
private String selectedPdbFileName;
+ private TFType localPdbTempfacType;
+
+ private String localPdbPaeMatrixFileName;
+
private boolean isValidPBDEntry;
private boolean cachedPDBExists;
List<SequenceI> seqsWithoutSourceDBRef = null;
- private boolean noChooserGUI = false;
+ private boolean showChooserGUI = true;
private static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
- this(selectedSeqs, selectedSeq, ap, false);
+ this(selectedSeqs, selectedSeq, ap, true);
}
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
- AlignmentPanel ap, boolean noChooserGUI)
+ AlignmentPanel ap, boolean showGUI)
{
// which FTS engine to use
data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
this.selectedSequence = selectedSeq;
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
- this.noChooserGUI = noChooserGUI;
+ this.showChooserGUI = showGUI;
init();
}
populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
discoverStructureViews();
updateProgressIndicator(null, startTime);
- mainFrame.setVisible(noChooserGUI);
+ mainFrame.setVisible(showChooserGUI);
updateCurrentView();
}
};
// 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)
{
- btn_queryTDB.setEnabled(false);
- 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;
};
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
// 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)));
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);
+ localPdbPaeMatrixFileName = guessPAEFilename();
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"))
+ {
+ 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
*/
{
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-")))
{
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
public static void openStructureFileForSequence(AlignmentPanel ap,
SequenceI seq, File sFile)
{
+ // Open the chooser headlessly. Not sure this is actually needed ?
StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
- ap, true);
+ ap, false);
StructureSelectionManager ssm = ap.getStructureSelectionManager();
PDBEntry fileEntry = null;
try
{ fileEntry }, ap, new SequenceI[] { seq });
sc.mainFrame.dispose();
- sc.noChooserGUI = false;
}
}
git://source.jalview.org / jalview.git / blobdiff