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 javax.swing.SwingUtilities;
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;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
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;
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;
};
// 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);
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ boolean guessTFType = localPdbPaeMatrixFileName == null;
localPdbPaeMatrixFileName = guessPAEFilename();
+ guessTFType |= localPdbPaeMatrixFileName != null;
+ Regex alphaFold = JmolParser.getNewAlphafoldValidator();
+ if (guessTFType
+ && alphaFold.search(new File(selectedPdbFileName).getName())
+ && !tempFacAsChanged)
+ {
+ // localPdbPaeMatrixFileName was null and now isn't and filename could
+ // well be AlphaFold and user hasn't adjusted the tempFacType
+ combo_tempFacAs.setSelectedItem(TFType.PLDDT);
+ }
validateSelections();
}
}
/**
- * 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();
private String guessPAEFilename()
{
- if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb"))
+ if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb")
+ || selectedPdbFileName.toLowerCase(Locale.ROOT)
+ .endsWith(".cif"))
{
String jsonExt = selectedPdbFileName.substring(0,
selectedPdbFileName.length() - 4) + ".json";
{
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
}
else if (currentView == VIEWS_FROM_FILE)
{
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
+ StructureChooser sc = StructureChooser.this;
+ TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem();
+ String paeFilename = sc.localPdbPaeMatrixFileName;
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ SequenceI userSelectedSeq = assSeqOpt.getSequence();
if (userSelectedSeq != null)
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
+ String pdbFilename = selectedPdbFileName;
- sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
- ap, new SequenceI[]
- { selectedSequence });
+ StructureChooser.openStructureFileForSequence(ssm, sc, ap,
+ 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);
MessageManager.getString(
"status.fetching_3d_structures_for_selected_entries"),
progressId);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel,
+ viewerType);
}
else
{
setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
pdbEntriesToView[0].getId()), progressId);
- theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ // Can we pass a pre-computeMappinged pdbFile?
+ theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel,
+ viewerType);
}
setProgressBar(null, progressId);
// remember the last viewer we used...
@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()
/**
* Open a single structure file for a given sequence
*/
- public static void openStructureFileForSequence(AlignmentPanel ap,
- SequenceI seq, File sFile)
+ public static void openStructureFileForSequence(
+ StructureSelectionManager ssm, StructureChooser sc,
+ AlignmentPanel ap, SequenceI seq, boolean prompt,
+ String sFilename, TFType tft, String paeFilename,
+ boolean doXferSettings)
{
- // Open the chooser headlessly. Not sure this is actually needed ?
- StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
- ap, false);
- StructureSelectionManager ssm = ap.getStructureSelectionManager();
- PDBEntry fileEntry = null;
- try
- {
- fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
- sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
- Desktop.instance);
- } catch (Exception e)
- {
- Console.error("Could not open structure file '"
- + sFile.getAbsolutePath() + "'");
- return;
+ 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)
+ {
+ StructureViewer sv = null;
+ boolean headless = forceHeadless;
+ if (sc == null)
+ {
+ // headless = true;
+ prompt = false;
+ sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
+ }
+ if (ssm == null)
+ {
+ ssm = ap.getStructureSelectionManager();
}
- StructureViewer sViewer = sc.launchStructureViewer(ssm,
- new PDBEntry[]
- { fileEntry }, ap, new SequenceI[] { seq });
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
+ 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();
+
+ 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();
+ }
+
}
}
git://source.jalview.org / jalview.git / blobdiff