import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
+import com.stevesoft.pat.Regex;
+
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.datamodel.PDBEntry;
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.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;
// 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);
+ 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
+ */
+ @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")
+ || selectedPdbFileName.toLowerCase(Locale.ROOT)
+ .endsWith(".cif"))
+ {
+ 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);
- setPdbOptionsEnabled(false);
+ // 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);
- setPdbOptionsEnabled(false);
+ // 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
}
else if (currentView == VIEWS_FROM_FILE)
{
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
+ TFType tft = (TFType) StructureChooser.this.combo_tempFacAs
+ .getSelectedItem();
+ String paeFilename = StructureChooser.this.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;
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(pdbFilename, DataSourceType.FILE,
+ selectedSequence, true, Desktop.instance, tft,
+ paeFilename);
+
+ /*
+ SequenceI[] seqArray = new SequenceI[] { selectedSequence };
+
+ StructureFile sf = ssm.computeMapping(true, seqArray, null,
+ selectedPdbFileName, DataSourceType.FILE, null, tft,
+ paeFilename);
+ StructureMapping[] sm = ssm.getMapping(fileEntry.getFile());
+ // DO SOMETHING WITH
+ File paeFile = paeFilename == null ? null : new File(paeFilename);
+ if (paeFilename != null && paeFile.exists())
+ {
+ AlignmentI al = StructureChooser.this.ap.getAlignment();
+ try
+ {
+ EBIAlfaFold.importPaeJSONAsContactMatrixToSequence(al,
+ paeFile, selectedSequence);
+ } catch (IOException | ParseException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ */
sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
ap, new SequenceI[]
{ selectedSequence });
for (SequenceI seq : sequences)
{
PDBEntry pdbe = pdbEntriesToView[p++];
+ Console.debug(
+ "##### pdbe=" + pdbe == null ? null : pdbe.toString());
+ Console.debug("##### pdbe.getFile()=" + pdbe == null ? null
+ : pdbe.getFile());
if (pdbe != null && pdbe.getFile() != null)
{
StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
pdbEntriesToView[0].getId()), progressId);
+ // Can we pass a pre-computeMappinged pdbFile?
theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
setProgressBar(null, progressId);