import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.io.File;
-import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
-import org.json.simple.parser.ParseException;
+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.AlignmentI;
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.FileFormatException;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.io.StructureFile;
import jalview.jbgui.FilterOption;
import jalview.jbgui.GStructureChooser;
import jalview.structure.StructureImportSettings.TFType;
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;
boolean guessTFType = localPdbPaeMatrixFileName == null;
localPdbPaeMatrixFileName = guessPAEFilename();
guessTFType |= localPdbPaeMatrixFileName != null;
+ Regex alphaFold = JmolParser.getNewAlphafoldValidator();
if (guessTFType
- && new File(selectedPdbFileName).getName().startsWith("AF-")
+ && alphaFold.search(new File(selectedPdbFileName).getName())
&& !tempFacAsChanged)
{
// localPdbPaeMatrixFileName was null and now isn't and filename could
}
/**
- * 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
}
else if (currentView == VIEWS_FROM_FILE)
{
-
- // TEMPFAC NOT WORKING
- TFType tft = (TFType) StructureChooser.this.combo_tempFacAs
- .getSelectedItem();
- if (tft != null && tft != TFType.DEFAULT)
- {
- ssm.setAddTempFacAnnot(true);
- }
-
+ 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);
-
- List<SequenceI> seqList = new ArrayList<>();
- seqList.add(selectedSequence);
- SequenceI[] seqArray = new SequenceI[] { selectedSequence };
- StructureFile sf = ssm.computeMapping(true, seqArray, null,
- selectedPdbFileName, DataSourceType.FILE, null);
- // EBIAlfaFold.addAlphaFoldPAEToStructure(pdbAlignment, pae, index,
- // structIdOrFile, isStructId);
- StructureMapping[] sm = ssm.getMapping(fileEntry.getFile());
- // DO SOMETHING WITH
- String paeFilename = StructureChooser.this.localPdbPaeMatrixFileName;
- File paeFile = paeFilename == null ? null : new File(paeFilename);
- if (paeFilename != null && paeFile.exists())
- {
- AlignmentI al = StructureChooser.this.ap.getAlignment();
- try
- {
- EBIAlfaFold.importPaeJSONAsContactMatrixToSequence(al,
- paeFile, -1, selectedSequence.getName());
- } catch (IOException | ParseException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
+ String pdbFilename = selectedPdbFileName;
- sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
- ap, new SequenceI[]
- { selectedSequence });
+ StructureChooser.openStructureFileForSequence(ssm, sc, ap,
+ selectedSequence, true, pdbFilename, tft, paeFilename);
}
SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
+ setProgressBar("Complete.", progress.hashCode());
closeAction(preferredHeight);
mainFrame.dispose();
}
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);
/**
* 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)
{
- // 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;
+ boolean headless = false;
+ if (sc == null)
+ {
+ headless = true;
+ sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
}
+ if (ssm == null)
+ ssm = ap.getStructureSelectionManager();
+
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
+ tft, paeFilename);
StructureViewer sViewer = sc.launchStructureViewer(ssm,
new PDBEntry[]
{ fileEntry }, ap, new SequenceI[] { seq });
- sc.mainFrame.dispose();
+ if (headless)
+ sc.mainFrame.dispose();
}
}
git://source.jalview.org / jalview.git / blobdiff