import java.awt.Container;
import java.io.File;
+import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.utils.UrlDownloadClient;
import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
Platform.cacheFileData(f);
}
}
+
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * Currently only used by Jmol - similar but different code used for Chimera/X
+ * and Pymol so still need to refactor
+ *
+ * @param structureViewer
+ * UI proxy for the structure viewer
+ * @return list of absolute paths to structures retrieved that need to be
+ * added to the display
+ */
+ public List<String> fetchPdbFiles(StructureViewerBase structureViewer)
+ {
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List<String> files = new ArrayList<>();
+ String pdbid = "";
+ try
+ {
+ String[] filesInViewer = getStructureFiles();
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ Pdb pdbclient = new Pdb();
+ EBIAlfaFold afclient = new EBIAlfaFold();
+
+ for (int pi = 0; pi < getPdbCount(); pi++)
+ {
+ String file = getPdbEntry(pi).getFile();
+ if (file == null)
+ {
+ // todo: extract block as method and pull up (also ChimeraViewFrame)
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ PDBEntry strucEntry = getPdbEntry(pi);
+ pdbid = strucEntry.getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ structureViewer.setProgressMessage(MessageManager
+ .formatMessage("status.fetching_pdb", new String[]
+ { pdbid }), hdl);
+ try
+ {
+ if (afclient.isValidReference(pdbid))
+ {
+ pdbseq = afclient.getSequenceRecords(pdbid);
+ } else {
+ if (strucEntry.hasRetrievalUrl())
+ {
+ File tmpFile = File.createTempFile(pdbid, ".cif");
+ String fromUrl = strucEntry.getRetrievalUrl();
+ UrlDownloadClient.download(fromUrl, tmpFile);
+
+ // may not need this check ?
+ file = tmpFile.getAbsolutePath();
+ if (file != null)
+ {
+ pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
+ }
+ } else {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
+ {
+ structureViewer.setProgressMessage(
+ MessageManager.getString("label.state_completed"), hdl);
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ getPdbEntry(pi).setFile(file);
+ files.add(file);
+ }
+ else
+ {
+ errormsgs.append("'").append(pdbid).append("' ");
+ }
+ }
+ else
+ {
+ if (filesInViewer != null && filesInViewer.length > 0)
+ {
+ structureViewer.setAddingStructures(true); // already files loaded.
+ for (int c = 0; c < filesInViewer.length; c++)
+ {
+ if (Platform.pathEquals(filesInViewer[c], file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.add(file);
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
+ }
+ if (errormsgs.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new String[]
+ { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return files;
+ }
+
}