X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=037b97e1ce9c889037047c5bbea7839cec939cd7;hb=551b3a8e53ff6b43f9d0bce08759e46f49373bed;hp=34ff7b3eabe13ff1e54a726248b860ef89f81e40;hpb=1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b;p=jalview.git diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java index 34ff7b3..037b97e 100644 --- a/src/jalview/gui/AppJmolBinding.java +++ b/src/jalview/gui/AppJmolBinding.java @@ -22,24 +22,30 @@ package jalview.gui; import java.awt.Container; import java.io.File; -import java.io.FileWriter; -import java.io.IOException; +import java.util.ArrayList; +import java.util.List; import java.util.Map; import javax.swing.JComponent; import org.jmol.api.JmolAppConsoleInterface; -import org.jmol.java.BS; import org.openscience.jmol.app.jmolpanel.console.AppConsole; 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 { @@ -93,6 +99,11 @@ public class AppJmolBinding extends JalviewJmolBinding @Override public void refreshGUI() { + if (getMappedStructureCount() == 0) + { + // too soon! + return; + } // appJmolWindow.repaint(); javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -100,6 +111,7 @@ public class AppJmolBinding extends JalviewJmolBinding public void run() { JalviewStructureDisplayI theViewer = getViewer(); + // invokes colourbySequence() via seqColour_ActionPerformed() theViewer.updateTitleAndMenus(); ((JComponent) theViewer).revalidate(); } @@ -143,7 +155,9 @@ public class AppJmolBinding extends JalviewJmolBinding Container consolePanel, String buttonsToShow) { jmolViewer.setJmolCallbackListener(this); - return new AppConsole(jmolViewer, consolePanel, buttonsToShow); + // BH comment: can't do this yet [for JS only, or generally?] + return Platform.isJS() ? null + : new AppConsole(jmolViewer, consolePanel, buttonsToShow); } @Override @@ -169,31 +183,149 @@ public class AppJmolBinding extends JalviewJmolBinding return null; } + @SuppressWarnings("unused") + public void cacheFiles(List files) + { + if (files == null) + { + return; + } + for (File f : files) + { + Platform.cacheFileData(f); + } + } + /** - * Overrides the default method to save a session to file, in order to - * guarantee it is done synchronously. Jmol command 'write STATE path' would - * execute asynchronously, so instead we get the state and write it directly - * here. + * 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 */ - @Override - protected void saveSession(File f) + public List fetchPdbFiles(StructureViewerBase structureViewer) { - String state = jmolViewer.getStateInfo(); - if (state != null) + // todo - record which pdbids were successfully imported. + StringBuilder errormsgs = new StringBuilder(); + + List files = new ArrayList<>(); + String pdbid = ""; + try { - try - { - FileWriter fw = new FileWriter(f); - fw.write(state); - fw.close(); - } catch (IOException e) + 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++) { - Cache.log.error("Error writing Jmol state: " + e.toString()); + 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("'"); } - else + if (errormsgs.length() > 0) { - Cache.log.error("Error requesting Jmol state to save"); + 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; } + }