X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=64ea4dca9020017952cb47802aa6fa178a66f530;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=9280caa42d0635708f6031e9c6ba3753e4ecd0c0;hpb=023163e0fe8837c1ddb75eb30abc058f7747b5c2;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 9280caa..64ea4dc 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -20,13 +20,14 @@ */ package jalview.gui; +import java.util.Locale; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; import java.io.File; -import java.util.ArrayList; import java.util.List; import java.util.Map; @@ -37,8 +38,7 @@ import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; +import jalview.bin.Console; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.datamodel.StructureViewerModel; @@ -52,9 +52,6 @@ import jalview.util.BrowserLauncher; import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.ws.dbsources.EBIAlfaFold; -import jalview.ws.dbsources.Pdb; -import jalview.ws.utils.UrlDownloadClient; public class AppJmol extends StructureViewerBase { @@ -187,8 +184,7 @@ public class AppJmol extends StructureViewerBase } private void openNewJmol(AlignmentPanel ap, boolean alignAdded, - PDBEntry[] pdbentrys, - SequenceI[][] seqs) + PDBEntry[] pdbentrys, SequenceI[][] seqs) { setProgressIndicator(ap.alignFrame); jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), @@ -206,7 +202,7 @@ public class AppJmol extends StructureViewerBase setSize(400, 400); // probably should be a configurable/dynamic default here initMenus(); addingStructures = false; - worker = new Thread(this); + worker = new Thread(this, "OpenJmol"); worker.start(); this.addInternalFrameListener(new InternalFrameAdapter() @@ -237,7 +233,6 @@ public class AppJmol extends StructureViewerBase openNewJmol(ap, alignAdded, pe, seqs); } - void initJmol(String command) { jmb.setFinishedInit(false); @@ -274,7 +269,7 @@ public class AppJmol extends StructureViewerBase _started = true; try { - List files = fetchPdbFiles(); + List files = jmb.fetchPdbFiles(this); if (files.size() > 0) { showFilesInViewer(files); @@ -312,10 +307,10 @@ public class AppJmol extends StructureViewerBase } catch (OutOfMemoryError oomerror) { new OOMWarning("When trying to open the Jmol viewer!", oomerror); - Cache.log.debug("File locations are " + filesString); + Console.debug("File locations are " + filesString); } catch (Exception ex) { - Cache.log.error("Couldn't open Jmol viewer!", ex); + Console.error("Couldn't open Jmol viewer!", ex); ex.printStackTrace(); return; } @@ -336,11 +331,11 @@ public class AppJmol extends StructureViewerBase { new OOMWarning("When trying to add structures to the Jmol viewer!", oomerror); - Cache.log.debug("File locations are " + filesString); + Console.debug("File locations are " + filesString); return; } catch (Exception ex) { - Cache.log.error("Couldn't add files to Jmol viewer!", ex); + Console.error("Couldn't add files to Jmol viewer!", ex); ex.printStackTrace(); return; } @@ -356,7 +351,7 @@ public class AppJmol extends StructureViewerBase { try { - Cache.log.debug("Waiting around for jmb notify."); + Console.debug("Waiting around for jmb notify."); waitTotal += waitFor; // Thread.sleep() throws an exception in JS @@ -420,132 +415,6 @@ public class AppJmol extends StructureViewerBase } /** - * 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). - * - * @return - */ - List fetchPdbFiles() - { - // todo - record which pdbids were successfully imported. - StringBuilder errormsgs = new StringBuilder(); - - List files = new ArrayList<>(); - String pdbid = ""; - try - { - String[] filesInViewer = jmb.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 < jmb.getPdbCount(); pi++) - { - String file = jmb.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 = jmb.getPdbEntry(pi); - pdbid = strucEntry.getId(); - long hdl = pdbid.hashCode() - System.currentTimeMillis(); - 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 - { - 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(); - jmb.getPdbEntry(pi).setFile(file); - files.add(file); - } - else - { - errormsgs.append("'").append(pdbid).append("' "); - } - } - else - { - if (filesInViewer != null && filesInViewer.length > 0) - { - addingStructures = 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; - } - - /** * Outputs the Jmol viewer image as an image file, after prompting the user to * choose a file and (for EPS) choice of Text or Lineart character rendering * (unless a preference for this is set) @@ -565,7 +434,8 @@ public class AppJmol extends StructureViewerBase jmb.jmolViewer.renderScreenImage(g, width, height); } }; - String view = MessageManager.getString("action.view").toLowerCase(); + String view = MessageManager.getString("action.view") + .toLowerCase(Locale.ROOT); ImageExporter exporter = new ImageExporter(writer, getProgressIndicator(), type, getTitle()); exporter.doExport(null, this, width, height, view); @@ -577,7 +447,7 @@ public class AppJmol extends StructureViewerBase try { BrowserLauncher // BH 2018 - .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/"); + .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { System.err.println("Show Jmol help failed with: " + ex.getMessage()); @@ -652,7 +522,8 @@ public class AppJmol extends StructureViewerBase } } } - else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit()) + else if (jmb == null || jmb.jmolViewer == null + || !jmb.isFinishedInit()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height);