X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=0aa4878d9263504541fa8bacf8f8a5ea6a76d328;hb=0ebbad305e982eeda562a1842362dc415c36cc8d;hp=9280caa42d0635708f6031e9c6ba3753e4ecd0c0;hpb=023163e0fe8837c1ddb75eb30abc058f7747b5c2;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 9280caa..0aa4878 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -25,10 +25,13 @@ import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.RenderingHints; import java.io.File; -import java.util.ArrayList; import java.util.List; +import java.util.Locale; import java.util.Map; +import java.util.concurrent.Executors; import javax.swing.JPanel; import javax.swing.JSplitPane; @@ -37,24 +40,22 @@ 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; import jalview.datamodel.StructureViewerModel.StructureData; -import jalview.fts.service.alphafold.AlphafoldRestClient; import jalview.gui.ImageExporter.ImageWriterI; import jalview.gui.StructureViewer.ViewerType; +import jalview.io.exceptions.ImageOutputException; import jalview.structure.StructureCommand; import jalview.structures.models.AAStructureBindingModel; import jalview.util.BrowserLauncher; import jalview.util.ImageMaker; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.ws.dbsources.EBIAlfaFold; -import jalview.ws.dbsources.Pdb; -import jalview.ws.utils.UrlDownloadClient; +import jalview.util.imagemaker.BitmapImageSizing; public class AppJmol extends StructureViewerBase { @@ -187,8 +188,7 @@ 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(), @@ -237,7 +237,6 @@ public class AppJmol extends StructureViewerBase openNewJmol(ap, alignAdded, pe, seqs); } - void initJmol(String command) { jmb.setFinishedInit(false); @@ -265,6 +264,8 @@ public class AppJmol extends StructureViewerBase } jmb.executeCommand(new StructureCommand(command), false); jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false); + jmb.executeCommand(new StructureCommand("set antialiasdisplay on"), + false); jmb.setFinishedInit(true); } @@ -274,7 +275,7 @@ public class AppJmol extends StructureViewerBase _started = true; try { - List files = fetchPdbFiles(); + List files = jmb.fetchPdbFiles(this); if (files.size() > 0) { showFilesInViewer(files); @@ -312,10 +313,10 @@ 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 +337,11 @@ 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 +357,7 @@ 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 @@ -366,9 +367,10 @@ public class AppJmol extends StructureViewerBase } if (waitTotal > waitMax) { - System.err.println("Timed out waiting for Jmol to load files after " - + waitTotal + "ms"); - // System.err.println("finished: " + jmb.isFinishedInit() + jalview.bin.Console.errPrintln( + "Timed out waiting for Jmol to load files after " + + waitTotal + "ms"); + // jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit() // + "; loaded: " + Arrays.toString(jmb.getPdbFile()) // + "; files: " + files.toString()); jmb.getStructureFiles(); @@ -420,155 +422,115 @@ 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). + * 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) * - * @return + * @param type */ - List fetchPdbFiles() + @Override + public void makePDBImage(ImageMaker.TYPE type) { - // 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) + makePDBImage(null, type, null, + BitmapImageSizing.defaultBitmapImageSizing()); + } catch (ImageOutputException ioex) { - 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); + Console.error("Unexpected error whilst writing " + type.toString(), + ioex); } - 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) - * - * @param type - */ - @Override - public void makePDBImage(ImageMaker.TYPE type) + public void makePDBImage(File file, ImageMaker.TYPE type, String renderer, + BitmapImageSizing userBis) throws ImageOutputException { int width = getWidth(); int height = getHeight(); + + BitmapImageSizing bis = ImageMaker.getScaleWidthHeight(width, height, + userBis); + float usescale = bis.scale(); + int usewidth = bis.width(); + int useheight = bis.height(); + ImageWriterI writer = new ImageWriterI() { @Override public void exportImage(Graphics g) throws Exception { - jmb.jmolViewer.renderScreenImage(g, width, height); + Graphics2D ig2 = (Graphics2D) g; + ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + if (type == TYPE.PNG && usescale > 0.0f) + { + // for a scaled image, this scales down a bigger image to give the + // right resolution + if (usescale > 0.0f) + { + ig2.scale(1 / usescale, 1 / usescale); + } + } + + jmb.jmolViewer.requestRepaintAndWait("image export"); + jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight); } }; - String view = MessageManager.getString("action.view").toLowerCase(); - ImageExporter exporter = new ImageExporter(writer, + String view = MessageManager.getString("action.view") + .toLowerCase(Locale.ROOT); + final ImageExporter exporter = new ImageExporter(writer, getProgressIndicator(), type, getTitle()); - exporter.doExport(null, this, width, height, view); + + final Throwable[] exceptions = new Throwable[1]; + exceptions[0] = null; + final AppJmol us = this; + try + { + Thread runner = Executors.defaultThreadFactory() + .newThread(new Runnable() + { + @Override + public void run() + { + try + { + exporter.doExport(file, us, width, height, view, + renderer, userBis); + } catch (Throwable t) + { + exceptions[0] = t; + } + } + }); + runner.start(); + long time = 0; + do + { + Thread.sleep(25); + } while (runner.isAlive() && time++ < 4000); + if (time >= 4000) + { + runner.interrupt(); + throw new ImageOutputException( + "Jmol took too long to export. Waited for 100 seconds."); + } + } catch (Throwable e) + { + throw new ImageOutputException( + "Unexpected error when generating image", e); + } + if (exceptions[0] != null) + { + if (exceptions[0] instanceof ImageOutputException) + { + throw ((ImageOutputException) exceptions[0]); + } + else + { + throw new ImageOutputException( + "Unexpected error when generating image", exceptions[0]); + } + } } @Override @@ -577,10 +539,11 @@ 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()); + jalview.bin.Console + .errPrintln("Show Jmol help failed with: " + ex.getMessage()); } } @@ -652,7 +615,8 @@ 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);