X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=950f1294aceaa5f57d96818348b18658e48cd419;hb=29bb043dfab1b0bdc1efca22f2e5e3d3e8549368;hp=7cf10e7d0bba59d73aa46eb98238b1303767d22c;hpb=7720585dc8cc56cdad2486b330ed37ddd0133531;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 7cf10e7..950f129 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -25,10 +25,19 @@ 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.lang.reflect.InvocationTargetException; import java.util.List; +import java.util.Locale; import java.util.Map; +import java.util.concurrent.Callable; +import java.util.concurrent.CompletableFuture; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.Future; +import java.util.concurrent.FutureTask; import javax.swing.JPanel; import javax.swing.JSplitPane; @@ -37,21 +46,22 @@ 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.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.Pdb; +import jalview.util.imagemaker.BitmapImageSizing; public class AppJmol extends StructureViewerBase { @@ -184,8 +194,7 @@ 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(), @@ -234,7 +243,6 @@ public class AppJmol extends StructureViewerBase openNewJmol(ap, alignAdded, pe, seqs); } - void initJmol(String command) { jmb.setFinishedInit(false); @@ -271,7 +279,7 @@ public class AppJmol extends StructureViewerBase _started = true; try { - List files = fetchPdbFiles(); + List files = jmb.fetchPdbFiles(this); if (files.size() > 0) { showFilesInViewer(files); @@ -309,10 +317,10 @@ 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; } @@ -333,11 +341,11 @@ 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; } @@ -353,7 +361,7 @@ 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 @@ -363,9 +371,9 @@ public class AppJmol extends StructureViewerBase } if (waitTotal > waitMax) { - System.err.println("Timed out waiting for Jmol to load files after " + jalview.bin.Console.errPrintln("Timed out waiting for Jmol to load files after " + waitTotal + "ms"); - // System.err.println("finished: " + jmb.isFinishedInit() + // jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit() // + "; loaded: " + Arrays.toString(jmb.getPdbFile()) // + "; files: " + files.toString()); jmb.getStructureFiles(); @@ -417,133 +425,102 @@ 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(); + try { + makePDBImage(null, type, null, + BitmapImageSizing.nullBitmapImageSizing()); + } catch (ImageOutputException ioex) { + Console.error("Unexpected error whilst writing "+type.toString(),ioex); + } + } - List files = new ArrayList<>(); - String pdbid = ""; - try + 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() { - String[] filesInViewer = jmb.getStructureFiles(); - // TODO: replace with reference fetching/transfer code (validate PDBentry - // as a DBRef?) - Pdb pdbclient = new Pdb(); - for (int pi = 0; pi < jmb.getPdbCount(); pi++) + @Override + public void exportImage(Graphics g) throws Exception { - String file = jmb.getPdbEntry(pi).getFile(); - if (file == null) + Graphics2D ig2 = (Graphics2D) g; + ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + if (type == TYPE.PNG && usescale > 0.0f) { - // todo: extract block as method and pull up (also ChimeraViewFrame) - // retrieve the pdb and store it locally - AlignmentI pdbseq = null; - pdbid = jmb.getPdbEntry(pi).getId(); - long hdl = pdbid.hashCode() - System.currentTimeMillis(); - setProgressMessage(MessageManager - .formatMessage("status.fetching_pdb", new String[] - { pdbid }), hdl); - try - { - 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) + // for a scaled image, this scales down a bigger image to give the + // right resolution + if (usescale > 0.0f) { - // 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("' "); + ig2.scale(1 / usescale, 1 / usescale); } } - else + + jmb.jmolViewer.antialiased = true; + jmb.jmolViewer.requestRepaintAndWait("image export"); + jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight); + } + }; + String view = MessageManager.getString("action.view") + .toLowerCase(Locale.ROOT); + final ImageExporter exporter = new ImageExporter(writer, + getProgressIndicator(), type, getTitle()); + + 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() { - if (filesInViewer != null && filesInViewer.length > 0) + try { - 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) + exporter.doExport(file, us, width, height, view, renderer, + userBis); + } catch (Throwable t) { - files.add(file); + exceptions[0] = t; } } - } - } 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) + }); + runner.start(); + do { Thread.sleep(25); } while (runner.isAlive()); + } catch (Throwable e) { - 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); + throw new ImageOutputException( + "Unexpected error when generating image", e); } - 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) - { - int width = getWidth(); - int height = getHeight(); - ImageWriterI writer = new ImageWriterI() + if (exceptions[0] != null) { - @Override - public void exportImage(Graphics g) throws Exception + if (exceptions[0] instanceof ImageOutputException) { - jmb.jmolViewer.renderScreenImage(g, width, height); + throw ((ImageOutputException) exceptions[0]); } - }; - String view = MessageManager.getString("action.view").toLowerCase(); - ImageExporter exporter = new ImageExporter(writer, - getProgressIndicator(), type, getTitle()); - exporter.doExport(null, this, width, height, view); + else + { + throw new ImageOutputException( + "Unexpected error when generating image", exceptions[0]); + } + } } @Override @@ -552,10 +529,10 @@ 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()); } } @@ -627,7 +604,8 @@ 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);