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Coverage Report

  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.gui

File AppJmol.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
30% of files have more coverage

Code metrics

58
224
24
2
689
541
74
0.33
9.33
12
3.08

Classes

Class Line # Actions
AppJmol 61 198 64
0.6840148668.4%
AppJmol.RenderPanel 611 26 10
0.4324324443.2%
 

Contributing tests

This file is covered by 47 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.gui;
22   
23    import java.awt.BorderLayout;
24    import java.awt.Color;
25    import java.awt.Dimension;
26    import java.awt.Font;
27    import java.awt.Graphics;
28    import java.awt.Graphics2D;
29    import java.awt.RenderingHints;
30    import java.io.File;
31    import java.util.List;
32    import java.util.Locale;
33    import java.util.Map;
34    import java.util.concurrent.Executors;
35   
36    import javax.swing.JPanel;
37    import javax.swing.JSplitPane;
38    import javax.swing.SwingUtilities;
39    import javax.swing.event.InternalFrameAdapter;
40    import javax.swing.event.InternalFrameEvent;
41   
42    import jalview.api.AlignmentViewPanel;
43    import jalview.bin.Console;
44    import jalview.datamodel.PDBEntry;
45    import jalview.datamodel.SequenceI;
46    import jalview.datamodel.StructureViewerModel;
47    import jalview.datamodel.StructureViewerModel.StructureData;
48    import jalview.ext.jmol.JmolCommands;
49    import jalview.gui.ImageExporter.ImageWriterI;
50    import jalview.gui.StructureViewer.ViewerType;
51    import jalview.io.exceptions.ImageOutputException;
52    import jalview.structure.StructureCommand;
53    import jalview.structures.models.AAStructureBindingModel;
54    import jalview.util.BrowserLauncher;
55    import jalview.util.ImageMaker;
56    import jalview.util.ImageMaker.TYPE;
57    import jalview.util.MessageManager;
58    import jalview.util.Platform;
59    import jalview.util.imagemaker.BitmapImageSizing;
60   
 
61    public class AppJmol extends StructureViewerBase
62    {
63    // ms to wait for Jmol to load files
64    private static final int JMOL_LOAD_TIMEOUT = 20000;
65   
66    private static final String SPACE = " ";
67   
68    private static final String QUOTE = "\"";
69   
70    AppJmolBinding jmb;
71   
72    JPanel scriptWindow;
73   
74    JSplitPane splitPane;
75   
76    RenderPanel renderPanel;
77   
78    /**
79    *
80    * @param files
81    * @param ids
82    * @param seqs
83    * @param ap
84    * @param usetoColour
85    * - add the alignment panel to the list used for colouring these
86    * structures
87    * @param useToAlign
88    * - add the alignment panel to the list used for aligning these
89    * structures
90    * @param leaveColouringToJmol
91    * - do not update the colours from any other source. Jmol is
92    * handling them
93    * @param loadStatus
94    * @param bounds
95    * @param viewid
96    */
 
97  7 toggle public AppJmol(StructureViewerModel viewerModel, AlignmentPanel ap,
98    String sessionFile, String viewid)
99    {
100  7 Map<File, StructureData> pdbData = viewerModel.getFileData();
101  7 PDBEntry[] pdbentrys = new PDBEntry[pdbData.size()];
102  7 SequenceI[][] seqs = new SequenceI[pdbData.size()][];
103  7 int i = 0;
104  7 for (StructureData data : pdbData.values())
105    {
106  7 PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
107    PDBEntry.Type.PDB, data.getFilePath());
108  7 pdbentrys[i] = pdbentry;
109  7 List<SequenceI> sequencesForPdb = data.getSeqList();
110  7 seqs[i] = sequencesForPdb
111    .toArray(new SequenceI[sequencesForPdb.size()]);
112  7 i++;
113    }
114   
115    // TODO: check if protocol is needed to be set, and if chains are
116    // autodiscovered.
117  7 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
118    pdbentrys, seqs, null);
119   
120  7 jmb.setLoadingFromArchive(true);
121  7 addAlignmentPanel(ap);
122  7 if (viewerModel.isAlignWithPanel())
123    {
124  0 useAlignmentPanelForSuperposition(ap);
125    }
126  7 initMenus();
127  7 boolean useToColour = viewerModel.isColourWithAlignPanel();
128  7 boolean leaveColouringToJmol = viewerModel.isColourByViewer();
129  7 if (leaveColouringToJmol || !useToColour)
130    {
131  7 jmb.setColourBySequence(false);
132  7 seqColour.setSelected(false);
133  7 viewerColour.setSelected(true);
134    }
135  0 else if (useToColour)
136    {
137  0 useAlignmentPanelForColourbyseq(ap);
138  0 jmb.setColourBySequence(true);
139  0 seqColour.setSelected(true);
140  0 viewerColour.setSelected(false);
141    }
142   
143  7 this.setBounds(viewerModel.getX(), viewerModel.getY(),
144    viewerModel.getWidth(), viewerModel.getHeight());
145  7 setViewId(viewid);
146   
147  7 this.addInternalFrameListener(new InternalFrameAdapter()
148    {
 
149  7 toggle @Override
150    public void internalFrameClosing(
151    InternalFrameEvent internalFrameEvent)
152    {
153  7 closeViewer(false);
154    }
155    });
156  7 StringBuilder cmd = new StringBuilder();
157  7 cmd.append(jmb.getCommandGenerator().loadFile(sessionFile));
158  7 initJmol(cmd.toString());
159    }
160   
 
161  62 toggle @Override
162    protected void initMenus()
163    {
164  62 super.initMenus();
165   
166  62 viewerColour
167    .setText(MessageManager.getString("label.colour_with_jmol"));
168  62 viewerColour.setToolTipText(MessageManager
169    .getString("label.let_jmol_manage_structure_colours"));
170    }
171   
172    /**
173    * display a single PDB structure in a new Jmol view
174    *
175    * @param pdbentry
176    * @param seq
177    * @param chains
178    * @param ap
179    */
 
180  50 toggle public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
181    final AlignmentPanel ap)
182    {
183  50 setProgressIndicator(ap.alignFrame);
184   
185  50 openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
186    new SequenceI[][]
187    { seq });
188    }
189   
 
190  55 toggle private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
191    PDBEntry[] pdbentrys, SequenceI[][] seqs)
192    {
193  55 setProgressIndicator(ap.alignFrame);
194  55 jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
195    pdbentrys, seqs, null);
196  55 addAlignmentPanel(ap);
197  55 useAlignmentPanelForColourbyseq(ap);
198   
199  55 alignAddedStructures = alignAdded;
200  55 if (pdbentrys.length > 1)
201    {
202  5 useAlignmentPanelForSuperposition(ap);
203    }
204   
205  55 jmb.setColourBySequence(true);
206  55 setSize(400, 400); // probably should be a configurable/dynamic default here
207  55 initMenus();
208  55 addingStructures = false;
209  55 worker = new Thread(this);
210  55 worker.start();
211   
212  55 this.addInternalFrameListener(new InternalFrameAdapter()
213    {
 
214  31 toggle @Override
215    public void internalFrameClosing(
216    InternalFrameEvent internalFrameEvent)
217    {
218  31 closeViewer(false);
219    }
220    });
221   
222    }
223   
224    /**
225    * create a new Jmol containing several structures optionally superimposed
226    * using the given alignPanel.
227    *
228    * @param ap
229    * @param alignAdded
230    * - true to superimpose
231    * @param pe
232    * @param seqs
233    */
 
234  5 toggle public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
235    SequenceI[][] seqs)
236    {
237  5 openNewJmol(ap, alignAdded, pe, seqs);
238    }
239   
 
240  62 toggle void initJmol(String command)
241    {
242  62 jmb.setFinishedInit(false);
243  62 renderPanel = new RenderPanel();
244    // TODO: consider waiting until the structure/view is fully loaded before
245    // displaying
246  62 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
247  62 jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
248    getBounds().width, getBounds().height);
249  62 if (scriptWindow == null)
250    {
251  62 BorderLayout bl = new BorderLayout();
252  62 bl.setHgap(0);
253  62 bl.setVgap(0);
254  62 scriptWindow = new JPanel(bl);
255  62 scriptWindow.setVisible(false);
256    }
257   
258  62 jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
259    null);
260    // jmb.newJmolPopup("Jmol");
261  62 if (command == null)
262    {
263  0 command = "";
264    }
265  62 jmb.executeCommand(new StructureCommand(command), false);
266  62 jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
267  62 jmb.executeCommand(new StructureCommand("set antialiasdisplay on"),
268    false);
269  62 jmb.setFinishedInit(true);
270    }
271   
 
272  60 toggle @Override
273    public void run()
274    {
275  60 _started = true;
276  60 try
277    {
278  60 List<String> files = jmb.fetchPdbFiles(this);
279  60 if (files.size() > 0)
280    {
281  60 showFilesInViewer(files);
282    }
283    } finally
284    {
285  60 _started = false;
286  60 worker = null;
287    }
288    }
289   
290    /**
291    * Either adds the given files to a structure viewer or opens a new viewer to
292    * show them
293    *
294    * @param files
295    * list of absolute paths to structure files
296    */
 
297  60 toggle void showFilesInViewer(List<String> files)
298    {
299  60 long lastnotify = jmb.getLoadNotifiesHandled();
300  60 StringBuilder fileList = new StringBuilder();
301  60 for (String s : files)
302    {
303  70 fileList.append(SPACE).append(QUOTE)
304    .append(JmolCommands.escapeQuotedFilename(s)).append(QUOTE);
305    }
306  60 String filesString = fileList.toString();
307   
308  60 if (!addingStructures)
309    {
310  55 try
311    {
312  55 initJmol("load FILES " + filesString);
313    } catch (OutOfMemoryError oomerror)
314    {
315  0 new OOMWarning("When trying to open the Jmol viewer!", oomerror);
316  0 Console.debug("File locations are " + filesString);
317    } catch (Exception ex)
318    {
319  0 Console.error("Couldn't open Jmol viewer!", ex);
320  0 ex.printStackTrace();
321  0 return;
322    }
323    }
324    else
325    {
326  5 StringBuilder cmd = new StringBuilder();
327  5 cmd.append("loadingJalviewdata=true\nload APPEND ");
328  5 cmd.append(filesString);
329  5 cmd.append("\nloadingJalviewdata=null");
330  5 final StructureCommand command = new StructureCommand(cmd.toString());
331  5 lastnotify = jmb.getLoadNotifiesHandled();
332   
333  5 try
334    {
335  5 jmb.executeCommand(command, false);
336    } catch (OutOfMemoryError oomerror)
337    {
338  0 new OOMWarning("When trying to add structures to the Jmol viewer!",
339    oomerror);
340  0 Console.debug("File locations are " + filesString);
341  0 return;
342    } catch (Exception ex)
343    {
344  0 Console.error("Couldn't add files to Jmol viewer!", ex);
345  0 ex.printStackTrace();
346  0 return;
347    }
348    }
349   
350    // need to wait around until script has finished
351  60 int waitMax = JMOL_LOAD_TIMEOUT;
352  60 int waitFor = 35;
353  60 int waitTotal = 0;
354  223 while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
355    : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
356    && jmb.getStructureFiles().length == files.size()))
357    {
358  163 try
359    {
360  163 Console.debug("Waiting around for jmb notify.");
361  163 waitTotal += waitFor;
362   
363    // Thread.sleep() throws an exception in JS
364  163 Thread.sleep(waitFor);
365    } catch (Exception e)
366    {
367    }
368  163 if (waitTotal > waitMax)
369    {
370  0 jalview.bin.Console.errPrintln(
371    "Timed out waiting for Jmol to load files after "
372    + waitTotal + "ms");
373    // jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit()
374    // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
375    // + "; files: " + files.toString());
376  0 jmb.getStructureFiles();
377  0 break;
378    }
379    }
380   
381    // refresh the sequence colours for the new structure(s)
382  60 for (AlignmentViewPanel ap : _colourwith)
383    {
384  59 jmb.updateColours(ap);
385    }
386    // do superposition if asked to
387  58 if (alignAddedStructures)
388    {
389  3 alignAddedStructures();
390    }
391  58 addingStructures = false;
392    }
393   
394    /**
395    * Queues a thread to align structures with Jalview alignments
396    */
 
397  3 toggle void alignAddedStructures()
398    {
399  3 javax.swing.SwingUtilities.invokeLater(new Runnable()
400    {
 
401  5 toggle @Override
402    public void run()
403    {
404  5 if (jmb.jmolViewer.isScriptExecuting())
405    {
406  2 SwingUtilities.invokeLater(this);
407  2 try
408    {
409  2 Thread.sleep(5);
410    } catch (InterruptedException q)
411    {
412    }
413  2 return;
414    }
415    else
416    {
417  3 alignStructsWithAllAlignPanels();
418    }
419    }
420    });
421   
422    }
423   
 
424  0 toggle public boolean isRepainting()
425    {
426  0 if (renderPanel != null && renderPanel.isVisible())
427    {
428  0 return renderPanel.repainting;
429    }
430  0 return false;
431    }
432   
433    /**
434    * Outputs the Jmol viewer image as an image file, after prompting the user to
435    * choose a file and (for EPS) choice of Text or Lineart character rendering
436    * (unless a preference for this is set)
437    *
438    * @param type
439    */
 
440  0 toggle @Override
441    public void makePDBImage(ImageMaker.TYPE type)
442    {
443  0 Runnable exporter = new Runnable()
444    {
 
445  0 toggle @Override
446    public void run()
447    {
448  0 while (!isRepainting())
449    {
450  0 try
451    {
452  0 Thread.sleep(2);
453    } catch (Exception q)
454    {
455    }
456    }
457  0 try
458    {
459  0 makePDBImage(null, type, null,
460    BitmapImageSizing.defaultBitmapImageSizing());
461    } catch (ImageOutputException ioex)
462    {
463  0 Console.error(
464    "Unexpected error whilst writing " + type.toString(),
465    ioex);
466    }
467    }
468    };
469   
470  0 Executors.newCachedThreadPool().execute(exporter);
471    }
472   
 
473  10 toggle public void makePDBImage(File file, ImageMaker.TYPE type, String renderer,
474    BitmapImageSizing userBis) throws ImageOutputException
475    {
476  10 int width = getWidth();
477  10 int height = getHeight();
478   
479  10 BitmapImageSizing bis = ImageMaker.getScaleWidthHeight(width, height,
480    userBis);
481  10 float usescale = bis.scale();
482  10 int usewidth = bis.width();
483  10 int useheight = bis.height();
484   
485  10 ImageWriterI writer = new ImageWriterI()
486    {
 
487  10 toggle @Override
488    public void exportImage(Graphics g) throws Exception
489    {
490  10 Graphics2D ig2 = (Graphics2D) g;
491  10 ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
492    RenderingHints.VALUE_ANTIALIAS_ON);
493  10 if (type == TYPE.PNG && usescale > 0.0f)
494    {
495    // for a scaled image, this scales down a bigger image to give the
496    // right resolution
497  4 if (usescale > 0.0f)
498    {
499  4 ig2.scale(1 / usescale, 1 / usescale);
500    }
501    }
502   
503  10 jmb.jmolViewer.requestRepaintAndWait("image export");
504  10 jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight);
505    }
506    };
507  10 String view = MessageManager.getString("action.view")
508    .toLowerCase(Locale.ROOT);
509  10 final ImageExporter exporter = new ImageExporter(writer,
510    getProgressIndicator(), type, getTitle());
511   
512  10 final Throwable[] exceptions = new Throwable[1];
513  10 exceptions[0] = null;
514  10 final AppJmol us = this;
515  10 try
516    {
517  10 Thread runner = Executors.defaultThreadFactory()
518    .newThread(new Runnable()
519    {
 
520  10 toggle @Override
521    public void run()
522    {
523  10 try
524    {
525  10 exporter.doExport(file, us, width, height, view,
526    renderer, userBis);
527    } catch (Throwable t)
528    {
529  0 exceptions[0] = t;
530    }
531    }
532    });
533  10 runner.start();
534  10 long time = 0;
535  10 do
536    {
537  402 Thread.sleep(25);
538  402 } while (runner.isAlive() && time++ < 4000);
539  10 if (time >= 4000)
540    {
541  0 runner.interrupt();
542  0 throw new ImageOutputException(
543    "Jmol took too long to export. Waited for 100 seconds.");
544    }
545    } catch (Throwable e)
546    {
547  0 throw new ImageOutputException(
548    "Unexpected error when generating image", e);
549    }
550  10 if (exceptions[0] != null)
551    {
552  0 if (exceptions[0] instanceof ImageOutputException)
553    {
554  0 throw ((ImageOutputException) exceptions[0]);
555    }
556    else
557    {
558  0 throw new ImageOutputException(
559    "Unexpected error when generating image", exceptions[0]);
560    }
561    }
562    }
563   
 
564  0 toggle @Override
565    public void showHelp_actionPerformed()
566    {
567  0 try
568    {
569  0 BrowserLauncher // BH 2018
570    .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
571    } catch (Exception ex)
572    {
573  0 jalview.bin.Console
574    .errPrintln("Show Jmol help failed with: " + ex.getMessage());
575    }
576    }
577   
 
578  0 toggle @Override
579    public void showConsole(boolean showConsole)
580    {
581  0 if (showConsole)
582    {
583  0 if (splitPane == null)
584    {
585  0 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
586  0 splitPane.setTopComponent(renderPanel);
587  0 splitPane.setBottomComponent(scriptWindow);
588  0 this.getContentPane().add(splitPane, BorderLayout.CENTER);
589  0 splitPane.setDividerLocation(getHeight() - 200);
590  0 scriptWindow.setVisible(true);
591  0 scriptWindow.validate();
592  0 splitPane.validate();
593    }
594   
595    }
596    else
597    {
598  0 if (splitPane != null)
599    {
600  0 splitPane.setVisible(false);
601    }
602   
603  0 splitPane = null;
604   
605  0 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
606    }
607   
608  0 validate();
609    }
610   
 
611    class RenderPanel extends JPanel
612    {
613    final Dimension currentSize = new Dimension();
614   
 
615  624 toggle @Override
616    public void paintComponent(Graphics g)
617    {
618  624 getSize(currentSize);
619   
620  624 if (jmb != null && jmb.hasFileLoadingError())
621    {
622  0 g.setColor(Color.black);
623  0 g.fillRect(0, 0, currentSize.width, currentSize.height);
624  0 g.setColor(Color.white);
625  0 g.setFont(new Font("Verdana", Font.BOLD, 14));
626  0 g.drawString(MessageManager.getString("label.error_loading_file")
627    + "...", 20, currentSize.height / 2);
628  0 StringBuffer sb = new StringBuffer();
629  0 int lines = 0;
630  0 for (int e = 0; e < jmb.getPdbCount(); e++)
631    {
632  0 sb.append(jmb.getPdbEntry(e).getId());
633  0 if (e < jmb.getPdbCount() - 1)
634    {
635  0 sb.append(",");
636    }
637   
638  0 if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
639    {
640  0 lines++;
641  0 g.drawString(sb.toString(), 20, currentSize.height / 2
642    - lines * g.getFontMetrics().getHeight());
643    }
644    }
645    }
646  624 else if (jmb == null || jmb.jmolViewer == null
647    || !jmb.isFinishedInit())
648    {
649  52 g.setColor(Color.black);
650  52 g.fillRect(0, 0, currentSize.width, currentSize.height);
651  52 g.setColor(Color.white);
652  52 g.setFont(new Font("Verdana", Font.BOLD, 14));
653  52 g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
654    20, currentSize.height / 2);
655    }
656    else
657    {
658  572 repainting = true;
659  572 synchronized (jmb)
660    {
661  572 jmb.jmolViewer.renderScreenImage(g, currentSize.width,
662    currentSize.height);
663   
664    }
665  572 repainting = false;
666    }
667    }
668   
669    volatile boolean repainting = false;
670    }
671   
 
672  2534 toggle @Override
673    public AAStructureBindingModel getBinding()
674    {
675  2534 return this.jmb;
676    }
677   
 
678  68 toggle @Override
679    public ViewerType getViewerType()
680    {
681  68 return ViewerType.JMOL;
682    }
683   
 
684  202 toggle @Override
685    protected String getViewerName()
686    {
687  202 return "Jmol";
688    }
689    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.