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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.bin

File Jalview.java

 

Coverage histogram

../../img/srcFileCovDistChart5.png
39% of files have more coverage

Code metrics

172
416
34
2
1,229
973
158
0.38
12.24
17
4.65

Classes

Class Line # Actions
Jalview 89 403 154
0.49256249.3%
Jalview.FeatureFetcher 138 13 4
0.00%
 

Contributing tests

This file is covered by 104 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.bin;
22   
23    import java.io.BufferedReader;
24    import java.io.File;
25    import java.io.FileOutputStream;
26    import java.io.IOException;
27    import java.io.InputStreamReader;
28    import java.io.OutputStreamWriter;
29    import java.io.PrintWriter;
30    import java.net.MalformedURLException;
31    import java.net.URI;
32    import java.net.URISyntaxException;
33    import java.net.URL;
34    import java.security.AllPermission;
35    import java.security.CodeSource;
36    import java.security.PermissionCollection;
37    import java.security.Permissions;
38    import java.security.Policy;
39    import java.util.HashMap;
40    import java.util.Map;
41    import java.util.Vector;
42    import java.util.logging.ConsoleHandler;
43    import java.util.logging.Level;
44    import java.util.logging.Logger;
45   
46    import javax.swing.UIManager;
47    import javax.swing.UIManager.LookAndFeelInfo;
48   
49    import com.threerings.getdown.util.LaunchUtil;
50   
51    import groovy.lang.Binding;
52    import groovy.util.GroovyScriptEngine;
53    import jalview.ext.so.SequenceOntology;
54    import jalview.gui.AlignFrame;
55    import jalview.gui.Desktop;
56    import jalview.gui.PromptUserConfig;
57    import jalview.io.AppletFormatAdapter;
58    import jalview.io.BioJsHTMLOutput;
59    import jalview.io.DataSourceType;
60    import jalview.io.FileFormat;
61    import jalview.io.FileFormatException;
62    import jalview.io.FileFormatI;
63    import jalview.io.FileLoader;
64    import jalview.io.HtmlSvgOutput;
65    import jalview.io.IdentifyFile;
66    import jalview.io.NewickFile;
67    import jalview.io.gff.SequenceOntologyFactory;
68    import jalview.schemes.ColourSchemeI;
69    import jalview.schemes.ColourSchemeProperty;
70    import jalview.util.MessageManager;
71    import jalview.util.Platform;
72    import jalview.ws.jws2.Jws2Discoverer;
73   
74    /**
75    * Main class for Jalview Application <br>
76    * <br>
77    * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
78    * jalview.bin.Jalview
79    *
80    * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
81    * jalview.bin.Jalview jalview.bin.Jalview
82    *
83    * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
84    * embellish '*' to e.g. '*.jar')
85    *
86    * @author $author$
87    * @version $Revision$
88    */
 
89    public class Jalview
90    {
 
91  19 toggle static
92    {
93  19 Platform.getURLCommandArguments();
94    }
95   
96    // singleton instance of this class
97   
98    private static Jalview instance;
99   
100    private Desktop desktop;
101   
102    public static AlignFrame currentAlignFrame;
103   
 
104  19 toggle static
105    {
106  19 if (!Platform.isJS())
107    /**
108    * Java only
109    *
110    * @j2sIgnore
111    */
112    {
113    // grab all the rights we can for the JVM
114  19 Policy.setPolicy(new Policy()
115    {
 
116  0 toggle @Override
117    public PermissionCollection getPermissions(CodeSource codesource)
118    {
119  0 Permissions perms = new Permissions();
120  0 perms.add(new AllPermission());
121  0 return (perms);
122    }
123   
 
124  0 toggle @Override
125    public void refresh()
126    {
127    }
128    });
129    }
130    }
131   
132    /**
133    * keep track of feature fetching tasks.
134    *
135    * @author JimP
136    *
137    */
 
138    class FeatureFetcher
139    {
140    /*
141    * TODO: generalise to track all jalview events to orchestrate batch processing
142    * events.
143    */
144   
145    private int queued = 0;
146   
147    private int running = 0;
148   
 
149  0 toggle public FeatureFetcher()
150    {
151   
152    }
153   
 
154  0 toggle public void addFetcher(final AlignFrame af,
155    final Vector<String> dasSources)
156    {
157  0 final long id = System.currentTimeMillis();
158  0 queued++;
159  0 final FeatureFetcher us = this;
160  0 new Thread(new Runnable()
161    {
162   
 
163  0 toggle @Override
164    public void run()
165    {
166  0 synchronized (us)
167    {
168  0 queued--;
169  0 running++;
170    }
171   
172  0 af.setProgressBar(MessageManager
173    .getString("status.das_features_being_retrived"), id);
174  0 af.featureSettings_actionPerformed(null);
175  0 af.setProgressBar(null, id);
176  0 synchronized (us)
177    {
178  0 running--;
179    }
180    }
181    }).start();
182    }
183   
 
184  0 toggle public synchronized boolean allFinished()
185    {
186  0 return queued == 0 && running == 0;
187    }
188   
189    }
190   
 
191  0 toggle public static Jalview getInstance()
192    {
193  0 return instance;
194    }
195   
196    /**
197    * main class for Jalview application
198    *
199    * @param args
200    * open <em>filename</em>
201    */
 
202  35 toggle public static void main(String[] args)
203    {
204    // setLogging(); // BH - for event debugging in JavaScript
205  35 instance = new Jalview();
206  35 instance.doMain(args);
207    }
208   
 
209  0 toggle private static void logClass(String name)
210    {
211    // BH - for event debugging in JavaScript
212  0 ConsoleHandler consoleHandler = new ConsoleHandler();
213  0 consoleHandler.setLevel(Level.ALL);
214  0 Logger logger = Logger.getLogger(name);
215  0 logger.setLevel(Level.ALL);
216  0 logger.addHandler(consoleHandler);
217    }
218   
 
219  0 toggle @SuppressWarnings("unused")
220    private static void setLogging()
221    {
222   
223    /**
224    * @j2sIgnore
225    *
226    */
227    {
228  0 System.out.println("not in js");
229    }
230   
231    // BH - for event debugging in JavaScript (Java mode only)
232  0 if (!Platform.isJS())
233    /**
234    * Java only
235    *
236    * @j2sIgnore
237    */
238    {
239  0 Logger.getLogger("").setLevel(Level.ALL);
240  0 logClass("java.awt.EventDispatchThread");
241  0 logClass("java.awt.EventQueue");
242  0 logClass("java.awt.Component");
243  0 logClass("java.awt.focus.Component");
244  0 logClass("java.awt.focus.DefaultKeyboardFocusManager");
245    }
246   
247    }
248   
249    /**
250    * @param args
251    */
 
252  35 toggle void doMain(String[] args)
253    {
254   
255  35 if (!Platform.isJS())
256    {
257  35 System.setSecurityManager(null);
258    }
259   
260  35 System.out
261    .println("Java version: " + System.getProperty("java.version"));
262  35 System.out.println("Java Home: " + System.getProperty("java.home"));
263  35 System.out.println(System.getProperty("os.arch") + " "
264    + System.getProperty("os.name") + " "
265    + System.getProperty("os.version"));
266  35 String val = System.getProperty("sys.install4jVersion");
267  35 if (val != null)
268    {
269  0 System.out.println("Install4j version: " + val);
270    }
271  35 val = System.getProperty("installer_template_version");
272  35 if (val != null)
273    {
274  0 System.out.println("Install4j template version: " + val);
275    }
276  35 val = System.getProperty("launcher_version");
277  35 if (val != null)
278    {
279  0 System.out.println("Launcher version: " + val);
280    }
281   
282    // report Jalview version
283  35 Cache.loadBuildProperties(true);
284   
285  35 ArgsParser aparser = new ArgsParser(args);
286  35 boolean headless = false;
287   
288  35 String usrPropsFile = aparser.getValue("props");
289  35 Cache.loadProperties(usrPropsFile); // must do this before
290  35 if (usrPropsFile != null)
291    {
292  11 System.out.println(
293    "CMD [-props " + usrPropsFile + "] executed successfully!");
294    }
295   
296  35 if (!Platform.isJS())
297    /**
298    * Java only
299    *
300    * @j2sIgnore
301    */
302    {
303  35 if (aparser.contains("help") || aparser.contains("h"))
304    {
305  0 showUsage();
306  0 System.exit(0);
307    }
308  35 if (aparser.contains("nodisplay") || aparser.contains("nogui")
309    || aparser.contains("headless"))
310    {
311  17 System.setProperty("java.awt.headless", "true");
312  17 headless = true;
313    }
314    // anything else!
315   
316  35 final String jabawsUrl = aparser.getValue("jabaws");
317  35 if (jabawsUrl != null)
318    {
319  1 try
320    {
321  1 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
322  1 System.out.println(
323    "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
324    } catch (MalformedURLException e)
325    {
326  0 System.err.println(
327    "Invalid jabaws parameter: " + jabawsUrl + " ignored");
328    }
329    }
330   
331    }
332  35 String defs = aparser.getValue("setprop");
333  35 while (defs != null)
334    {
335  0 int p = defs.indexOf('=');
336  0 if (p == -1)
337    {
338  0 System.err.println("Ignoring invalid setprop argument : " + defs);
339    }
340    else
341    {
342  0 System.out.println("Executing setprop argument: " + defs);
343  0 if (Platform.isJS())
344    {
345  0 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
346    }
347    }
348  0 defs = aparser.getValue("setprop");
349    }
350  35 if (System.getProperty("java.awt.headless") != null
351    && System.getProperty("java.awt.headless").equals("true"))
352    {
353  17 headless = true;
354    }
355  35 System.setProperty("http.agent",
356    "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
357  35 try
358    {
359  35 Cache.initLogger();
360    } catch (NoClassDefFoundError error)
361    {
362  0 error.printStackTrace();
363  0 System.out.println("\nEssential logging libraries not found."
364    + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
365  0 System.exit(0);
366    }
367   
368  35 desktop = null;
369   
370    // property laf = "crossplatform", "system", "gtk", "metal" or "mac"
371    // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
372    // try Quaqua/Vaqua.
373  35 String lafProp = System.getProperty("laf");
374  35 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
375  35 String laf = "none";
376  35 if (lafProp != null)
377    {
378  0 laf = lafProp;
379    }
380  35 else if (lafSetting != null)
381    {
382  0 laf = lafSetting;
383    }
384  35 boolean lafSet = false;
385  35 switch (laf)
386    {
387  0 case "crossplatform":
388  0 lafSet = setCrossPlatformLookAndFeel();
389  0 if (!lafSet)
390    {
391  0 System.err.println("Could not set requested laf=" + laf);
392    }
393  0 break;
394  0 case "system":
395  0 lafSet = setSystemLookAndFeel();
396  0 if (!lafSet)
397    {
398  0 System.err.println("Could not set requested laf=" + laf);
399    }
400  0 break;
401  0 case "gtk":
402  0 lafSet = setGtkLookAndFeel();
403    {
404  0 System.err.println("Could not set requested laf=" + laf);
405    }
406  0 break;
407  0 case "metal":
408  0 lafSet = setMetalLookAndFeel();
409    {
410  0 System.err.println("Could not set requested laf=" + laf);
411    }
412  0 break;
413  0 case "nimbus":
414  0 lafSet = setNimbusLookAndFeel();
415    {
416  0 System.err.println("Could not set requested laf=" + laf);
417    }
418  0 break;
419  0 case "quaqua":
420  0 lafSet = setQuaquaLookAndFeel();
421    {
422  0 System.err.println("Could not set requested laf=" + laf);
423    }
424  0 break;
425  0 case "vaqua":
426  0 lafSet = setVaquaLookAndFeel();
427    {
428  0 System.err.println("Could not set requested laf=" + laf);
429    }
430  0 break;
431  0 case "mac":
432  0 lafSet = setMacLookAndFeel();
433  0 if (!lafSet)
434    {
435  0 System.err.println("Could not set requested laf=" + laf);
436    }
437  0 break;
438  35 case "none":
439  35 break;
440  0 default:
441  0 System.err.println("Requested laf=" + laf + " not implemented");
442    }
443  35 if (!lafSet)
444    {
445  35 setSystemLookAndFeel();
446  35 if (Platform.isLinux() && !Platform.isJS())
447    {
448  35 setMetalLookAndFeel();
449    }
450  35 if (Platform.isAMacAndNotJS())
451    {
452  0 setMacLookAndFeel();
453    }
454    }
455   
456    /*
457    * configure 'full' SO model if preferences say to, else use the default (full SO)
458    * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
459    */
460  35 boolean soDefault = !Platform.isJS();
461  35 if (Cache.getDefault("USE_FULL_SO", soDefault))
462    {
463  35 SequenceOntologyFactory.setInstance(new SequenceOntology());
464    }
465   
466  35 if (!headless)
467    {
468  18 desktop = new Desktop();
469  18 desktop.setInBatchMode(true); // indicate we are starting up
470   
471  18 try
472    {
473  18 JalviewTaskbar.setTaskbar(this);
474    } catch (Throwable t)
475    {
476  0 System.out.println("Error setting Taskbar: " + t.getMessage());
477    }
478   
479  18 desktop.setVisible(true);
480   
481  18 if (!Platform.isJS())
482    /**
483    * Java only
484    *
485    * @j2sIgnore
486    */
487    {
488  18 desktop.startServiceDiscovery();
489  18 if (!aparser.contains("nousagestats"))
490    {
491  17 startUsageStats(desktop);
492    }
493    else
494    {
495  1 System.err.println("CMD [-nousagestats] executed successfully!");
496    }
497   
498  18 if (!aparser.contains("noquestionnaire"))
499    {
500  16 String url = aparser.getValue("questionnaire");
501  16 if (url != null)
502    {
503    // Start the desktop questionnaire prompter with the specified
504    // questionnaire
505  0 Cache.log.debug("Starting questionnaire url at " + url);
506  0 desktop.checkForQuestionnaire(url);
507  0 System.out.println("CMD questionnaire[-" + url
508    + "] executed successfully!");
509    }
510    else
511    {
512  16 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
513    {
514    // Start the desktop questionnaire prompter with the specified
515    // questionnaire
516    // String defurl =
517    // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
518    // //
519  0 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
520  0 Cache.log.debug(
521    "Starting questionnaire with default url: " + defurl);
522  0 desktop.checkForQuestionnaire(defurl);
523    }
524    }
525    }
526    else
527    {
528  2 System.err
529    .println("CMD [-noquestionnaire] executed successfully!");
530    }
531   
532  18 if (!aparser.contains("nonews"))
533    {
534  6 desktop.checkForNews();
535    }
536   
537  18 BioJsHTMLOutput.updateBioJS();
538    }
539    }
540   
541    // Move any new getdown-launcher-new.jar into place over old
542    // getdown-launcher.jar
543  35 String appdirString = System.getProperty("getdownappdir");
544  35 if (appdirString != null && appdirString.length() > 0)
545    {
546  0 final File appdir = new File(appdirString);
547  0 new Thread()
548    {
 
549  0 toggle @Override
550    public void run()
551    {
552  0 LaunchUtil.upgradeGetdown(
553    new File(appdir, "getdown-launcher-old.jar"),
554    new File(appdir, "getdown-launcher.jar"),
555    new File(appdir, "getdown-launcher-new.jar"));
556    }
557    }.start();
558    }
559   
560  35 String file = null, data = null;
561  35 FileFormatI format = null;
562  35 DataSourceType protocol = null;
563  35 FileLoader fileLoader = new FileLoader(!headless);
564   
565  35 String groovyscript = null; // script to execute after all loading is
566    // completed one way or another
567    // extract groovy argument and execute if necessary
568  35 groovyscript = aparser.getValue("groovy", true);
569  35 file = aparser.getValue("open", true);
570   
571  35 if (file == null && desktop == null)
572    {
573  0 System.out.println("No files to open!");
574  0 System.exit(1);
575    }
576  35 long progress = -1;
577    // Finally, deal with the remaining input data.
578  35 if (file != null)
579    {
580  18 if (!headless)
581    {
582  1 desktop.setProgressBar(
583    MessageManager
584    .getString("status.processing_commandline_args"),
585    progress = System.currentTimeMillis());
586    }
587  18 System.out.println("CMD [-open " + file + "] executed successfully!");
588   
589  18 if (!Platform.isJS())
590    /**
591    * ignore in JavaScript -- can't just file existence - could load it?
592    *
593    * @j2sIgnore
594    */
595    {
596  18 if (!file.startsWith("http://") && !file.startsWith("https://"))
597    // BH 2019 added https check for Java
598    {
599  18 if (!(new File(file)).exists())
600    {
601  0 System.out.println("Can't find " + file);
602  0 if (headless)
603    {
604  0 System.exit(1);
605    }
606    }
607    }
608    }
609   
610  18 protocol = AppletFormatAdapter.checkProtocol(file);
611   
612  18 try
613    {
614  18 format = new IdentifyFile().identify(file, protocol);
615    } catch (FileFormatException e1)
616    {
617    // TODO ?
618    }
619   
620  18 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
621    format);
622  18 if (af == null)
623    {
624  1 System.out.println("error");
625    }
626    else
627    {
628  17 setCurrentAlignFrame(af);
629  17 data = aparser.getValue("colour", true);
630  17 if (data != null)
631    {
632  1 data.replaceAll("%20", " ");
633   
634  1 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
635    af.getViewport(), af.getViewport().getAlignment(), data);
636   
637  1 if (cs != null)
638    {
639  1 System.out.println(
640    "CMD [-color " + data + "] executed successfully!");
641    }
642  1 af.changeColour(cs);
643    }
644   
645    // Must maintain ability to use the groups flag
646  17 data = aparser.getValue("groups", true);
647  17 if (data != null)
648    {
649  0 af.parseFeaturesFile(data,
650    AppletFormatAdapter.checkProtocol(data));
651    // System.out.println("Added " + data);
652  0 System.out.println(
653    "CMD groups[-" + data + "] executed successfully!");
654    }
655  17 data = aparser.getValue("features", true);
656  17 if (data != null)
657    {
658  1 af.parseFeaturesFile(data,
659    AppletFormatAdapter.checkProtocol(data));
660    // System.out.println("Added " + data);
661  1 System.out.println(
662    "CMD [-features " + data + "] executed successfully!");
663    }
664   
665  17 data = aparser.getValue("annotations", true);
666  17 if (data != null)
667    {
668  1 af.loadJalviewDataFile(data, null, null, null);
669    // System.out.println("Added " + data);
670  1 System.out.println(
671    "CMD [-annotations " + data + "] executed successfully!");
672    }
673    // set or clear the sortbytree flag.
674  17 if (aparser.contains("sortbytree"))
675    {
676  1 af.getViewport().setSortByTree(true);
677  1 if (af.getViewport().getSortByTree())
678    {
679  1 System.out.println("CMD [-sortbytree] executed successfully!");
680    }
681    }
682  17 if (aparser.contains("no-annotation"))
683    {
684  0 af.getViewport().setShowAnnotation(false);
685  0 if (!af.getViewport().isShowAnnotation())
686    {
687  0 System.out.println("CMD no-annotation executed successfully!");
688    }
689    }
690  17 if (aparser.contains("nosortbytree"))
691    {
692  1 af.getViewport().setSortByTree(false);
693  1 if (!af.getViewport().getSortByTree())
694    {
695  1 System.out
696    .println("CMD [-nosortbytree] executed successfully!");
697    }
698    }
699  17 data = aparser.getValue("tree", true);
700  17 if (data != null)
701    {
702  1 try
703    {
704  1 System.out.println(
705    "CMD [-tree " + data + "] executed successfully!");
706  1 NewickFile nf = new NewickFile(data,
707    AppletFormatAdapter.checkProtocol(data));
708  1 af.getViewport()
709    .setCurrentTree(af.showNewickTree(nf, data).getTree());
710    } catch (IOException ex)
711    {
712  0 System.err.println("Couldn't add tree " + data);
713  0 ex.printStackTrace(System.err);
714    }
715    }
716    // TODO - load PDB structure(s) to alignment JAL-629
717    // (associate with identical sequence in alignment, or a specified
718    // sequence)
719  17 if (groovyscript != null)
720    {
721    // Execute the groovy script after we've done all the rendering stuff
722    // and before any images or figures are generated.
723  0 System.out.println("Executing script " + groovyscript);
724  0 executeGroovyScript(groovyscript, af);
725  0 System.out.println("CMD groovy[" + groovyscript
726    + "] executed successfully!");
727  0 groovyscript = null;
728    }
729  17 String imageName = "unnamed.png";
730  33 while (aparser.getSize() > 1)
731    {
732  16 String outputFormat = aparser.nextValue();
733  16 file = aparser.nextValue();
734   
735  16 if (outputFormat.equalsIgnoreCase("png"))
736    {
737  1 af.createPNG(new File(file));
738  1 imageName = (new File(file)).getName();
739  1 System.out.println("Creating PNG image: " + file);
740  1 continue;
741    }
742  15 else if (outputFormat.equalsIgnoreCase("svg"))
743    {
744  1 File imageFile = new File(file);
745  1 imageName = imageFile.getName();
746  1 af.createSVG(imageFile);
747  1 System.out.println("Creating SVG image: " + file);
748  1 continue;
749    }
750  14 else if (outputFormat.equalsIgnoreCase("html"))
751    {
752  1 File imageFile = new File(file);
753  1 imageName = imageFile.getName();
754  1 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
755  1 htmlSVG.exportHTML(file);
756   
757  1 System.out.println("Creating HTML image: " + file);
758  1 continue;
759    }
760  13 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
761    {
762  0 if (file == null)
763    {
764  0 System.err.println("The output html file must not be null");
765  0 return;
766    }
767  0 try
768    {
769  0 BioJsHTMLOutput.refreshVersionInfo(
770    BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
771    } catch (URISyntaxException e)
772    {
773  0 e.printStackTrace();
774    }
775  0 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
776  0 bjs.exportHTML(file);
777  0 System.out
778    .println("Creating BioJS MSA Viwer HTML file: " + file);
779  0 continue;
780    }
781  13 else if (outputFormat.equalsIgnoreCase("imgMap"))
782    {
783  0 af.createImageMap(new File(file), imageName);
784  0 System.out.println("Creating image map: " + file);
785  0 continue;
786    }
787  13 else if (outputFormat.equalsIgnoreCase("eps"))
788    {
789  5 File outputFile = new File(file);
790  5 System.out.println(
791    "Creating EPS file: " + outputFile.getAbsolutePath());
792  5 af.createEPS(outputFile);
793  5 continue;
794    }
795   
796  8 af.saveAlignment(file, format);
797  8 if (af.isSaveAlignmentSuccessful())
798    {
799  8 System.out.println("Written alignment in " + format
800    + " format to " + file);
801    }
802    else
803    {
804  0 System.out.println("Error writing file " + file + " in "
805    + format + " format!!");
806    }
807   
808    }
809   
810  17 while (aparser.getSize() > 0)
811    {
812  0 System.out.println("Unknown arg: " + aparser.nextValue());
813    }
814    }
815    }
816  35 AlignFrame startUpAlframe = null;
817    // We'll only open the default file if the desktop is visible.
818    // And the user
819    // ////////////////////
820   
821  35 if (!Platform.isJS() && !headless && file == null
822    && Cache.getDefault("SHOW_STARTUP_FILE", true))
823    /**
824    * Java only
825    *
826    * @j2sIgnore
827    */
828    {
829  0 file = Cache.getDefault("STARTUP_FILE",
830    Cache.getDefault("www.jalview.org", "http://www.jalview.org")
831    + "/examples/exampleFile_2_7.jar");
832  0 if (file.equals(
833    "http://www.jalview.org/examples/exampleFile_2_3.jar"))
834    {
835    // hardwire upgrade of the startup file
836  0 file.replace("_2_3.jar", "_2_7.jar");
837    // and remove the stale setting
838  0 Cache.removeProperty("STARTUP_FILE");
839    }
840   
841  0 protocol = DataSourceType.FILE;
842   
843  0 if (file.indexOf("http:") > -1)
844    {
845  0 protocol = DataSourceType.URL;
846    }
847   
848  0 if (file.endsWith(".jar"))
849    {
850  0 format = FileFormat.Jalview;
851    }
852    else
853    {
854  0 try
855    {
856  0 format = new IdentifyFile().identify(file, protocol);
857    } catch (FileFormatException e)
858    {
859    // TODO what?
860    }
861    }
862   
863  0 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
864    format);
865    // extract groovy arguments before anything else.
866    }
867   
868    // Once all other stuff is done, execute any groovy scripts (in order)
869  35 if (groovyscript != null)
870    {
871  0 if (Cache.groovyJarsPresent())
872    {
873  0 System.out.println("Executing script " + groovyscript);
874  0 executeGroovyScript(groovyscript, startUpAlframe);
875    }
876    else
877    {
878  0 System.err.println(
879    "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
880    + groovyscript);
881    }
882    }
883    // and finally, turn off batch mode indicator - if the desktop still exists
884  35 if (desktop != null)
885    {
886  18 if (progress != -1)
887    {
888  1 desktop.setProgressBar(null, progress);
889    }
890  18 desktop.setInBatchMode(false);
891    }
892    }
893   
 
894  0 toggle private static boolean setCrossPlatformLookAndFeel()
895    {
896  0 return setGenericLookAndFeel(false);
897    }
898   
 
899  35 toggle private static boolean setSystemLookAndFeel()
900    {
901  35 return setGenericLookAndFeel(true);
902    }
903   
 
904  35 toggle private static boolean setGenericLookAndFeel(boolean system)
905    {
906  35 boolean set = false;
907  35 try
908    {
909  35 UIManager.setLookAndFeel(
910  35 system ? UIManager.getSystemLookAndFeelClassName()
911    : UIManager.getCrossPlatformLookAndFeelClassName());
912  35 set = true;
913    } catch (Exception ex)
914    {
915  0 System.err.println("Unexpected Look and Feel Exception");
916  0 ex.printStackTrace();
917    }
918  35 return set;
919    }
920   
 
921  35 toggle private static boolean setSpecificLookAndFeel(String name,
922    String className, boolean nameStartsWith)
923    {
924  35 boolean set = false;
925  35 try
926    {
927  35 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
928    {
929  35 if (info.getName() != null && nameStartsWith
930    ? info.getName().toLowerCase()
931    .startsWith(name.toLowerCase())
932    : info.getName().toLowerCase().equals(name.toLowerCase()))
933    {
934  35 className = info.getClassName();
935  35 break;
936    }
937    }
938  35 UIManager.setLookAndFeel(className);
939  35 set = true;
940    } catch (Exception ex)
941    {
942  0 System.err.println("Unexpected Look and Feel Exception");
943  0 ex.printStackTrace();
944    }
945  35 return set;
946    }
947   
 
948  0 toggle private static boolean setGtkLookAndFeel()
949    {
950  0 return setSpecificLookAndFeel("gtk",
951    "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
952    }
953   
 
954  35 toggle private static boolean setMetalLookAndFeel()
955    {
956  35 return setSpecificLookAndFeel("metal",
957    "javax.swing.plaf.metal.MetalLookAndFeel", false);
958    }
959   
 
960  0 toggle private static boolean setNimbusLookAndFeel()
961    {
962  0 return setSpecificLookAndFeel("nimbus",
963    "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
964    }
965   
 
966  0 toggle private static boolean setQuaquaLookAndFeel()
967    {
968  0 return setSpecificLookAndFeel("quaqua",
969    ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
970    .getName(),
971    false);
972    }
973   
 
974  0 toggle private static boolean setVaquaLookAndFeel()
975    {
976  0 return setSpecificLookAndFeel("vaqua",
977    "org.violetlib.aqua.AquaLookAndFeel", false);
978    }
979   
 
980  0 toggle private static boolean setMacLookAndFeel()
981    {
982  0 boolean set = false;
983  0 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
984    "Jalview");
985  0 System.setProperty("apple.laf.useScreenMenuBar", "true");
986  0 set = setQuaquaLookAndFeel();
987  0 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
988    .toLowerCase().contains("quaqua"))
989    {
990  0 set = setVaquaLookAndFeel();
991    }
992  0 return set;
993    }
994   
 
995  0 toggle private static void showUsage()
996    {
997  0 System.out.println(
998    "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
999    + "-nodisplay\tRun Jalview without User Interface.\n"
1000    + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1001    + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1002    + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1003    + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1004    + "-features FILE\tUse the given file to mark features on the alignment.\n"
1005    + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1006    + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1007    + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1008    + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1009    + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1010    + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1011    + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1012    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1013    + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1014    + "-png FILE\tCreate PNG image FILE from alignment.\n"
1015    + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1016    + "-html FILE\tCreate HTML file from alignment.\n"
1017    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1018    + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1019    + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1020    + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1021    + "-noquestionnaire\tTurn off questionnaire check.\n"
1022    + "-nonews\tTurn off check for Jalview news.\n"
1023    + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1024    + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1025    // +
1026    // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1027    // after all other properties files have been read\n\t
1028    // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1029    // passed in correctly)"
1030    + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1031    + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1032    + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
1033    + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
1034    + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
1035    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
1036    }
1037   
 
1038  17 toggle private static void startUsageStats(final Desktop desktop)
1039    {
1040    /**
1041    * start a User Config prompt asking if we can log usage statistics.
1042    */
1043  17 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1044    "USAGESTATS", "Jalview Usage Statistics",
1045    "Do you want to help make Jalview better by enabling "
1046    + "the collection of usage statistics with Google Analytics ?"
1047    + "\n\n(you can enable or disable usage tracking in the preferences)",
1048    new Runnable()
1049    {
 
1050  0 toggle @Override
1051    public void run()
1052    {
1053  0 Cache.log.debug(
1054    "Initialising googletracker for usage stats.");
1055  0 Cache.initGoogleTracker();
1056  0 Cache.log.debug("Tracking enabled.");
1057    }
1058    }, new Runnable()
1059    {
 
1060  5 toggle @Override
1061    public void run()
1062    {
1063  5 Cache.log.debug("Not enabling Google Tracking.");
1064    }
1065    }, null, true);
1066  17 desktop.addDialogThread(prompter);
1067    }
1068   
1069    /**
1070    * Locate the given string as a file and pass it to the groovy interpreter.
1071    *
1072    * @param groovyscript
1073    * the script to execute
1074    * @param jalviewContext
1075    * the Jalview Desktop object passed in to the groovy binding as the
1076    * 'Jalview' object.
1077    */
 
1078  0 toggle private void executeGroovyScript(String groovyscript, AlignFrame af)
1079    {
1080    /**
1081    * for scripts contained in files
1082    */
1083  0 File tfile = null;
1084    /**
1085    * script's URI
1086    */
1087  0 URL sfile = null;
1088  0 if (groovyscript.trim().equals("STDIN"))
1089    {
1090    // read from stdin into a tempfile and execute it
1091  0 try
1092    {
1093  0 tfile = File.createTempFile("jalview", "groovy");
1094  0 PrintWriter outfile = new PrintWriter(
1095    new OutputStreamWriter(new FileOutputStream(tfile)));
1096  0 BufferedReader br = new BufferedReader(
1097    new InputStreamReader(System.in));
1098  0 String line = null;
1099  0 while ((line = br.readLine()) != null)
1100    {
1101  0 outfile.write(line + "\n");
1102    }
1103  0 br.close();
1104  0 outfile.flush();
1105  0 outfile.close();
1106   
1107    } catch (Exception ex)
1108    {
1109  0 System.err.println("Failed to read from STDIN into tempfile "
1110  0 + ((tfile == null) ? "(tempfile wasn't created)"
1111    : tfile.toString()));
1112  0 ex.printStackTrace();
1113  0 return;
1114    }
1115  0 try
1116    {
1117  0 sfile = tfile.toURI().toURL();
1118    } catch (Exception x)
1119    {
1120  0 System.err.println(
1121    "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1122    + tfile.toURI());
1123  0 x.printStackTrace();
1124  0 return;
1125    }
1126    }
1127    else
1128    {
1129  0 try
1130    {
1131  0 sfile = new URI(groovyscript).toURL();
1132    } catch (Exception x)
1133    {
1134  0 tfile = new File(groovyscript);
1135  0 if (!tfile.exists())
1136    {
1137  0 System.err.println("File '" + groovyscript + "' does not exist.");
1138  0 return;
1139    }
1140  0 if (!tfile.canRead())
1141    {
1142  0 System.err.println("File '" + groovyscript + "' cannot be read.");
1143  0 return;
1144    }
1145  0 if (tfile.length() < 1)
1146    {
1147  0 System.err.println("File '" + groovyscript + "' is empty.");
1148  0 return;
1149    }
1150  0 try
1151    {
1152  0 sfile = tfile.getAbsoluteFile().toURI().toURL();
1153    } catch (Exception ex)
1154    {
1155  0 System.err.println("Failed to create a file URL for "
1156    + tfile.getAbsoluteFile());
1157  0 return;
1158    }
1159    }
1160    }
1161  0 try
1162    {
1163  0 Map<String, java.lang.Object> vbinding = new HashMap<>();
1164  0 vbinding.put("Jalview", this);
1165  0 if (af != null)
1166    {
1167  0 vbinding.put("currentAlFrame", af);
1168    }
1169  0 Binding gbinding = new Binding(vbinding);
1170  0 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1171  0 gse.run(sfile.toString(), gbinding);
1172  0 if ("STDIN".equals(groovyscript))
1173    {
1174    // delete temp file that we made -
1175    // only if it was successfully executed
1176  0 tfile.delete();
1177    }
1178    } catch (Exception e)
1179    {
1180  0 System.err.println("Exception Whilst trying to execute file " + sfile
1181    + " as a groovy script.");
1182  0 e.printStackTrace(System.err);
1183   
1184    }
1185    }
1186   
 
1187  434 toggle public static boolean isHeadlessMode()
1188    {
1189  434 String isheadless = System.getProperty("java.awt.headless");
1190  434 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1191    {
1192  37 return true;
1193    }
1194  397 return false;
1195    }
1196   
 
1197  0 toggle public AlignFrame[] getAlignFrames()
1198    {
1199  0 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1200    : Desktop.getAlignFrames();
1201   
1202    }
1203   
1204    /**
1205    * Quit method delegates to Desktop.quit - unless running in headless mode
1206    * when it just ends the JVM
1207    */
 
1208  0 toggle public void quit()
1209    {
1210  0 if (desktop != null)
1211    {
1212  0 desktop.quit();
1213    }
1214    else
1215    {
1216  0 System.exit(0);
1217    }
1218    }
1219   
 
1220  0 toggle public static AlignFrame getCurrentAlignFrame()
1221    {
1222  0 return Jalview.currentAlignFrame;
1223    }
1224   
 
1225  413 toggle public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1226    {
1227  413 Jalview.currentAlignFrame = currentAlignFrame;
1228    }
1229    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.