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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.bin

File Jalview.java

 

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47% of files have more coverage

Code metrics

188
390
23
2
1,193
944
154
0.39
16.96
11.5
6.7

Classes

Class Line # Actions
Jalview 78 377 150 449
0.2311643823.1%
Jalview.FeatureFetcher 134 13 4 17
0.00%
 

Contributing tests

This file is covered by 85 tests. .

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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 jalview.ext.so.SequenceOntology;
24    import jalview.gui.AlignFrame;
25    import jalview.gui.Desktop;
26    import jalview.gui.PromptUserConfig;
27    import jalview.io.AppletFormatAdapter;
28    import jalview.io.BioJsHTMLOutput;
29    import jalview.io.DataSourceType;
30    import jalview.io.FileFormat;
31    import jalview.io.FileFormatException;
32    import jalview.io.FileFormatI;
33    import jalview.io.FileLoader;
34    import jalview.io.HtmlSvgOutput;
35    import jalview.io.IdentifyFile;
36    import jalview.io.NewickFile;
37    import jalview.io.gff.SequenceOntologyFactory;
38    import jalview.schemes.ColourSchemeI;
39    import jalview.schemes.ColourSchemeProperty;
40    import jalview.util.MessageManager;
41    import jalview.util.Platform;
42    import jalview.ws.jws2.Jws2Discoverer;
43   
44    import java.io.BufferedReader;
45    import java.io.File;
46    import java.io.FileOutputStream;
47    import java.io.IOException;
48    import java.io.InputStreamReader;
49    import java.io.OutputStreamWriter;
50    import java.io.PrintWriter;
51    import java.net.MalformedURLException;
52    import java.net.URI;
53    import java.net.URISyntaxException;
54    import java.net.URL;
55    import java.security.AllPermission;
56    import java.security.CodeSource;
57    import java.security.PermissionCollection;
58    import java.security.Permissions;
59    import java.security.Policy;
60    import java.util.HashMap;
61    import java.util.Map;
62    import java.util.Vector;
63   
64    import javax.swing.LookAndFeel;
65    import javax.swing.UIManager;
66   
67    import groovy.lang.Binding;
68    import groovy.util.GroovyScriptEngine;
69   
70    /**
71    * Main class for Jalview Application <br>
72    * <br>
73    * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
74    *
75    * @author $author$
76    * @version $Revision$
77    */
 
78    public class Jalview
79    {
80   
81    // BH 6/19/2018 starting to work on JS version - just discovering issues
82   
83    /*
84    * singleton instance of this class
85    */
86    private static Jalview instance;
87   
88    private Desktop desktop;
89   
90    public static AlignFrame currentAlignFrame;
91   
92    /**
93    * Answers true if Jalview is running as Javascript, else false. The value is
94    * set at compile time.
95    *
96    * @return
97    */
 
98  81048 toggle public static boolean isJS()
99    {
100  81048 return /** @j2sNative true || */
101    false;
102    }
103   
 
104  1 toggle static
105    {
106  1 if (!isJS())
107    { // BH 2018
108    // grab all the rights we can the JVM
109  1 Policy.setPolicy(new Policy()
110    {
 
111  0 toggle @Override
112    public PermissionCollection getPermissions(CodeSource codesource)
113    {
114  0 Permissions perms = new Permissions();
115  0 perms.add(new AllPermission());
116  0 return (perms);
117    }
118   
 
119  0 toggle @Override
120    public void refresh()
121    {
122    }
123    });
124   
125    }
126    }
127   
128    /**
129    * keep track of feature fetching tasks.
130    *
131    * @author JimP
132    *
133    */
 
134    class FeatureFetcher
135    {
136    /*
137    * TODO: generalise to track all jalview events to orchestrate batch
138    * processing events.
139    */
140   
141    private int queued = 0;
142   
143    private int running = 0;
144   
 
145  0 toggle public FeatureFetcher()
146    {
147   
148    }
149   
 
150  0 toggle public void addFetcher(final AlignFrame af,
151    final Vector<String> dasSources)
152    {
153  0 final long id = System.currentTimeMillis();
154  0 queued++;
155  0 final FeatureFetcher us = this;
156  0 new Thread(new Runnable()
157    {
158   
 
159  0 toggle @Override
160    public void run()
161    {
162  0 synchronized (us)
163    {
164  0 queued--;
165  0 running++;
166    }
167   
168  0 af.setProgressBar(MessageManager
169    .getString("status.das_features_being_retrived"), id);
170  0 af.featureSettings_actionPerformed(null);
171  0 af.setProgressBar(null, id);
172  0 synchronized (us)
173    {
174  0 running--;
175    }
176    }
177    }).start();
178    }
179   
 
180  0 toggle public synchronized boolean allFinished()
181    {
182  0 return queued == 0 && running == 0;
183    }
184   
185    }
186   
 
187  0 toggle public static Jalview getInstance()
188    {
189  0 return instance;
190    }
191   
192    /**
193    * main class for Jalview application
194    *
195    * @param args
196    * open <em>filename</em>
197    */
 
198  11 toggle public static void main(String[] args)
199    {
200  11 instance = new Jalview();
201  11 instance.doMain(args);
202    }
203   
204    /**
205    * @param args
206    */
 
207  11 toggle void doMain(String[] args)
208    {
209   
210  11 if (!isJS())
211    {
212  11 System.setSecurityManager(null);
213    }
214   
215  11 System.out
216    .println("Java version: " + System.getProperty("java.version"));
217  11 System.out.println(System.getProperty("os.arch") + " "
218    + System.getProperty("os.name") + " "
219    + System.getProperty("os.version"));
220   
221  11 ArgsParser aparser = new ArgsParser(args);
222  11 boolean headless = false;
223   
224  11 String usrPropsFile = aparser.getValue("props");
225  11 Cache.loadProperties(usrPropsFile); // must do this before
226  11 if (usrPropsFile != null)
227    {
228  7 System.out.println(
229    "CMD [-props " + usrPropsFile + "] executed successfully!");
230    }
231   
232    /**
233    * BH 2018 ignoring this section for JS
234    *
235    * @j2sNative
236    */
237    {
238  11 if (aparser.contains("help") || aparser.contains("h"))
239    {
240  0 showUsage();
241  0 System.exit(0);
242    }
243  11 if (aparser.contains("nodisplay") || aparser.contains("nogui")
244    || aparser.contains("headless"))
245    {
246  0 System.setProperty("java.awt.headless", "true");
247  0 headless = true;
248    }
249    // anything else!
250   
251  11 final String jabawsUrl = aparser.getValue("jabaws");
252  11 if (jabawsUrl != null)
253    {
254  0 try
255    {
256  0 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
257  0 System.out.println(
258    "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
259    } catch (MalformedURLException e)
260    {
261  0 System.err.println(
262    "Invalid jabaws parameter: " + jabawsUrl + " ignored");
263    }
264    }
265   
266    }
267  11 String defs = aparser.getValue("setprop");
268  11 while (defs != null)
269    {
270  0 int p = defs.indexOf('=');
271  0 if (p == -1)
272    {
273  0 System.err.println("Ignoring invalid setprop argument : " + defs);
274    }
275    else
276    {
277  0 System.out.println("Executing setprop argument: " + defs);
278    // DISABLED FOR SECURITY REASONS
279    // TODO: add a property to allow properties to be overriden by cli args
280    // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
281    }
282  0 defs = aparser.getValue("setprop");
283    }
284  11 if (System.getProperty("java.awt.headless") != null
285    && System.getProperty("java.awt.headless").equals("true"))
286    {
287  0 headless = true;
288    }
289  11 System.setProperty("http.agent",
290    "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
291  11 try
292    {
293  11 Cache.initLogger();
294    } catch (NoClassDefFoundError error)
295    {
296  0 error.printStackTrace();
297  0 System.out.println("\nEssential logging libraries not found."
298    + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
299  0 System.exit(0);
300    }
301   
302  11 desktop = null;
303   
304  11 try
305    {
306  11 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
307    } catch (Exception ex)
308    {
309  0 System.err.println("Unexpected Look and Feel Exception");
310  0 ex.printStackTrace();
311    }
312  11 if (Platform.isAMac())
313    {
314   
315  0 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
316    .getLookAndFeel();
317  0 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
318    "Jalview");
319  0 System.setProperty("apple.laf.useScreenMenuBar", "true");
320  0 if (lookAndFeel != null)
321    {
322  0 try
323    {
324  0 UIManager.setLookAndFeel(lookAndFeel);
325    } catch (Throwable e)
326    {
327  0 System.err.println(
328    "Failed to set QuaQua look and feel: " + e.toString());
329    }
330    }
331  0 if (lookAndFeel == null || !(lookAndFeel.getClass()
332    .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
333    || !UIManager.getLookAndFeel().getClass().toString()
334    .toLowerCase().contains("quaqua"))
335    {
336  0 try
337    {
338  0 System.err.println(
339    "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
340  0 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
341    } catch (Throwable e)
342    {
343  0 System.err.println(
344    "Failed to reset look and feel: " + e.toString());
345    }
346    }
347    }
348   
349    /*
350    * configure 'full' SO model if preferences say to,
351    * else use the default (SO Lite)
352    */
353  11 if (Cache.getDefault("USE_FULL_SO", false))
354    {
355  0 SequenceOntologyFactory.setInstance(new SequenceOntology());
356    }
357   
358  11 if (!headless)
359    {
360  11 desktop = new Desktop();
361  11 desktop.setInBatchMode(true); // indicate we are starting up
362  11 desktop.setVisible(true);
363   
364    /**
365    * BH 2018 JS bypass this section
366    *
367    * @j2sNative
368    *
369    */
370    {
371  11 desktop.startServiceDiscovery();
372  11 if (!aparser.contains("nousagestats"))
373    {
374  11 startUsageStats(desktop);
375    }
376    else
377    {
378  0 System.err.println("CMD [-nousagestats] executed successfully!");
379    }
380   
381  11 if (!aparser.contains("noquestionnaire"))
382    {
383  10 String url = aparser.getValue("questionnaire");
384  10 if (url != null)
385    {
386    // Start the desktop questionnaire prompter with the specified
387    // questionnaire
388  0 Cache.log.debug("Starting questionnaire url at " + url);
389  0 desktop.checkForQuestionnaire(url);
390  0 System.out.println("CMD questionnaire[-" + url
391    + "] executed successfully!");
392    }
393    else
394    {
395  10 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
396    {
397    // Start the desktop questionnaire prompter with the specified
398    // questionnaire
399    // String defurl =
400    // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
401    // //
402  4 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
403  4 Cache.log.debug(
404    "Starting questionnaire with default url: " + defurl);
405  4 desktop.checkForQuestionnaire(defurl);
406    }
407    }
408    }
409    else
410    {
411  1 System.err
412    .println("CMD [-noquestionnaire] executed successfully!");
413    }
414   
415  11 if (!aparser.contains("nonews"))
416    {
417  4 desktop.checkForNews();
418    }
419   
420  11 BioJsHTMLOutput.updateBioJS();
421    }
422    }
423   
424  11 String file = null, data = null;
425  11 FileFormatI format = null;
426  11 DataSourceType protocol = null;
427  11 FileLoader fileLoader = new FileLoader(!headless);
428  11 Vector<String> getFeatures = null; // vector of das source nicknames to
429    // fetch
430    // features from
431    // loading is done.
432  11 String groovyscript = null; // script to execute after all loading is
433    // completed one way or another
434    // extract groovy argument and execute if necessary
435  11 groovyscript = aparser.getValue("groovy", true);
436  11 file = aparser.getValue("open", true);
437   
438  11 if (file == null && desktop == null)
439    {
440  0 System.out.println("No files to open!");
441  0 System.exit(1);
442    }
443  11 String vamsasImport = aparser.getValue("vdoc");
444  11 String vamsasSession = aparser.getValue("vsess");
445  11 if (vamsasImport != null || vamsasSession != null)
446    {
447  0 if (desktop == null || headless)
448    {
449  0 System.out.println(
450    "Headless vamsas sessions not yet supported. Sorry.");
451  0 System.exit(1);
452    }
453    // if we have a file, start a new session and import it.
454  0 boolean inSession = false;
455  0 if (vamsasImport != null)
456    {
457  0 try
458    {
459  0 DataSourceType viprotocol = AppletFormatAdapter
460    .checkProtocol(vamsasImport);
461  0 if (viprotocol == DataSourceType.FILE)
462    {
463  0 inSession = desktop.vamsasImport(new File(vamsasImport));
464    }
465  0 else if (viprotocol == DataSourceType.URL)
466    {
467  0 inSession = desktop.vamsasImport(new URL(vamsasImport));
468    }
469   
470    } catch (Exception e)
471    {
472  0 System.err.println("Exeption when importing " + vamsasImport
473    + " as a vamsas document.");
474  0 e.printStackTrace();
475    }
476  0 if (!inSession)
477    {
478  0 System.err.println("Failed to import " + vamsasImport
479    + " as a vamsas document.");
480    }
481    else
482    {
483  0 System.out.println("Imported Successfully into new session "
484    + desktop.getVamsasApplication().getCurrentSession());
485    }
486    }
487  0 if (vamsasSession != null)
488    {
489  0 if (vamsasImport != null)
490    {
491    // close the newly imported session and import the Jalview specific
492    // remnants into the new session later on.
493  0 desktop.vamsasStop_actionPerformed(null);
494    }
495    // now join the new session
496  0 try
497    {
498  0 if (desktop.joinVamsasSession(vamsasSession))
499    {
500  0 System.out.println(
501    "Successfully joined vamsas session " + vamsasSession);
502    }
503    else
504    {
505  0 System.err.println("WARNING: Failed to join vamsas session "
506    + vamsasSession);
507    }
508    } catch (Exception e)
509    {
510  0 System.err.println(
511    "ERROR: Failed to join vamsas session " + vamsasSession);
512  0 e.printStackTrace();
513    }
514  0 if (vamsasImport != null)
515    {
516    // the Jalview specific remnants can now be imported into the new
517    // session at the user's leisure.
518  0 Cache.log.info(
519    "Skipping Push for import of data into existing vamsas session."); // TODO:
520    // enable
521    // this
522    // when
523    // debugged
524    // desktop.getVamsasApplication().push_update();
525    }
526    }
527    }
528  11 long progress = -1;
529    // Finally, deal with the remaining input data.
530  11 if (file != null)
531    {
532  0 if (!headless)
533    {
534  0 desktop.setProgressBar(
535    MessageManager
536    .getString("status.processing_commandline_args"),
537    progress = System.currentTimeMillis());
538    }
539  0 System.out.println("CMD [-open " + file + "] executed successfully!");
540   
541  0 if (!isJS() && !file.startsWith("http://"))
542    {
543  0 if (!(new File(file)).exists())
544    {
545  0 System.out.println("Can't find " + file);
546  0 if (headless)
547    {
548  0 System.exit(1);
549    }
550    }
551    }
552   
553  0 protocol = AppletFormatAdapter.checkProtocol(file);
554   
555  0 try
556    {
557  0 format = new IdentifyFile().identify(file, protocol);
558    } catch (FileFormatException e1)
559    {
560    // TODO ?
561    }
562   
563  0 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
564    format);
565  0 if (af == null)
566    {
567  0 System.out.println("error");
568    }
569    else
570    {
571  0 setCurrentAlignFrame(af);
572  0 data = aparser.getValue("colour", true);
573  0 if (data != null)
574    {
575  0 data.replaceAll("%20", " ");
576   
577  0 ColourSchemeI cs = ColourSchemeProperty
578    .getColourScheme(af.getViewport().getAlignment(), data);
579   
580  0 if (cs != null)
581    {
582  0 System.out.println(
583    "CMD [-color " + data + "] executed successfully!");
584    }
585  0 af.changeColour(cs);
586    }
587   
588    // Must maintain ability to use the groups flag
589  0 data = aparser.getValue("groups", true);
590  0 if (data != null)
591    {
592  0 af.parseFeaturesFile(data,
593    AppletFormatAdapter.checkProtocol(data));
594    // System.out.println("Added " + data);
595  0 System.out.println(
596    "CMD groups[-" + data + "] executed successfully!");
597    }
598  0 data = aparser.getValue("features", true);
599  0 if (data != null)
600    {
601  0 af.parseFeaturesFile(data,
602    AppletFormatAdapter.checkProtocol(data));
603    // System.out.println("Added " + data);
604  0 System.out.println(
605    "CMD [-features " + data + "] executed successfully!");
606    }
607   
608  0 data = aparser.getValue("annotations", true);
609  0 if (data != null)
610    {
611  0 af.loadJalviewDataFile(data, null, null, null);
612    // System.out.println("Added " + data);
613  0 System.out.println(
614    "CMD [-annotations " + data + "] executed successfully!");
615    }
616    // set or clear the sortbytree flag.
617  0 if (aparser.contains("sortbytree"))
618    {
619  0 af.getViewport().setSortByTree(true);
620  0 if (af.getViewport().getSortByTree())
621    {
622  0 System.out.println("CMD [-sortbytree] executed successfully!");
623    }
624    }
625  0 if (aparser.contains("no-annotation"))
626    {
627  0 af.getViewport().setShowAnnotation(false);
628  0 if (!af.getViewport().isShowAnnotation())
629    {
630  0 System.out.println("CMD no-annotation executed successfully!");
631    }
632    }
633  0 if (aparser.contains("nosortbytree"))
634    {
635  0 af.getViewport().setSortByTree(false);
636  0 if (!af.getViewport().getSortByTree())
637    {
638  0 System.out
639    .println("CMD [-nosortbytree] executed successfully!");
640    }
641    }
642  0 data = aparser.getValue("tree", true);
643  0 if (data != null)
644    {
645  0 try
646    {
647  0 System.out.println(
648    "CMD [-tree " + data + "] executed successfully!");
649  0 NewickFile nf = new NewickFile(data,
650    AppletFormatAdapter.checkProtocol(data));
651  0 af.getViewport()
652    .setCurrentTree(af.showNewickTree(nf, data).getTree());
653    } catch (IOException ex)
654    {
655  0 System.err.println("Couldn't add tree " + data);
656  0 ex.printStackTrace(System.err);
657    }
658    }
659    // TODO - load PDB structure(s) to alignment JAL-629
660    // (associate with identical sequence in alignment, or a specified
661    // sequence)
662   
663  0 getFeatures = checkDasArguments(aparser);
664  0 if (af != null && getFeatures != null)
665    {
666  0 FeatureFetcher ff = startFeatureFetching(getFeatures);
667  0 if (ff != null)
668    {
669  0 while (!ff.allFinished() || af.operationInProgress())
670    {
671    // wait around until fetching is finished.
672  0 try
673    {
674  0 Thread.sleep(100);
675    } catch (Exception e)
676    {
677   
678    }
679    }
680    }
681  0 getFeatures = null; // have retrieved features - forget them now.
682    }
683  0 if (groovyscript != null)
684    {
685    // Execute the groovy script after we've done all the rendering stuff
686    // and before any images or figures are generated.
687  0 System.out.println("Executing script " + groovyscript);
688  0 executeGroovyScript(groovyscript, af);
689  0 System.out.println("CMD groovy[" + groovyscript
690    + "] executed successfully!");
691  0 groovyscript = null;
692    }
693  0 String imageName = "unnamed.png";
694  0 while (aparser.getSize() > 1)
695    {
696  0 String outputFormat = aparser.nextValue();
697  0 file = aparser.nextValue();
698   
699  0 if (outputFormat.equalsIgnoreCase("png"))
700    {
701  0 af.createPNG(new File(file));
702  0 imageName = (new File(file)).getName();
703  0 System.out.println("Creating PNG image: " + file);
704  0 continue;
705    }
706  0 else if (outputFormat.equalsIgnoreCase("svg"))
707    {
708  0 File imageFile = new File(file);
709  0 imageName = imageFile.getName();
710  0 af.createSVG(imageFile);
711  0 System.out.println("Creating SVG image: " + file);
712  0 continue;
713    }
714  0 else if (outputFormat.equalsIgnoreCase("html"))
715    {
716  0 File imageFile = new File(file);
717  0 imageName = imageFile.getName();
718  0 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
719  0 htmlSVG.exportHTML(file);
720   
721  0 System.out.println("Creating HTML image: " + file);
722  0 continue;
723    }
724  0 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
725    {
726  0 if (file == null)
727    {
728  0 System.err.println("The output html file must not be null");
729  0 return;
730    }
731  0 try
732    {
733  0 BioJsHTMLOutput.refreshVersionInfo(
734    BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
735    } catch (URISyntaxException e)
736    {
737  0 e.printStackTrace();
738    }
739  0 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
740  0 bjs.exportHTML(file);
741  0 System.out
742    .println("Creating BioJS MSA Viwer HTML file: " + file);
743  0 continue;
744    }
745  0 else if (outputFormat.equalsIgnoreCase("imgMap"))
746    {
747  0 af.createImageMap(new File(file), imageName);
748  0 System.out.println("Creating image map: " + file);
749  0 continue;
750    }
751  0 else if (outputFormat.equalsIgnoreCase("eps"))
752    {
753  0 File outputFile = new File(file);
754  0 System.out.println(
755    "Creating EPS file: " + outputFile.getAbsolutePath());
756  0 af.createEPS(outputFile);
757  0 continue;
758    }
759   
760  0 af.saveAlignment(file, format);
761  0 if (af.isSaveAlignmentSuccessful())
762    {
763  0 System.out.println("Written alignment in " + format
764    + " format to " + file);
765    }
766    else
767    {
768  0 System.out.println("Error writing file " + file + " in "
769    + format + " format!!");
770    }
771   
772    }
773   
774  0 while (aparser.getSize() > 0)
775    {
776  0 System.out.println("Unknown arg: " + aparser.nextValue());
777    }
778    }
779    }
780  11 AlignFrame startUpAlframe = null;
781    // We'll only open the default file if the desktop is visible.
782    // And the user
783    // ////////////////////
784   
785  11 if (/** @j2sNative false && */ // BH 2018
786  11 !headless && file == null && vamsasImport == null
787    && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
788    {
789  4 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
790    jalview.bin.Cache.getDefault("www.jalview.org",
791    "http://www.jalview.org")
792    + "/examples/exampleFile_2_7.jar");
793  4 if (file.equals(
794    "http://www.jalview.org/examples/exampleFile_2_3.jar"))
795    {
796    // hardwire upgrade of the startup file
797  0 file.replace("_2_3.jar", "_2_7.jar");
798    // and remove the stale setting
799  0 jalview.bin.Cache.removeProperty("STARTUP_FILE");
800    }
801   
802  4 protocol = DataSourceType.FILE;
803   
804  4 if (file.indexOf("http:") > -1)
805    {
806  4 protocol = DataSourceType.URL;
807    }
808   
809  4 if (file.endsWith(".jar"))
810    {
811  4 format = FileFormat.Jalview;
812    }
813    else
814    {
815  0 try
816    {
817  0 format = new IdentifyFile().identify(file, protocol);
818    } catch (FileFormatException e)
819    {
820    // TODO what?
821    }
822    }
823   
824  4 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
825    format);
826  4 getFeatures = checkDasArguments(aparser);
827    // extract groovy arguments before anything else.
828    }
829    // If the user has specified features to be retrieved,
830    // or a groovy script to be executed, do them if they
831    // haven't been done already
832    // fetch features for the default alignment
833  11 if (getFeatures != null)
834    {
835  0 if (startUpAlframe != null)
836    {
837  0 startFeatureFetching(getFeatures);
838    }
839    }
840    // Once all other stuff is done, execute any groovy scripts (in order)
841  11 if (groovyscript != null)
842    {
843  0 if (Cache.groovyJarsPresent())
844    {
845  0 System.out.println("Executing script " + groovyscript);
846  0 executeGroovyScript(groovyscript, startUpAlframe);
847    }
848    else
849    {
850  0 System.err.println(
851    "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
852    + groovyscript);
853    }
854    }
855    // and finally, turn off batch mode indicator - if the desktop still exists
856  11 if (desktop != null)
857    {
858  11 if (progress != -1)
859    {
860  0 desktop.setProgressBar(null, progress);
861    }
862  11 desktop.setInBatchMode(false);
863    }
864    }
865   
 
866  0 toggle private static void showUsage()
867    {
868  0 System.out.println(
869    "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
870    + "-nodisplay\tRun Jalview without User Interface.\n"
871    + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
872    + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
873    + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
874    + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
875    + "-features FILE\tUse the given file to mark features on the alignment.\n"
876    + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
877    + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
878    + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
879    + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
880    + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
881    + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
882    + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
883    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
884    + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
885    + "-png FILE\tCreate PNG image FILE from alignment.\n"
886    + "-svg FILE\tCreate SVG image FILE from alignment.\n"
887    + "-html FILE\tCreate HTML file from alignment.\n"
888    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
889    + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
890    + "-eps FILE\tCreate EPS file FILE from alignment.\n"
891    + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
892    + "-noquestionnaire\tTurn off questionnaire check.\n"
893    + "-nonews\tTurn off check for Jalview news.\n"
894    + "-nousagestats\tTurn off google analytics tracking for this session.\n"
895    + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
896    // +
897    // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
898    // after all other properties files have been read\n\t
899    // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
900    // passed in correctly)"
901    + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
902    + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
903    + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
904    + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
905    + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
906    // +
907    // "-vdoc vamsas-document\tImport vamsas document into new
908    // session or join existing session with same URN\n"
909    // + "-vses vamsas-session\tJoin session with given URN\n"
910    + "-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"
911    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
912    }
913   
 
914  11 toggle private static void startUsageStats(final Desktop desktop)
915    {
916    /**
917    * start a User Config prompt asking if we can log usage statistics.
918    */
919  11 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
920    "USAGESTATS", "Jalview Usage Statistics",
921    "Do you want to help make Jalview better by enabling "
922    + "the collection of usage statistics with Google Analytics ?"
923    + "\n\n(you can enable or disable usage tracking in the preferences)",
924    new Runnable()
925    {
 
926  0 toggle @Override
927    public void run()
928    {
929  0 Cache.log.debug(
930    "Initialising googletracker for usage stats.");
931  0 Cache.initGoogleTracker();
932  0 Cache.log.debug("Tracking enabled.");
933    }
934    }, new Runnable()
935    {
 
936  2 toggle @Override
937    public void run()
938    {
939  2 Cache.log.debug("Not enabling Google Tracking.");
940    }
941    }, null, true);
942  11 desktop.addDialogThread(prompter);
943    }
944   
945    /**
946    * Locate the given string as a file and pass it to the groovy interpreter.
947    *
948    * @param groovyscript
949    * the script to execute
950    * @param jalviewContext
951    * the Jalview Desktop object passed in to the groovy binding as the
952    * 'Jalview' object.
953    */
 
954  0 toggle private void executeGroovyScript(String groovyscript, AlignFrame af)
955    {
956    /**
957    * for scripts contained in files
958    */
959  0 File tfile = null;
960    /**
961    * script's URI
962    */
963  0 URL sfile = null;
964  0 if (groovyscript.trim().equals("STDIN"))
965    {
966    // read from stdin into a tempfile and execute it
967  0 try
968    {
969  0 tfile = File.createTempFile("jalview", "groovy");
970  0 PrintWriter outfile = new PrintWriter(
971    new OutputStreamWriter(new FileOutputStream(tfile)));
972  0 BufferedReader br = new BufferedReader(
973    new InputStreamReader(System.in));
974  0 String line = null;
975  0 while ((line = br.readLine()) != null)
976    {
977  0 outfile.write(line + "\n");
978    }
979  0 br.close();
980  0 outfile.flush();
981  0 outfile.close();
982   
983    } catch (Exception ex)
984    {
985  0 System.err.println("Failed to read from STDIN into tempfile "
986  0 + ((tfile == null) ? "(tempfile wasn't created)"
987    : tfile.toString()));
988  0 ex.printStackTrace();
989  0 return;
990    }
991  0 try
992    {
993  0 sfile = tfile.toURI().toURL();
994    } catch (Exception x)
995    {
996  0 System.err.println(
997    "Unexpected Malformed URL Exception for temporary file created from STDIN: "
998    + tfile.toURI());
999  0 x.printStackTrace();
1000  0 return;
1001    }
1002    }
1003    else
1004    {
1005  0 try
1006    {
1007  0 sfile = new URI(groovyscript).toURL();
1008    } catch (Exception x)
1009    {
1010  0 tfile = new File(groovyscript);
1011  0 if (!tfile.exists())
1012    {
1013  0 System.err.println("File '" + groovyscript + "' does not exist.");
1014  0 return;
1015    }
1016  0 if (!tfile.canRead())
1017    {
1018  0 System.err.println("File '" + groovyscript + "' cannot be read.");
1019  0 return;
1020    }
1021  0 if (tfile.length() < 1)
1022    {
1023  0 System.err.println("File '" + groovyscript + "' is empty.");
1024  0 return;
1025    }
1026  0 try
1027    {
1028  0 sfile = tfile.getAbsoluteFile().toURI().toURL();
1029    } catch (Exception ex)
1030    {
1031  0 System.err.println("Failed to create a file URL for "
1032    + tfile.getAbsoluteFile());
1033  0 return;
1034    }
1035    }
1036    }
1037  0 try
1038    {
1039  0 Map<String, Object> vbinding = new HashMap<>();
1040  0 vbinding.put("Jalview", this);
1041  0 if (af != null)
1042    {
1043  0 vbinding.put("currentAlFrame", af);
1044    }
1045  0 Binding gbinding = new Binding(vbinding);
1046  0 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1047  0 gse.run(sfile.toString(), gbinding);
1048  0 if ("STDIN".equals(groovyscript))
1049    {
1050    // delete temp file that we made -
1051    // only if it was successfully executed
1052  0 tfile.delete();
1053    }
1054    } catch (Exception e)
1055    {
1056  0 System.err.println("Exception Whilst trying to execute file " + sfile
1057    + " as a groovy script.");
1058  0 e.printStackTrace(System.err);
1059   
1060    }
1061    }
1062   
1063    /**
1064    * Check commandline for any das server definitions or any fetchfrom switches
1065    *
1066    * @return vector of DAS source nicknames to retrieve from
1067    */
 
1068  4 toggle private static Vector<String> checkDasArguments(ArgsParser aparser)
1069    {
1070  4 Vector<String> source = null;
1071  4 String data;
1072  4 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
1073  ? while ((data = aparser.getValue("dasserver", true)) != null)
1074    {
1075  0 String nickname = null;
1076  0 String url = null;
1077  0 int pos = data.indexOf('=');
1078    // determine capabilities
1079  0 if (pos > 0)
1080    {
1081  0 nickname = data.substring(0, pos);
1082    }
1083  0 url = data.substring(pos + 1);
1084  0 if (url != null && (url.startsWith("http:")
1085    || url.startsWith("sequence:http:")))
1086    {
1087  0 if (nickname == null)
1088    {
1089  0 nickname = url;
1090    }
1091  0 if (locsources == null)
1092    {
1093  0 locsources = "";
1094    }
1095    else
1096    {
1097  0 locsources += "\t";
1098    }
1099  0 locsources = locsources + nickname + "|" + url;
1100  0 System.err.println(
1101    "NOTE! dasserver parameter not yet really supported (got args of "
1102    + nickname + "|" + url);
1103  0 if (source == null)
1104    {
1105  0 source = new Vector<>();
1106    }
1107  0 source.addElement(nickname);
1108    }
1109  0 System.out.println(
1110    "CMD [-dasserver " + data + "] executed successfully!");
1111    } // loop until no more server entries are found.
1112  4 if (locsources != null && locsources.indexOf('|') > -1)
1113    {
1114  0 Cache.log.debug("Setting local source list in properties file to:\n"
1115    + locsources);
1116  0 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
1117    }
1118  ? while ((data = aparser.getValue("fetchfrom", true)) != null)
1119    {
1120  0 System.out.println("adding source '" + data + "'");
1121  0 if (source == null)
1122    {
1123  0 source = new Vector<>();
1124    }
1125  0 source.addElement(data);
1126    }
1127  4 return source;
1128    }
1129   
1130    /**
1131    * start a feature fetcher for every alignment frame
1132    *
1133    * @param dasSources
1134    */
 
1135  0 toggle private FeatureFetcher startFeatureFetching(
1136    final Vector<String> dasSources)
1137    {
1138  0 FeatureFetcher ff = new FeatureFetcher();
1139  0 AlignFrame afs[] = Desktop.getAlignFrames();
1140  0 if (afs == null || afs.length == 0)
1141    {
1142  0 return null;
1143    }
1144  0 for (int i = 0; i < afs.length; i++)
1145    {
1146  0 ff.addFetcher(afs[i], dasSources);
1147    }
1148  0 return ff;
1149    }
1150   
 
1151  298 toggle public static boolean isHeadlessMode()
1152    {
1153  298 String isheadless = System.getProperty("java.awt.headless");
1154  298 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1155    {
1156  0 return true;
1157    }
1158  298 return false;
1159    }
1160   
 
1161  0 toggle public AlignFrame[] getAlignFrames()
1162    {
1163  0 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1164    : Desktop.getAlignFrames();
1165   
1166    }
1167   
1168    /**
1169    * Quit method delegates to Desktop.quit - unless running in headless mode
1170    * when it just ends the JVM
1171    */
 
1172  0 toggle public void quit()
1173    {
1174  0 if (desktop != null)
1175    {
1176  0 desktop.quit();
1177    }
1178    else
1179    {
1180  0 System.exit(0);
1181    }
1182    }
1183   
 
1184  0 toggle public static AlignFrame getCurrentAlignFrame()
1185    {
1186  0 return Jalview.currentAlignFrame;
1187    }
1188   
 
1189  341 toggle public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1190    {
1191  341 Jalview.currentAlignFrame = currentAlignFrame;
1192    }
1193    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.