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Coverage Report

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

File Cache.java

 

Coverage histogram

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

Code metrics

106
300
27
1
1,189
737
114
0.38
11.11
27
4.22

Classes

Class Line # Actions
Cache 215 300 114
0.4919168749.2%
 

Contributing tests

This file is covered by 246 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 jalview.datamodel.PDBEntry;
24    import jalview.gui.UserDefinedColours;
25    import jalview.schemes.ColourSchemeLoader;
26    import jalview.schemes.ColourSchemes;
27    import jalview.schemes.UserColourScheme;
28    import jalview.structure.StructureImportSettings;
29    import jalview.urls.IdOrgSettings;
30    import jalview.util.ColorUtils;
31    import jalview.util.Platform;
32    import jalview.ws.sifts.SiftsSettings;
33   
34    import java.awt.Color;
35    import java.io.BufferedReader;
36    import java.io.File;
37    import java.io.FileInputStream;
38    import java.io.FileOutputStream;
39    import java.io.InputStream;
40    import java.io.InputStreamReader;
41    import java.net.URL;
42    import java.text.DateFormat;
43    import java.text.SimpleDateFormat;
44    import java.util.Collections;
45    import java.util.Date;
46    import java.util.Enumeration;
47    import java.util.Locale;
48    import java.util.Properties;
49    import java.util.StringTokenizer;
50    import java.util.TreeSet;
51    import java.util.regex.Pattern;
52   
53    import javax.swing.LookAndFeel;
54    import javax.swing.UIManager;
55   
56    import org.apache.log4j.ConsoleAppender;
57    import org.apache.log4j.Level;
58    import org.apache.log4j.Logger;
59    import org.apache.log4j.SimpleLayout;
60   
61    /**
62    * Stores and retrieves Jalview Application Properties Lists and fields within
63    * list entries are separated by '|' symbols unless otherwise stated (|) clauses
64    * are alternative values for a tag. <br>
65    * <br>
66    * Current properties include:
67    * <ul>
68    * <br>
69    * logs.Axis.Level - one of the stringified Levels for log4j controlling the
70    * logging level for axis (used for web services) <br>
71    * </li>
72    * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
73    * the logging level for castor (used for serialization) <br>
74    * </li>
75    * <li>logs.Jalview.Level - Cache.log stringified level. <br>
76    * </li>
77    * <li>SCREEN_WIDTH</li>
78    * <li>SCREEN_HEIGHT</li>
79    * <li>SCREEN_Y=285</li>
80    * <li>SCREEN_X=371</li>
81    * <li>SHOW_FULLSCREEN boolean</li>
82    * <li>FONT_NAME java font name for alignment text display</li>
83    * <li>FONT_SIZE size of displayed alignment text</li>
84    * <li>FONT_STYLE style of font displayed (sequence labels are always
85    * italic)</li>
86    * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
87    * <li>LAST_DIRECTORY last directory for browsing alignment</li>
88    * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
89    * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
90    * <li>SHOW_IDENTITY show percentage identity annotation</li>
91    * <li>SHOW_QUALITY show alignment quality annotation</li>
92    * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
93    * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
94    * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
95    * LABEL_AND_SEQUENCE</li>
96    * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
97    * sequence annotations</li>
98    * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
99    * annotation row</li>
100    * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
101    * <li>DEFAULT_FILE_FORMAT file format used to save</li>
102    * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
103    * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
104    * <li>VERSION the version of the jalview build</li>
105    * <li>BUILD_DATE date of this build</li>
106    * <li>LATEST_VERSION the latest jalview version advertised on the
107    * www.jalview.org</li>
108    * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
109    * descriptions</li>
110    * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
111    * suffix to file</li>
112    * <li>RECENT_URL list of recently retrieved URLs</li>
113    * <li>RECENT_FILE list of recently opened files</li>
114    * <li>USE_PROXY flag for whether a http proxy is to be used</li>
115    * <li>PROXY_SERVER the proxy</li>
116    * <li>PROXY_PORT</li>
117    * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
118    * service</li>
119    * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
120    * service</li>
121    * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
122    * collecting usage statistics</li>
123    * <li>SHOW_OVERVIEW boolean for overview window display</li>
124    * <li>ANTI_ALIAS boolean for smooth fonts</li>
125    * <li>RIGHT_ALIGN_IDS boolean</li>
126    * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
127    * <li>PAD_GAPS boolean</li>
128    * <li>ID_ITALICS boolean</li>
129    * <li>SHOW_JV_SUFFIX</li>
130    * <li>WRAP_ALIGNMENT</li>
131    * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
132    * style check</li>
133    * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
134    * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
135    * $SEQUENCE_ID$</li>
136    * <li>STORED_LINKS list of name|url pairs which user has entered but are not
137    * currently used
138    * <li>DEFAULT_LINK name of single url to be used when user double clicks a
139    * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
140    * <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see
141    * jalview.utils.GroupURLLink for more info</li>
142    * <li>DEFAULT_BROWSER for unix</li>
143    * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
144    * (false)</li>
145    * <li>VERSION_CHECK (true) check for the latest release version from
146    * www.jalview.org (or the alias given by the www.jalview.org property)</li>
147    * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
148    * ID tooltip</li>
149    * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
150    * ID tooltip</li>
151    * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
152    * displayed as '.'</li>
153    * <li>SORT_BY_TREE (false) sort the current alignment view according to the
154    * order of a newly displayed tree</li>
155    * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
156    * sequence ID strings before attempting retrieval from any datasource</li>
157    * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
158    * alignment.</li>
159    * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
160    * in the alignment.</li>
161    * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
162    * histogram.</li>
163    * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
164    * logo.</li>
165    * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
166    * logo normalised to row height rather than histogram height.</li>
167    * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
168    * respond to selections made in other alignments containing the same sequences.
169    * </li>
170    * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
171    * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
172    * warning dialog box is displayed.</li>
173    * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
174    * when shading by annotation</li>
175    * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
176    * when shading by annotation</li>
177    * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
178    * requests to be redirected to a mirror of http://www.jalview.org</li>
179    * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
180    * alignment figure to accommodate even the longest sequence ID or annotation
181    * label.</li>
182    * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
183    * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
184    * will override this).</li>
185    * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
186    * record</li>
187    * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
188    * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
189    * display</li>
190    * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
191    * display</li>
192    * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
193    * display</li>
194    * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
195    * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
196    * </li>
197    *
198    * </ul>
199    * Deprecated settings:
200    * <ul>
201    * *
202    * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
203    * startup (JWS1 services only)</li>
204    * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
205    * (JWS1 services only)</li>
206    * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
207    * services in the desktop GUI</li>
208    * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
209    * panel in web service preferences</li>
210    * </ul>
211    *
212    * @author $author$
213    * @version $Revision$
214    */
 
215    public class Cache
216    {
217    /**
218    * property giving log4j level for CASTOR loggers
219    */
220    public static final String CASTORLOGLEVEL = "logs.Castor.level";
221   
222    /**
223    * property giving log4j level for AXIS loggers
224    */
225    public static final String AXISLOGLEVEL = "logs.Axis.level";
226   
227    /**
228    * property giving log4j level for Jalview Log
229    */
230    public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
231   
232    /**
233    * Sifts settings
234    */
235    public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
236    .getProperty("user.home") + File.separatorChar
237    + ".sifts_downloads" + File.separatorChar;
238   
239    private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
240   
241    private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
242   
243    /**
244    * Identifiers.org download settings
245    */
246    private static final String ID_ORG_FILE = System.getProperty("user.home")
247    + File.separatorChar + ".identifiers.org.ids.json";
248   
249    /**
250    * Allowed values are PDB or mmCIF
251    */
252    private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
253    .toString();
254   
255    private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
256    .toString();
257   
258    /*
259    * a date formatter using a fixed (rather than the user's) locale;
260    * this ensures that date properties can be written and re-read successfully
261    * even if the user changes their locale setting
262    */
263    private static final DateFormat date_format = SimpleDateFormat
264    .getDateTimeInstance(SimpleDateFormat.MEDIUM,
265    SimpleDateFormat.MEDIUM, Locale.UK);
266   
267    /**
268    * Initialises the Jalview Application Log
269    */
270    public static Logger log;
271   
272    /** Jalview Properties */
273    public static Properties applicationProperties = new Properties()
274    {
275    // override results in properties output in alphabetical order
 
276  0 toggle @Override
277    public synchronized Enumeration<Object> keys()
278    {
279  0 return Collections.enumeration(new TreeSet<>(super.keySet()));
280    }
281    };
282   
283    /** Default file is ~/.jalview_properties */
284    static String propertiesFile;
285   
286    private static boolean propsAreReadOnly = Platform.isJS();
287   
288    private final static String JS_PROPERTY_PREFIX = "jalview_";
289   
 
290  51 toggle public static void initLogger()
291    {
292  51 if (log != null)
293    {
294  32 return;
295    }
296  19 try
297    {
298    // TODO: redirect stdout and stderr here in order to grab the output of
299    // the log
300   
301  19 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
302    "System.err");
303  19 ap.setName("JalviewLogger");
304  19 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
305    // log output
306  19 Logger laxis = Logger.getLogger("org.apache.axis");
307  19 Logger lcastor = Logger.getLogger("org.exolab.castor");
308  19 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
309   
310  19 laxis.setLevel(Level.toLevel(
311    Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
312  19 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
313    Level.INFO.toString())));
314  19 lcastor = Logger.getLogger("org.exolab.castor.xml");
315  19 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
316    Level.INFO.toString())));
317    // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
318    // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
319    // Level.INFO.toString())));
320    // we shouldn't need to do this
321  19 org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.INFO);
322   
323  19 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
324    .getDefault("logs.Jalview.level", Level.INFO.toString())));
325    // laxis.addAppender(ap);
326    // lcastor.addAppender(ap);
327    // jalview.bin.Cache.log.addAppender(ap);
328    // Tell the user that debug is enabled
329  19 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
330    } catch (Exception ex)
331    {
332  0 System.err.println("Problems initializing the log4j system\n");
333  0 ex.printStackTrace(System.err);
334    }
335    }
336   
337    /**
338    * Loads properties from the given properties file. Any existing properties
339    * are first cleared.
340    */
 
341  110 toggle public static void loadProperties(String propsFile)
342    {
343  110 propertiesFile = propsFile;
344  110 if (propsFile == null && !propsAreReadOnly)
345    {
346  17 propertiesFile = System.getProperty("user.home") + File.separatorChar
347    + ".jalview_properties";
348    }
349    else
350    {
351    // don't corrupt the file we've been given.
352  93 propsAreReadOnly = true;
353    }
354   
355  110 if (propertiesFile == null)
356    { // BH 2019
357  7 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
358    applicationProperties);
359    }
360    else
361    {
362  103 try
363    {
364  103 InputStream fis;
365  103 try
366    {
367  103 fis = new java.net.URL(propertiesFile).openStream();
368  0 System.out.println(
369    "Loading jalview properties from : " + propertiesFile);
370  0 System.out.println(
371    "Disabling Jalview writing to user's local properties file.");
372  0 propsAreReadOnly = true;
373   
374    } catch (Exception ex)
375    {
376  103 fis = null;
377    }
378  103 if (fis == null)
379    {
380  103 fis = new FileInputStream(propertiesFile);
381    }
382  103 applicationProperties.clear();
383  103 applicationProperties.load(fis);
384   
385    // remove any old build properties
386   
387  103 deleteBuildProperties();
388  103 fis.close();
389    } catch (Exception ex)
390    {
391  0 System.out.println("Error reading properties file: " + ex);
392    }
393    }
394  110 if (getDefault("USE_PROXY", false))
395    {
396  0 String proxyServer = getDefault("PROXY_SERVER", ""),
397    proxyPort = getDefault("PROXY_PORT", "8080");
398   
399  0 System.out.println("Using proxyServer: " + proxyServer
400    + " proxyPort: " + proxyPort);
401   
402  0 System.setProperty("http.proxyHost", proxyServer);
403  0 System.setProperty("http.proxyPort", proxyPort);
404    }
405   
406    // LOAD THE AUTHORS FROM THE authors.props file
407  110 String authorDetails = resolveResourceURLFor("/authors.props");
408   
409  110 try
410    {
411  110 if (authorDetails != null)
412    {
413  110 URL localJarFileURL = new URL(authorDetails);
414  110 InputStream in = localJarFileURL.openStream();
415  110 applicationProperties.load(in);
416  110 in.close();
417    }
418    } catch (Exception ex)
419    {
420  0 System.out.println("Error reading author details: " + ex);
421  0 authorDetails = null;
422    }
423  110 if (authorDetails == null)
424    {
425  0 applicationProperties.remove("AUTHORS");
426  0 applicationProperties.remove("AUTHORFNAMES");
427  0 applicationProperties.remove("YEAR");
428    }
429   
430  110 loadBuildProperties(false);
431   
432  110 SiftsSettings
433    .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
434   
435  110 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
436    .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
437   
438  110 SiftsSettings.setFailSafePIDThreshold(
439    jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
440    DEFAULT_FAIL_SAFE_PID_THRESHOLD));
441   
442  110 SiftsSettings.setCacheThresholdInDays(
443    jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
444    DEFAULT_CACHE_THRESHOLD_IN_DAYS));
445   
446  110 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
447    "http://www.jalview.org/services/identifiers"));
448  110 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
449   
450  110 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
451    .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
452  110 StructureImportSettings
453    .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
454    // StructureImportSettings
455    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
456    // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
457   
458  110 String jnlpVersion = System.getProperty("jalview.version");
459   
460    // jnlpVersion will be null if a latest version check for the channel needs to
461    // be done
462    // Dont do this check if running in headless mode
463   
464  110 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
465    && (System.getProperty("java.awt.headless") == null || System
466    .getProperty("java.awt.headless").equals("false")))
467    {
468  4 new Thread()
469    {
 
470  4 toggle @Override
471    public void run()
472    {
473  4 String orgtimeout = System
474    .getProperty("sun.net.client.defaultConnectTimeout");
475  4 if (orgtimeout == null)
476    {
477  4 orgtimeout = "30";
478  4 System.out.println("# INFO: Setting default net timeout to "
479    + orgtimeout + " seconds.");
480    }
481  4 String remoteVersion = null;
482  4 try
483    {
484  4 System.setProperty("sun.net.client.defaultConnectTimeout",
485    "5000");
486  4 java.net.URL url = new java.net.URL(Cache
487    .getDefault("www.jalview.org", "http://www.jalview.org")
488    + "/webstart/jalview.jnlp");
489  4 BufferedReader in = new BufferedReader(
490    new InputStreamReader(url.openStream()));
491  4 String line = null;
492  ? while ((line = in.readLine()) != null)
493    {
494  272 if (line.indexOf("jalview.version") == -1)
495    {
496  268 continue;
497    }
498   
499  4 line = line.substring(line.indexOf("value=") + 7);
500  4 line = line.substring(0, line.lastIndexOf("\""));
501  4 remoteVersion = line;
502  4 break;
503    }
504    } catch (Exception ex)
505    {
506  0 System.out.println(
507    "Non-fatal exception when checking version at www.jalview.org :");
508  0 System.out.println(ex);
509  0 remoteVersion = getProperty("VERSION");
510    }
511  4 System.setProperty("sun.net.client.defaultConnectTimeout",
512    orgtimeout);
513   
514  4 setProperty("LATEST_VERSION", remoteVersion);
515    }
516    }.start();
517    }
518    else
519    {
520  106 if (jnlpVersion != null)
521    {
522  0 setProperty("LATEST_VERSION", jnlpVersion);
523    }
524    else
525    {
526  106 applicationProperties.remove("LATEST_VERSION");
527    }
528    }
529   
530    // LOAD USERDEFINED COLOURS
531  110 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
532  110 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
533    false);
534    }
535   
536    /**
537    * construct a resource URL for the given absolute resource pathname
538    *
539    * @param resourcePath
540    * @return
541    */
 
542  255 toggle private static String resolveResourceURLFor(String resourcePath)
543    {
544  255 String url = null;
545  255 if (Platform.isJS() || !Cache.class.getProtectionDomain()
546    .getCodeSource().getLocation().toString().endsWith(".jar"))
547    {
548  255 try
549    {
550  255 url = Cache.class.getResource(resourcePath).toString();
551    } catch (Exception ex)
552    {
553  0 System.err.println("Failed to resolve resource " + resourcePath + ": "
554    + ex.getMessage());
555    }
556    }
557    else
558    {
559  0 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
560    .getLocation().toString().concat("!" + resourcePath));
561    }
562  255 return url;
563    }
564   
 
565  145 toggle public static void loadBuildProperties(boolean reportVersion)
566    {
567  145 String codeInstallation = getProperty("INSTALLATION");
568  145 boolean printVersion = codeInstallation == null;
569   
570    /*
571    * read build properties - from the Jalview jar for a Java distribution,
572    * or from codebase file in test or JalviewJS context
573    */
574  145 try
575    {
576  145 String buildDetails = resolveResourceURLFor("/.build_properties");
577  145 URL localJarFileURL = new URL(buildDetails);
578  145 InputStream in = localJarFileURL.openStream();
579  145 applicationProperties.load(in);
580  145 in.close();
581    } catch (Exception ex)
582    {
583  0 System.out.println("Error reading build details: " + ex);
584  0 applicationProperties.remove("VERSION");
585    }
586  145 String codeVersion = getProperty("VERSION");
587  145 codeInstallation = getProperty("INSTALLATION");
588   
589  145 if (codeVersion == null)
590    {
591    // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
592  0 codeVersion = "Test";
593  0 codeInstallation = "";
594    }
595    else
596    {
597  145 codeInstallation = " (" + codeInstallation + ")";
598    }
599  145 setProperty("VERSION", codeVersion);
600  145 new BuildDetails(codeVersion, null, codeInstallation);
601  145 if (printVersion && reportVersion)
602    {
603  18 System.out
604    .println("Jalview Version: " + codeVersion + codeInstallation);
605    }
606    }
607   
 
608  103 toggle private static void deleteBuildProperties()
609    {
610  103 applicationProperties.remove("LATEST_VERSION");
611  103 applicationProperties.remove("VERSION");
612  103 applicationProperties.remove("AUTHORS");
613  103 applicationProperties.remove("AUTHORFNAMES");
614  103 applicationProperties.remove("YEAR");
615  103 applicationProperties.remove("BUILD_DATE");
616  103 applicationProperties.remove("INSTALLATION");
617    }
618   
619    /**
620    * Gets Jalview application property of given key. Returns null if key not
621    * found
622    *
623    * @param key
624    * Name of property
625    *
626    * @return Property value
627    */
 
628  21943 toggle public static String getProperty(String key)
629    {
630  21943 String prop = applicationProperties.getProperty(key);
631  21942 if (prop == null && Platform.isJS())
632    {
633  0 prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
634    + "_" + JS_PROPERTY_PREFIX + key);
635    }
636  21942 return prop;
637    }
638   
639    /**
640    * These methods are used when checking if the saved preference is different
641    * to the default setting
642    */
643   
 
644  15591 toggle public static boolean getDefault(String property, boolean def)
645    {
646  15591 String string = getProperty(property);
647  15591 if (string != null)
648    {
649  10278 def = Boolean.valueOf(string).booleanValue();
650    }
651   
652  15591 return def;
653    }
654   
 
655  0 toggle public static int getDefault(String property, int def)
656    {
657  0 String string = getProperty(property);
658  0 if (string != null)
659    {
660  0 try
661    {
662  0 def = Integer.parseInt(string);
663    } catch (NumberFormatException e)
664    {
665  0 System.out.println("Error parsing int property '" + property
666    + "' with value '" + string + "'");
667    }
668    }
669   
670  0 return def;
671    }
672   
673    /**
674    * Answers the value of the given property, or the supplied default value if
675    * the property is not set
676    */
 
677  4653 toggle public static String getDefault(String property, String def)
678    {
679  4653 String value = getProperty(property);
680  4653 return value == null ? def : value;
681    }
682   
683    /**
684    * Stores property in the file "HOME_DIR/.jalview_properties"
685    *
686    * @param key
687    * Name of object
688    * @param obj
689    * String value of property
690    *
691    * @return previous value of property (or null)
692    */
 
693  355 toggle public static Object setProperty(String key, String obj)
694    {
695  355 Object oldValue = null;
696  355 try
697    {
698  355 oldValue = applicationProperties.setProperty(key, obj);
699  355 if (propertiesFile != null && !propsAreReadOnly)
700    {
701  57 FileOutputStream out = new FileOutputStream(propertiesFile);
702  57 applicationProperties.store(out, "---JalviewX Properties File---");
703  57 out.close();
704    }
705    } catch (Exception ex)
706    {
707  0 System.out.println(
708    "Error setting property: " + key + " " + obj + "\n" + ex);
709    }
710  355 return oldValue;
711    }
712   
713    /**
714    * remove the specified property from the jalview properties file
715    *
716    * @param string
717    */
 
718  0 toggle public static void removeProperty(String string)
719    {
720  0 applicationProperties.remove(string);
721  0 saveProperties();
722    }
723   
724    /**
725    * save the properties to the jalview properties path
726    */
 
727  0 toggle public static void saveProperties()
728    {
729  0 if (!propsAreReadOnly)
730    {
731  0 try
732    {
733  0 FileOutputStream out = new FileOutputStream(propertiesFile);
734  0 applicationProperties.store(out, "---JalviewX Properties File---");
735  0 out.close();
736    } catch (Exception ex)
737    {
738  0 System.out.println("Error saving properties: " + ex);
739    }
740    }
741    }
742   
743    /**
744    * internal vamsas class discovery state
745    */
746    private static int vamsasJarsArePresent = -1;
747   
748    /**
749    * Searches for vamsas client classes on class path.
750    *
751    * @return true if vamsas client is present on classpath
752    */
 
753  0 toggle public static boolean vamsasJarsPresent()
754    {
755  0 if (vamsasJarsArePresent == -1)
756    {
757  0 try
758    {
759  0 if (jalview.jbgui.GDesktop.class.getClassLoader()
760    .loadClass("uk.ac.vamsas.client.VorbaId") != null)
761    {
762  0 jalview.bin.Cache.log.debug(
763    "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
764  0 vamsasJarsArePresent = 1;
765  0 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
766  0 lvclient.setLevel(Level.toLevel(Cache
767    .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
768   
769  0 lvclient.addAppender(log.getAppender("JalviewLogger"));
770    // Tell the user that debug is enabled
771  0 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
772    }
773    } catch (Exception e)
774    {
775  0 vamsasJarsArePresent = 0;
776  0 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
777    }
778    }
779  0 return (vamsasJarsArePresent > 0);
780    }
781   
782    /**
783    * internal vamsas class discovery state
784    */
785    private static int groovyJarsArePresent = -1;
786   
787    /**
788    * Searches for vamsas client classes on class path.
789    *
790    * @return true if vamsas client is present on classpath
791    */
 
792  0 toggle public static boolean groovyJarsPresent()
793    {
794  0 if (groovyJarsArePresent == -1)
795    {
796  0 try
797    {
798  0 if (Cache.class.getClassLoader()
799    .loadClass("groovy.lang.GroovyObject") != null)
800    {
801  0 jalview.bin.Cache.log.debug(
802    "Found Groovy (groovy.lang.GroovyObject can be loaded)");
803  0 groovyJarsArePresent = 1;
804  0 Logger lgclient = Logger.getLogger("groovy");
805  0 lgclient.setLevel(Level.toLevel(Cache
806    .getDefault("logs.Groovy.Level", Level.INFO.toString())));
807   
808  0 lgclient.addAppender(log.getAppender("JalviewLogger"));
809    // Tell the user that debug is enabled
810  0 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
811    }
812    } catch (Error e)
813    {
814  0 groovyJarsArePresent = 0;
815  0 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
816    } catch (Exception e)
817    {
818  0 groovyJarsArePresent = 0;
819  0 jalview.bin.Cache.log.debug("Groovy Classes are not present");
820    }
821    }
822  0 return (groovyJarsArePresent > 0);
823    }
824   
825    /**
826    * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
827    * enabled.
828    */
829    protected static Object tracker = null;
830   
831    protected static Class trackerfocus = null;
832   
833    protected static Class jgoogleanalyticstracker = null;
834   
835    /**
836    * Initialise the google tracker if it is not done already.
837    */
 
838  0 toggle public static void initGoogleTracker()
839    {
840  0 if (tracker == null)
841    {
842  0 if (jgoogleanalyticstracker == null)
843    {
844    // try to get the tracker class
845  0 try
846    {
847  0 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
848    "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
849  0 trackerfocus = Cache.class.getClassLoader()
850    .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
851    } catch (Exception e)
852    {
853  0 log.debug(
854    "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
855  0 tracker = null;
856  0 jgoogleanalyticstracker = null;
857  0 trackerfocus = null;
858  0 return;
859    }
860    }
861    // now initialise tracker
862  0 Exception re = null, ex = null;
863  0 Error err = null;
864  0 String vrs = "No Version Accessible";
865  0 try
866    {
867    // Google analytics tracking code for Library Finder
868  0 tracker = jgoogleanalyticstracker
869    .getConstructor(new Class[]
870    { String.class, String.class, String.class })
871    .newInstance(new Object[]
872    { "Jalview Desktop",
873    (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
874    + jalview.bin.Cache.getDefault("BUILD_DATE",
875    "unknown")),
876    "UA-9060947-1" });
877  0 jgoogleanalyticstracker
878    .getMethod("trackAsynchronously", new Class[]
879    { trackerfocus })
880    .invoke(tracker, new Object[]
881    { trackerfocus.getConstructor(new Class[] { String.class })
882    .newInstance(new Object[]
883    { "Application Started." }) });
884    } catch (RuntimeException e)
885    {
886  0 re = e;
887    } catch (Exception e)
888    {
889  0 ex = e;
890    } catch (Error e)
891    {
892  0 err = e;
893    }
894  0 if (re != null || ex != null || err != null)
895    {
896  0 if (log != null)
897    {
898  0 if (re != null)
899    {
900  0 log.debug("Caught runtime exception in googletracker init:",
901    re);
902    }
903  0 if (ex != null)
904    {
905  0 log.warn(
906    "Failed to initialise GoogleTracker for Jalview Desktop with version "
907    + vrs,
908    ex);
909    }
910  0 if (err != null)
911    {
912  0 log.error(
913    "Whilst initing GoogleTracker for Jalview Desktop version "
914    + vrs,
915    err);
916    }
917    }
918    else
919    {
920  0 if (re != null)
921    {
922  0 System.err.println(
923    "Debug: Caught runtime exception in googletracker init:"
924    + vrs);
925  0 re.printStackTrace();
926    }
927  0 if (ex != null)
928    {
929  0 System.err.println(
930    "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
931    + vrs);
932  0 ex.printStackTrace();
933    }
934   
935  0 if (err != null)
936    {
937  0 System.err.println(
938    "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
939    + vrs);
940  0 err.printStackTrace();
941    }
942    }
943    }
944    else
945    {
946  0 log.debug("Successfully initialised tracker.");
947    }
948    }
949    }
950   
951    /**
952    * get the user's default colour if available
953    *
954    * @param property
955    * @param defcolour
956    * @return
957    */
 
958  0 toggle public static Color getDefaultColour(String property, Color defcolour)
959    {
960  0 String colprop = getProperty(property);
961  0 if (colprop == null)
962    {
963  0 return defcolour;
964    }
965  0 Color col = ColorUtils.parseColourString(colprop);
966  0 if (col == null)
967    {
968  0 log.warn("Couldn't parse '" + colprop + "' as a colour for "
969    + property);
970    }
971  0 return (col == null) ? defcolour : col;
972    }
973   
974    /**
975    * store a colour as a Jalview user default property
976    *
977    * @param property
978    * @param colour
979    */
 
980  0 toggle public static void setColourProperty(String property, Color colour)
981    {
982  0 setProperty(property, jalview.util.Format.getHexString(colour));
983    }
984   
985    /**
986    * Stores a formatted date in a jalview property, using a fixed locale.
987    *
988    * @param propertyName
989    * @param date
990    * @return the formatted date string
991    */
 
992  17 toggle public static String setDateProperty(String propertyName, Date date)
993    {
994  17 String formatted = date_format.format(date);
995  17 setProperty(propertyName, formatted);
996  17 return formatted;
997    }
998   
999    /**
1000    * Reads a date stored in a Jalview property, parses it (using a fixed locale
1001    * format) and returns as a Date, or null if parsing fails
1002    *
1003    * @param propertyName
1004    * @return
1005    *
1006    */
 
1007  6 toggle public static Date getDateProperty(String propertyName)
1008    {
1009  6 String val = getProperty(propertyName);
1010  6 if (val != null)
1011    {
1012  6 try
1013    {
1014  6 return date_format.parse(val);
1015    } catch (Exception ex)
1016    {
1017  2 System.err.println("Invalid or corrupt date in property '"
1018    + propertyName + "' : value was '" + val + "'");
1019    }
1020    }
1021  2 return null;
1022    }
1023   
1024    /**
1025    * get and parse a property as an integer. send any parsing problems to
1026    * System.err
1027    *
1028    * @param property
1029    * @return null or Integer
1030    */
 
1031  16 toggle public static Integer getIntegerProperty(String property)
1032    {
1033  16 String val = getProperty(property);
1034  ? if (val != null && (val = val.trim()).length() > 0)
1035    {
1036  0 try
1037    {
1038  0 return Integer.valueOf(val);
1039    } catch (NumberFormatException x)
1040    {
1041  0 System.err.println("Invalid integer in property '" + property
1042    + "' (value was '" + val + "')");
1043    }
1044    }
1045  16 return null;
1046    }
1047   
1048    /**
1049    * Set the specified value, or remove it if null or empty. Does not save the
1050    * properties file.
1051    *
1052    * @param propName
1053    * @param value
1054    */
 
1055  0 toggle public static void setOrRemove(String propName, String value)
1056    {
1057  0 if (propName == null)
1058    {
1059  0 return;
1060    }
1061  0 if (value == null || value.trim().length() < 1)
1062    {
1063  0 Cache.applicationProperties.remove(propName);
1064    }
1065    else
1066    {
1067  0 Cache.applicationProperties.setProperty(propName, value);
1068    }
1069    }
1070   
1071    /**
1072    * Loads in user colour schemes from files.
1073    *
1074    * @param files
1075    * a '|'-delimited list of file paths
1076    */
 
1077  110 toggle public static void initUserColourSchemes(String files)
1078    {
1079  110 if (files == null || files.length() == 0)
1080    {
1081  110 return;
1082    }
1083   
1084    // In case colours can't be loaded, we'll remove them
1085    // from the default list here.
1086  0 StringBuffer coloursFound = new StringBuffer();
1087  0 StringTokenizer st = new StringTokenizer(files, "|");
1088  0 while (st.hasMoreElements())
1089    {
1090  0 String file = st.nextToken();
1091  0 try
1092    {
1093  0 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1094  0 if (ucs != null)
1095    {
1096  0 if (coloursFound.length() > 0)
1097    {
1098  0 coloursFound.append("|");
1099    }
1100  0 coloursFound.append(file);
1101  0 ColourSchemes.getInstance().registerColourScheme(ucs);
1102    }
1103    } catch (Exception ex)
1104    {
1105  0 System.out.println("Error loading User ColourFile\n" + ex);
1106    }
1107    }
1108  0 if (!files.equals(coloursFound.toString()))
1109    {
1110  0 if (coloursFound.toString().length() > 1)
1111    {
1112  0 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1113    coloursFound.toString());
1114    }
1115    else
1116    {
1117  0 applicationProperties
1118    .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1119    }
1120    }
1121    }
1122   
1123    /**
1124    * Initial logging information helper for various versions output
1125    *
1126    * @param prefix
1127    * @param value
1128    * @param defaultValue
1129    */
 
1130  72 toggle private static void appendIfNotNull(StringBuilder sb, String prefix,
1131    String value, String suffix, String defaultValue)
1132    {
1133  72 if (value == null && defaultValue == null)
1134    {
1135  54 return;
1136    }
1137  18 String line = prefix + (value != null ? value : defaultValue) + suffix;
1138  18 sb.append(line);
1139    }
1140   
1141    /**
1142    *
1143    * @return Jalview version, build details and JVM platform version for console
1144    */
 
1145  18 toggle public static String getVersionDetailsForConsole()
1146    {
1147  18 StringBuilder sb = new StringBuilder();
1148  18 sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
1149  18 sb.append("\n");
1150  18 sb.append("Jalview Installation: "
1151    + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1152  18 sb.append("\n");
1153  18 sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1154  18 sb.append("\n");
1155  18 sb.append("Java version: " + System.getProperty("java.version"));
1156  18 sb.append("\n");
1157  18 sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
1158  18 sb.append("\n");
1159  18 appendIfNotNull(sb, "Install4j version: ",
1160    System.getProperty("sys.install4jVersion"), "\n", null);
1161  18 appendIfNotNull(sb, "Install4j template version: ",
1162    System.getProperty("installer_template_version"), "\n", null);
1163  18 appendIfNotNull(sb, "Launcher version: ",
1164    System.getProperty("launcher_version"), "\n", null);
1165  18 LookAndFeel laf = UIManager.getLookAndFeel();
1166  18 String lafName = laf == null?"Not obtained":laf.getName();
1167  18 String lafClass = laf == null?"unknown":laf.getClass().getName();
1168  18 appendIfNotNull(sb, "LookAndFeel: ", lafName+" ("+lafClass+")", "\n", null);
1169    // Not displayed in release version ( determined by possible version number regex 9[9.]*9[.-_a9]* )
1170  18 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$", jalview.bin.Cache.getDefault("VERSION", "TEST"))) {
1171  0 appendIfNotNull(sb, "Getdown appdir: ",
1172    System.getProperty("getdownappdir"), "\n", null);
1173  0 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1174    "\n", "unknown");
1175    }
1176  18 return sb.toString();
1177    }
1178   
1179    /**
1180    *
1181    * @return build details as reported in splashscreen
1182    */
 
1183  188 toggle public static String getBuildDetailsForSplash()
1184    {
1185    // consider returning more human friendly info
1186    // eg 'built from Source' or update channel
1187  188 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1188    }
1189    }
  • 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.