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package jalview.bin; |
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import jalview.datamodel.PDBEntry; |
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import jalview.gui.UserDefinedColours; |
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import jalview.schemes.ColourSchemeLoader; |
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import jalview.schemes.ColourSchemes; |
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import jalview.schemes.UserColourScheme; |
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import jalview.structure.StructureImportSettings; |
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import jalview.urls.IdOrgSettings; |
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import jalview.util.ColorUtils; |
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import jalview.ws.sifts.SiftsSettings; |
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import java.awt.Color; |
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import java.io.BufferedReader; |
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import java.io.File; |
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import java.io.FileInputStream; |
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import java.io.FileOutputStream; |
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import java.io.InputStream; |
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import java.io.InputStreamReader; |
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import java.text.DateFormat; |
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import java.text.SimpleDateFormat; |
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import java.util.Collections; |
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import java.util.Date; |
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import java.util.Enumeration; |
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import java.util.Locale; |
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import java.util.Properties; |
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import java.util.StringTokenizer; |
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import java.util.TreeSet; |
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import org.apache.log4j.ConsoleAppender; |
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import org.apache.log4j.Level; |
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import org.apache.log4j.Logger; |
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import org.apache.log4j.SimpleLayout; |
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@author |
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@version |
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| 42.7% |
Uncovered Elements: 185 (323) |
Complexity: 83 |
Complexity Density: 0.37 |
|
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public class Cache |
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{ |
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public static final String CASTORLOGLEVEL = "logs.Castor.level"; |
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public static final String AXISLOGLEVEL = "logs.Axis.level"; |
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public static final String JALVIEWLOGLEVEL = "logs.Jalview.level"; |
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public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE"; |
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public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL"; |
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public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE"; |
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public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System |
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.getProperty("user.home") + File.separatorChar |
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+ ".sifts_downloads" + File.separatorChar; |
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private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2"; |
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private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30"; |
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private static final String ID_ORG_FILE = System.getProperty("user.home") |
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+ File.separatorChar + ".identifiers.org.ids.json"; |
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private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF |
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.toString(); |
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private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER |
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.toString(); |
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private static final DateFormat date_format = SimpleDateFormat |
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.getDateTimeInstance(SimpleDateFormat.MEDIUM, |
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SimpleDateFormat.MEDIUM, Locale.UK); |
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public static Logger log; |
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public static Properties applicationProperties = new Properties() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public synchronized Enumeration<Object> keys() |
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{ |
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return Collections.enumeration(new TreeSet<>(super.keySet())); |
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} |
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}; |
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static String propertiesFile; |
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private static boolean propsAreReadOnly = |
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false; |
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|
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| 89.5% |
Uncovered Elements: 2 (19) |
Complexity: 3 |
Complexity Density: 0.18 |
|
292 |
13 |
public static void initLogger()... |
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{ |
294 |
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if (log != null) |
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{ |
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return; |
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} |
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1 |
try |
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{ |
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|
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ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), |
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"System.err"); |
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ap.setName("JalviewLogger"); |
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org.apache.log4j.Logger.getRootLogger().addAppender(ap); |
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|
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1 |
Logger laxis = Logger.getLogger("org.apache.axis"); |
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Logger lcastor = Logger.getLogger("org.exolab.castor"); |
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jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview"); |
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|
312 |
1 |
laxis.setLevel(Level.toLevel( |
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Cache.getDefault("logs.Axis.Level", Level.INFO.toString()))); |
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1 |
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", |
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Level.INFO.toString()))); |
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1 |
lcastor = Logger.getLogger("org.exolab.castor.xml"); |
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1 |
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", |
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Level.INFO.toString()))); |
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320 |
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1 |
jalview.bin.Cache.log.setLevel(Level.toLevel(Cache |
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.getDefault("logs.Jalview.level", Level.INFO.toString()))); |
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326 |
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1 |
jalview.bin.Cache.log.debug("Jalview Debugging Output Follows."); |
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} catch (Exception ex) |
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{ |
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System.err.println("Problems initializing the log4j system\n"); |
332 |
0 |
ex.printStackTrace(System.err); |
333 |
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} |
334 |
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} |
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336 |
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337 |
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338 |
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339 |
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| 74.1% |
Uncovered Elements: 21 (81) |
Complexity: 14 |
Complexity Density: 0.2 |
|
340 |
69 |
public static void loadProperties(String propsFile)... |
341 |
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{ |
342 |
69 |
propertiesFile = propsFile; |
343 |
69 |
if (propsFile == null) |
344 |
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{ |
345 |
4 |
propertiesFile = System.getProperty("user.home") + File.separatorChar |
346 |
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+ ".jalview_properties"; |
347 |
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} |
348 |
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else |
349 |
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{ |
350 |
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|
351 |
65 |
propsAreReadOnly = true; |
352 |
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} |
353 |
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|
354 |
69 |
try |
355 |
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{ |
356 |
69 |
InputStream fis; |
357 |
69 |
try |
358 |
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{ |
359 |
69 |
fis = new java.net.URL(propertiesFile).openStream(); |
360 |
0 |
System.out.println( |
361 |
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"Loading jalview properties from : " + propertiesFile); |
362 |
0 |
System.out.println( |
363 |
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"Disabling Jalview writing to user's local properties file."); |
364 |
0 |
propsAreReadOnly = true; |
365 |
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|
366 |
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} catch (Exception ex) |
367 |
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{ |
368 |
69 |
fis = null; |
369 |
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} |
370 |
69 |
if (fis == null) |
371 |
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{ |
372 |
69 |
fis = new FileInputStream(propertiesFile); |
373 |
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} |
374 |
69 |
applicationProperties.clear(); |
375 |
69 |
applicationProperties.load(fis); |
376 |
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|
377 |
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|
378 |
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|
379 |
69 |
deleteBuildProperties(); |
380 |
69 |
fis.close(); |
381 |
|
} catch (Exception ex) |
382 |
|
{ |
383 |
0 |
System.out.println("Error reading properties file: " + ex); |
384 |
|
} |
385 |
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|
386 |
69 |
if (getDefault("USE_PROXY", false)) |
387 |
|
{ |
388 |
0 |
String proxyServer = getDefault("PROXY_SERVER", ""), |
389 |
|
proxyPort = getDefault("PROXY_PORT", "8080"); |
390 |
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|
391 |
0 |
System.out.println("Using proxyServer: " + proxyServer |
392 |
|
+ " proxyPort: " + proxyPort); |
393 |
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|
394 |
0 |
System.setProperty("http.proxyHost", proxyServer); |
395 |
0 |
System.setProperty("http.proxyPort", proxyPort); |
396 |
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} |
397 |
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|
398 |
|
|
399 |
69 |
try |
400 |
|
{ |
401 |
69 |
String authorDetails = |
402 |
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"jar:" |
403 |
|
.concat(Cache.class.getProtectionDomain().getCodeSource() |
404 |
|
.getLocation().toString().concat("!/authors.props")); |
405 |
|
|
406 |
69 |
java.net.URL localJarFileURL = new java.net.URL(authorDetails); |
407 |
|
|
408 |
69 |
InputStream in = localJarFileURL.openStream(); |
409 |
0 |
applicationProperties.load(in); |
410 |
0 |
in.close(); |
411 |
|
} catch (Exception ex) |
412 |
|
{ |
413 |
69 |
System.out.println("Error reading author details: " + ex); |
414 |
69 |
applicationProperties.remove("AUTHORS"); |
415 |
69 |
applicationProperties.remove("AUTHORFNAMES"); |
416 |
69 |
applicationProperties.remove("YEAR"); |
417 |
|
} |
418 |
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|
419 |
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|
420 |
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|
421 |
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|
422 |
69 |
try |
423 |
|
{ |
424 |
69 |
String buildDetails = |
425 |
|
"jar:".concat(Cache.class.getProtectionDomain() |
426 |
|
.getCodeSource().getLocation().toString() |
427 |
|
.concat("!/.build_properties")); |
428 |
|
|
429 |
69 |
java.net.URL localJarFileURL = new java.net.URL(buildDetails); |
430 |
|
|
431 |
69 |
InputStream in = localJarFileURL.openStream(); |
432 |
0 |
applicationProperties.load(in); |
433 |
0 |
in.close(); |
434 |
|
} catch (Exception ex) |
435 |
|
{ |
436 |
69 |
System.out.println("Error reading build details: " + ex); |
437 |
69 |
applicationProperties.remove("VERSION"); |
438 |
|
} |
439 |
|
|
440 |
69 |
String jnlpVersion = System.getProperty("jalview.version"); |
441 |
69 |
String codeVersion = getProperty("VERSION"); |
442 |
69 |
String codeInstallation = getProperty("INSTALLATION"); |
443 |
69 |
if (codeVersion == null) |
444 |
|
{ |
445 |
|
|
446 |
69 |
codeVersion = "Test"; |
447 |
69 |
jnlpVersion = "Test"; |
448 |
69 |
codeInstallation = ""; |
449 |
|
} |
450 |
|
else |
451 |
|
{ |
452 |
0 |
codeInstallation = " (" + codeInstallation + ")"; |
453 |
|
} |
454 |
69 |
new BuildDetails(codeVersion, null, codeInstallation); |
455 |
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|
456 |
69 |
SiftsSettings |
457 |
|
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); |
458 |
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|
459 |
69 |
SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache |
460 |
|
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); |
461 |
|
|
462 |
69 |
SiftsSettings.setFailSafePIDThreshold( |
463 |
|
jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold", |
464 |
|
DEFAULT_FAIL_SAFE_PID_THRESHOLD)); |
465 |
|
|
466 |
69 |
SiftsSettings.setCacheThresholdInDays( |
467 |
|
jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", |
468 |
|
DEFAULT_CACHE_THRESHOLD_IN_DAYS)); |
469 |
|
|
470 |
69 |
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", |
471 |
|
"http://www.jalview.org/services/identifiers")); |
472 |
69 |
IdOrgSettings.setDownloadLocation(ID_ORG_FILE); |
473 |
|
|
474 |
69 |
System.out |
475 |
|
.println("Jalview Version: " + codeVersion + codeInstallation); |
476 |
|
|
477 |
69 |
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache |
478 |
|
.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); |
479 |
69 |
StructureImportSettings |
480 |
|
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); |
481 |
|
|
482 |
|
|
483 |
|
|
484 |
|
|
485 |
|
|
486 |
69 |
if (jnlpVersion == null && getDefault("VERSION_CHECK", true) |
487 |
|
&& (System.getProperty("java.awt.headless") == null || System |
488 |
|
.getProperty("java.awt.headless").equals("false"))) |
489 |
|
{ |
490 |
|
|
|
|
| 0% |
Uncovered Elements: 29 (29) |
Complexity: 5 |
Complexity Density: 0.23 |
|
491 |
|
class VersionChecker extends Thread |
492 |
|
{ |
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 5 |
Complexity Density: 0.23 |
|
493 |
0 |
@Override... |
494 |
|
public void run() |
495 |
|
{ |
496 |
0 |
String orgtimeout = System |
497 |
|
.getProperty("sun.net.client.defaultConnectTimeout"); |
498 |
0 |
if (orgtimeout == null) |
499 |
|
{ |
500 |
0 |
orgtimeout = "30"; |
501 |
0 |
System.out.println("# INFO: Setting default net timeout to " |
502 |
|
+ orgtimeout + " seconds."); |
503 |
|
} |
504 |
0 |
String remoteVersion = null; |
505 |
0 |
try |
506 |
|
{ |
507 |
0 |
System.setProperty("sun.net.client.defaultConnectTimeout", |
508 |
|
"5000"); |
509 |
0 |
java.net.URL url = new java.net.URL(Cache |
510 |
|
.getDefault("www.jalview.org", "http://www.jalview.org") |
511 |
|
+ "/webstart/jalview.jnlp"); |
512 |
0 |
BufferedReader in = new BufferedReader( |
513 |
|
new InputStreamReader(url.openStream())); |
514 |
0 |
String line = null; |
515 |
0 |
while ((line = in.readLine()) != null) |
516 |
|
{ |
517 |
0 |
if (line.indexOf("jalview.version") == -1) |
518 |
|
{ |
519 |
0 |
continue; |
520 |
|
} |
521 |
|
|
522 |
0 |
line = line.substring(line.indexOf("value=") + 7); |
523 |
0 |
line = line.substring(0, line.lastIndexOf("\"")); |
524 |
0 |
remoteVersion = line; |
525 |
0 |
break; |
526 |
|
} |
527 |
|
} catch (Exception ex) |
528 |
|
{ |
529 |
0 |
System.out.println( |
530 |
|
"Non-fatal exception when checking version at www.jalview.org :"); |
531 |
0 |
System.out.println(ex); |
532 |
0 |
remoteVersion = getProperty("VERSION"); |
533 |
|
} |
534 |
0 |
System.setProperty("sun.net.client.defaultConnectTimeout", |
535 |
|
orgtimeout); |
536 |
|
|
537 |
0 |
setProperty("LATEST_VERSION", remoteVersion); |
538 |
|
} |
539 |
|
} |
540 |
|
|
541 |
0 |
VersionChecker vc = new VersionChecker(); |
542 |
0 |
vc.start(); |
543 |
|
} |
544 |
|
else |
545 |
|
{ |
546 |
69 |
if (jnlpVersion != null) |
547 |
|
{ |
548 |
69 |
setProperty("LATEST_VERSION", jnlpVersion); |
549 |
|
} |
550 |
|
else |
551 |
|
{ |
552 |
0 |
applicationProperties.remove("LATEST_VERSION"); |
553 |
|
} |
554 |
|
} |
555 |
|
|
556 |
69 |
setProperty("VERSION", codeVersion); |
557 |
|
|
558 |
|
|
559 |
69 |
jalview.bin.Cache |
560 |
|
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); |
561 |
69 |
jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", |
562 |
|
false); |
563 |
|
} |
564 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
|
565 |
69 |
private static void deleteBuildProperties()... |
566 |
|
{ |
567 |
69 |
applicationProperties.remove("LATEST_VERSION"); |
568 |
69 |
applicationProperties.remove("VERSION"); |
569 |
69 |
applicationProperties.remove("AUTHORS"); |
570 |
69 |
applicationProperties.remove("AUTHORFNAMES"); |
571 |
69 |
applicationProperties.remove("YEAR"); |
572 |
69 |
applicationProperties.remove("BUILD_DATE"); |
573 |
69 |
applicationProperties.remove("INSTALLATION"); |
574 |
|
} |
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
@param |
581 |
|
|
582 |
|
|
583 |
|
@return |
584 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
585 |
16103 |
public static String getProperty(String key)... |
586 |
|
{ |
587 |
16103 |
return applicationProperties.getProperty(key); |
588 |
|
} |
589 |
|
|
590 |
|
|
591 |
|
|
592 |
|
|
593 |
|
|
594 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
595 |
11754 |
public static boolean getDefault(String property, boolean def)... |
596 |
|
{ |
597 |
11754 |
String string = getProperty(property); |
598 |
11753 |
if (string != null) |
599 |
|
{ |
600 |
4486 |
def = Boolean.valueOf(string).booleanValue(); |
601 |
|
} |
602 |
|
|
603 |
11754 |
return def; |
604 |
|
} |
605 |
|
|
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
610 |
3272 |
public static String getDefault(String property, String def)... |
611 |
|
{ |
612 |
3273 |
String value = getProperty(property); |
613 |
3275 |
return value == null ? def : value; |
614 |
|
} |
615 |
|
|
616 |
|
|
617 |
|
|
618 |
|
|
619 |
|
@param |
620 |
|
|
621 |
|
@param |
622 |
|
|
623 |
|
|
624 |
|
@return |
625 |
|
|
|
|
| 54.5% |
Uncovered Elements: 5 (11) |
Complexity: 3 |
Complexity Density: 0.33 |
|
626 |
267 |
public static Object setProperty(String key, String obj)... |
627 |
|
{ |
628 |
267 |
Object oldValue = null; |
629 |
267 |
try |
630 |
|
{ |
631 |
267 |
oldValue = applicationProperties.setProperty(key, obj); |
632 |
267 |
if (!propsAreReadOnly) |
633 |
|
{ |
634 |
0 |
FileOutputStream out = new FileOutputStream(propertiesFile); |
635 |
0 |
applicationProperties.store(out, "---JalviewX Properties File---"); |
636 |
0 |
out.close(); |
637 |
|
} |
638 |
|
} catch (Exception ex) |
639 |
|
{ |
640 |
0 |
System.out.println( |
641 |
|
"Error setting property: " + key + " " + obj + "\n" + ex); |
642 |
|
} |
643 |
267 |
return oldValue; |
644 |
|
} |
645 |
|
|
646 |
|
|
647 |
|
|
648 |
|
|
649 |
|
@param |
650 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
651 |
0 |
public static void removeProperty(String string)... |
652 |
|
{ |
653 |
0 |
applicationProperties.remove(string); |
654 |
0 |
saveProperties(); |
655 |
|
} |
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
660 |
0 |
public static void saveProperties()... |
661 |
|
{ |
662 |
0 |
if (!propsAreReadOnly) |
663 |
|
{ |
664 |
0 |
try |
665 |
|
{ |
666 |
0 |
FileOutputStream out = new FileOutputStream(propertiesFile); |
667 |
0 |
applicationProperties.store(out, "---JalviewX Properties File---"); |
668 |
0 |
out.close(); |
669 |
|
} catch (Exception ex) |
670 |
|
{ |
671 |
0 |
System.out.println("Error saving properties: " + ex); |
672 |
|
} |
673 |
|
} |
674 |
|
} |
675 |
|
|
676 |
|
|
677 |
|
|
678 |
|
|
679 |
|
private static int vamsasJarsArePresent = -1; |
680 |
|
|
681 |
|
|
682 |
|
|
683 |
|
|
684 |
|
@return |
685 |
|
|
|
|
| 81.2% |
Uncovered Elements: 3 (16) |
Complexity: 4 |
Complexity Density: 0.33 |
|
686 |
11 |
public static boolean vamsasJarsPresent()... |
687 |
|
{ |
688 |
11 |
if (vamsasJarsArePresent == -1) |
689 |
|
{ |
690 |
1 |
try |
691 |
|
{ |
692 |
1 |
if (jalview.jbgui.GDesktop.class.getClassLoader() |
693 |
|
.loadClass("uk.ac.vamsas.client.VorbaId") != null) |
694 |
|
{ |
695 |
1 |
jalview.bin.Cache.log.debug( |
696 |
|
"Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)"); |
697 |
1 |
vamsasJarsArePresent = 1; |
698 |
1 |
Logger lvclient = Logger.getLogger("uk.ac.vamsas"); |
699 |
1 |
lvclient.setLevel(Level.toLevel(Cache |
700 |
|
.getDefault("logs.Vamsas.Level", Level.INFO.toString()))); |
701 |
|
|
702 |
1 |
lvclient.addAppender(log.getAppender("JalviewLogger")); |
703 |
|
|
704 |
1 |
lvclient.debug("Jalview Vamsas Client Debugging Output Follows."); |
705 |
|
} |
706 |
|
} catch (Exception e) |
707 |
|
{ |
708 |
0 |
vamsasJarsArePresent = 0; |
709 |
0 |
jalview.bin.Cache.log.debug("Vamsas Classes are not present"); |
710 |
|
} |
711 |
|
} |
712 |
11 |
return (vamsasJarsArePresent > 0); |
713 |
|
} |
714 |
|
|
715 |
|
|
716 |
|
|
717 |
|
|
718 |
|
private static int groovyJarsArePresent = -1; |
719 |
|
|
720 |
|
|
721 |
|
|
722 |
|
|
723 |
|
@return |
724 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 5 |
Complexity Density: 0.36 |
|
725 |
0 |
public static boolean groovyJarsPresent()... |
726 |
|
{ |
727 |
0 |
if (groovyJarsArePresent == -1) |
728 |
|
{ |
729 |
0 |
try |
730 |
|
{ |
731 |
0 |
if (Cache.class.getClassLoader() |
732 |
|
.loadClass("groovy.lang.GroovyObject") != null) |
733 |
|
{ |
734 |
0 |
jalview.bin.Cache.log.debug( |
735 |
|
"Found Groovy (groovy.lang.GroovyObject can be loaded)"); |
736 |
0 |
groovyJarsArePresent = 1; |
737 |
0 |
Logger lgclient = Logger.getLogger("groovy"); |
738 |
0 |
lgclient.setLevel(Level.toLevel(Cache |
739 |
|
.getDefault("logs.Groovy.Level", Level.INFO.toString()))); |
740 |
|
|
741 |
0 |
lgclient.addAppender(log.getAppender("JalviewLogger")); |
742 |
|
|
743 |
0 |
lgclient.debug("Jalview Groovy Client Debugging Output Follows."); |
744 |
|
} |
745 |
|
} catch (Error e) |
746 |
|
{ |
747 |
0 |
groovyJarsArePresent = 0; |
748 |
0 |
jalview.bin.Cache.log.debug("Groovy Classes are not present", e); |
749 |
|
} catch (Exception e) |
750 |
|
{ |
751 |
0 |
groovyJarsArePresent = 0; |
752 |
0 |
jalview.bin.Cache.log.debug("Groovy Classes are not present"); |
753 |
|
} |
754 |
|
} |
755 |
0 |
return (groovyJarsArePresent > 0); |
756 |
|
} |
757 |
|
|
758 |
|
|
759 |
|
|
760 |
|
|
761 |
|
|
762 |
|
protected static Object tracker = null; |
763 |
|
|
764 |
|
protected static Class trackerfocus = null; |
765 |
|
|
766 |
|
protected static Class jgoogleanalyticstracker = null; |
767 |
|
|
768 |
|
|
769 |
|
|
770 |
|
|
|
|
| 0% |
Uncovered Elements: 57 (57) |
Complexity: 17 |
Complexity Density: 0.46 |
|
771 |
0 |
public static void initGoogleTracker()... |
772 |
|
{ |
773 |
0 |
if (tracker == null) |
774 |
|
{ |
775 |
0 |
if (jgoogleanalyticstracker == null) |
776 |
|
{ |
777 |
|
|
778 |
0 |
try |
779 |
|
{ |
780 |
0 |
jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass( |
781 |
|
"com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker"); |
782 |
0 |
trackerfocus = Cache.class.getClassLoader() |
783 |
|
.loadClass("com.boxysystems.jgoogleanalytics.FocusPoint"); |
784 |
|
} catch (Exception e) |
785 |
|
{ |
786 |
0 |
log.debug( |
787 |
|
"com.boxysystems.jgoogleanalytics package is not present - tracking not enabled."); |
788 |
0 |
tracker = null; |
789 |
0 |
jgoogleanalyticstracker = null; |
790 |
0 |
trackerfocus = null; |
791 |
0 |
return; |
792 |
|
} |
793 |
|
} |
794 |
|
|
795 |
0 |
Exception re = null, ex = null; |
796 |
0 |
Error err = null; |
797 |
0 |
String vrs = "No Version Accessible"; |
798 |
0 |
try |
799 |
|
{ |
800 |
|
|
801 |
0 |
tracker = jgoogleanalyticstracker |
802 |
|
.getConstructor(new Class[] |
803 |
|
{ String.class, String.class, String.class }) |
804 |
|
.newInstance(new Object[] |
805 |
|
{ "Jalview Desktop", |
806 |
|
(vrs = jalview.bin.Cache.getProperty("VERSION") + "_" |
807 |
|
+ jalview.bin.Cache.getDefault("BUILD_DATE", |
808 |
|
"unknown")), |
809 |
|
"UA-9060947-1" }); |
810 |
0 |
jgoogleanalyticstracker |
811 |
|
.getMethod("trackAsynchronously", new Class[] |
812 |
|
{ trackerfocus }) |
813 |
|
.invoke(tracker, new Object[] |
814 |
|
{ trackerfocus.getConstructor(new Class[] { String.class }) |
815 |
|
.newInstance(new Object[] |
816 |
|
{ "Application Started." }) }); |
817 |
|
} catch (RuntimeException e) |
818 |
|
{ |
819 |
0 |
re = e; |
820 |
|
} catch (Exception e) |
821 |
|
{ |
822 |
0 |
ex = e; |
823 |
|
} catch (Error e) |
824 |
|
{ |
825 |
0 |
err = e; |
826 |
|
} |
827 |
0 |
if (re != null || ex != null || err != null) |
828 |
|
{ |
829 |
0 |
if (log != null) |
830 |
|
{ |
831 |
0 |
if (re != null) |
832 |
|
{ |
833 |
0 |
log.debug("Caught runtime exception in googletracker init:", |
834 |
|
re); |
835 |
|
} |
836 |
0 |
if (ex != null) |
837 |
|
{ |
838 |
0 |
log.warn( |
839 |
|
"Failed to initialise GoogleTracker for Jalview Desktop with version " |
840 |
|
+ vrs, |
841 |
|
ex); |
842 |
|
} |
843 |
0 |
if (err != null) |
844 |
|
{ |
845 |
0 |
log.error( |
846 |
|
"Whilst initing GoogleTracker for Jalview Desktop version " |
847 |
|
+ vrs, |
848 |
|
err); |
849 |
|
} |
850 |
|
} |
851 |
|
else |
852 |
|
{ |
853 |
0 |
if (re != null) |
854 |
|
{ |
855 |
0 |
System.err.println( |
856 |
|
"Debug: Caught runtime exception in googletracker init:" |
857 |
|
+ vrs); |
858 |
0 |
re.printStackTrace(); |
859 |
|
} |
860 |
0 |
if (ex != null) |
861 |
|
{ |
862 |
0 |
System.err.println( |
863 |
|
"Warning: Failed to initialise GoogleTracker for Jalview Desktop with version " |
864 |
|
+ vrs); |
865 |
0 |
ex.printStackTrace(); |
866 |
|
} |
867 |
|
|
868 |
0 |
if (err != null) |
869 |
|
{ |
870 |
0 |
System.err.println( |
871 |
|
"ERROR: Whilst initing GoogleTracker for Jalview Desktop version " |
872 |
|
+ vrs); |
873 |
0 |
err.printStackTrace(); |
874 |
|
} |
875 |
|
} |
876 |
|
} |
877 |
|
else |
878 |
|
{ |
879 |
0 |
log.debug("Successfully initialised tracker."); |
880 |
|
} |
881 |
|
} |
882 |
|
} |
883 |
|
|
884 |
|
|
885 |
|
|
886 |
|
|
887 |
|
@param |
888 |
|
@param |
889 |
|
@return |
890 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
891 |
0 |
public static Color getDefaultColour(String property, Color defcolour)... |
892 |
|
{ |
893 |
0 |
String colprop = getProperty(property); |
894 |
0 |
if (colprop == null) |
895 |
|
{ |
896 |
0 |
return defcolour; |
897 |
|
} |
898 |
0 |
Color col = ColorUtils.parseColourString(colprop); |
899 |
0 |
if (col == null) |
900 |
|
{ |
901 |
0 |
log.warn("Couldn't parse '" + colprop + "' as a colour for " |
902 |
|
+ property); |
903 |
|
} |
904 |
0 |
return (col == null) ? defcolour : col; |
905 |
|
} |
906 |
|
|
907 |
|
|
908 |
|
|
909 |
|
|
910 |
|
@param |
911 |
|
@param |
912 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
913 |
0 |
public static void setColourProperty(String property, Color colour)... |
914 |
|
{ |
915 |
0 |
setProperty(property, jalview.util.Format.getHexString(colour)); |
916 |
|
} |
917 |
|
|
918 |
|
|
919 |
|
|
920 |
|
|
921 |
|
@param |
922 |
|
@param |
923 |
|
@return |
924 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
925 |
10 |
public static String setDateProperty(String propertyName, Date date)... |
926 |
|
{ |
927 |
10 |
String formatted = date_format.format(date); |
928 |
10 |
setProperty(propertyName, formatted); |
929 |
10 |
return formatted; |
930 |
|
} |
931 |
|
|
932 |
|
|
933 |
|
|
934 |
|
|
935 |
|
|
936 |
|
@param |
937 |
|
@return |
938 |
|
|
939 |
|
|
|
|
| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
940 |
3 |
public static Date getDateProperty(String propertyName)... |
941 |
|
{ |
942 |
3 |
String val = getProperty(propertyName); |
943 |
3 |
if (val != null) |
944 |
|
{ |
945 |
3 |
try |
946 |
|
{ |
947 |
3 |
return date_format.parse(val); |
948 |
|
} catch (Exception ex) |
949 |
|
{ |
950 |
1 |
System.err.println("Invalid or corrupt date in property '" |
951 |
|
+ propertyName + "' : value was '" + val + "'"); |
952 |
|
} |
953 |
|
} |
954 |
1 |
return null; |
955 |
|
} |
956 |
|
|
957 |
|
|
958 |
|
|
959 |
|
|
960 |
|
|
961 |
|
@param |
962 |
|
@return |
963 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 4 |
Complexity Density: 0.67 |
|
964 |
0 |
public static Integer getIntegerProperty(String property)... |
965 |
|
{ |
966 |
0 |
String val = getProperty(property); |
967 |
0 |
if (val != null && (val = val.trim()).length() > 0) |
968 |
|
{ |
969 |
0 |
try |
970 |
|
{ |
971 |
0 |
return Integer.valueOf(val); |
972 |
|
} catch (NumberFormatException x) |
973 |
|
{ |
974 |
0 |
System.err.println("Invalid integer in property '" + property |
975 |
|
+ "' (value was '" + val + "')"); |
976 |
|
} |
977 |
|
} |
978 |
0 |
return null; |
979 |
|
} |
980 |
|
|
981 |
|
|
982 |
|
|
983 |
|
|
984 |
|
|
985 |
|
@param |
986 |
|
@param |
987 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 4 |
Complexity Density: 0.8 |
|
988 |
0 |
public static void setOrRemove(String propName, String value)... |
989 |
|
{ |
990 |
0 |
if (propName == null) |
991 |
|
{ |
992 |
0 |
return; |
993 |
|
} |
994 |
0 |
if (value == null || value.trim().length() < 1) |
995 |
|
{ |
996 |
0 |
Cache.applicationProperties.remove(propName); |
997 |
|
} |
998 |
|
else |
999 |
|
{ |
1000 |
0 |
Cache.applicationProperties.setProperty(propName, value); |
1001 |
|
} |
1002 |
|
} |
1003 |
|
|
1004 |
|
|
1005 |
|
|
1006 |
|
|
1007 |
|
@param |
1008 |
|
|
1009 |
|
|
|
|
| 10% |
Uncovered Elements: 27 (30) |
Complexity: 9 |
Complexity Density: 0.5 |
|
1010 |
69 |
public static void initUserColourSchemes(String files)... |
1011 |
|
{ |
1012 |
69 |
if (files == null || files.length() == 0) |
1013 |
|
{ |
1014 |
69 |
return; |
1015 |
|
} |
1016 |
|
|
1017 |
|
|
1018 |
|
|
1019 |
0 |
StringBuffer coloursFound = new StringBuffer(); |
1020 |
0 |
StringTokenizer st = new StringTokenizer(files, "|"); |
1021 |
0 |
while (st.hasMoreElements()) |
1022 |
|
{ |
1023 |
0 |
String file = st.nextToken(); |
1024 |
0 |
try |
1025 |
|
{ |
1026 |
0 |
UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file); |
1027 |
0 |
if (ucs != null) |
1028 |
|
{ |
1029 |
0 |
if (coloursFound.length() > 0) |
1030 |
|
{ |
1031 |
0 |
coloursFound.append("|"); |
1032 |
|
} |
1033 |
0 |
coloursFound.append(file); |
1034 |
0 |
ColourSchemes.getInstance().registerColourScheme(ucs); |
1035 |
|
} |
1036 |
|
} catch (Exception ex) |
1037 |
|
{ |
1038 |
0 |
System.out.println("Error loading User ColourFile\n" + ex); |
1039 |
|
} |
1040 |
|
} |
1041 |
0 |
if (!files.equals(coloursFound.toString())) |
1042 |
|
{ |
1043 |
0 |
if (coloursFound.toString().length() > 1) |
1044 |
|
{ |
1045 |
0 |
setProperty(UserDefinedColours.USER_DEFINED_COLOURS, |
1046 |
|
coloursFound.toString()); |
1047 |
|
} |
1048 |
|
else |
1049 |
|
{ |
1050 |
0 |
applicationProperties |
1051 |
|
.remove(UserDefinedColours.USER_DEFINED_COLOURS); |
1052 |
|
} |
1053 |
|
} |
1054 |
|
} |
1055 |
|
} |