#j2s.compiler.nonqualified.classes = null
#j2s.compiler.mode = debug
#a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made
-j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j.
+#j2s.class.replacements = org.apache.logging.log4j.->jalview.javascript.log4j.
j2s.template.html = utils/jalviewjs/template.html
j2s_coretemplate_html = utils/jalviewjs/coretemplate.html
#output file name for logging methods declared - delete the file to regenerate a listing
}
else
{
- Cache.log.error(
+ Cache.error(
"JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString());
}
}
}
} catch (IOException | NullPointerException e)
{
- Cache.log.error(
+ Cache.error(
"Error reading genetic codes data file " + fileName + ": "
+ e.getMessage());
}
}
} catch (IOException e)
{
- Cache.log.error(
+ Cache.error(
"Error reading nucleotide ambiguity codes data file: "
+ e.getMessage());
}
line.lastIndexOf(QUOTE));
if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
{
- Cache.log.error("wrong data length in code table: " + line);
+ Cache.error("wrong data length in code table: " + line);
}
else
{
eigenMatrix.tqli();
} catch (Exception q)
{
- Cache.log.error("Error computing PCA: " + q.getMessage());
+ Cache.error("Error computing PCA: " + q.getMessage());
q.printStackTrace();
}
}
*/
package jalview.analysis;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
if (one2many.contains(nam))
{
// countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // if (Cache.isDebugEnabled())
+ // Cache.debug("One 2 many relationship for
// "+nam.getName());
}
else
j.setPlaceholder(true);
}
}
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+ // if (Cache.isDebugEnabled() && countOne2Many>0) {
+ // Cache.debug("There were "+countOne2Many+" alignment
// sequence ids (out of "+one2many.size()+" unique ids) linked to two or
// more leaves.");
// }
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
-import org.apache.logging.log4j.Level;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.core.config.Configurator;
-import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
-import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
-import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFactory;
-import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
-
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
+import jalview.log.JLogger;
+import jalview.log.JLoggerLog4j;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
/**
* Initialises the Jalview Application Log
*/
- public static Logger log;
+
+ public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
+
+ public static JLoggerLog4j log;
// save the proxy properties set at startup
public final static String[] startupProxyProperties = {
private final static String JS_PROPERTY_PREFIX = "jalview_";
- public static void initLogger()
+ public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
+
+ public static JLogger.LogLevel getCachedLogLevel()
+ {
+ return getCachedLogLevel(JALVIEWLOGLEVEL);
+ }
+
+ public static JLogger.LogLevel getCachedLogLevel(String key)
+ {
+ return JLogger.toLevel(Cache.getDefault(key, "INFO"));
+ }
+
+ public static boolean initLogger()
{
if (log != null)
{
- return;
+ return true;
}
try
{
- // configure the root logger to stderr
- ConfigurationBuilder<BuiltConfiguration> builder = ConfigurationBuilderFactory
- .newConfigurationBuilder();
- AppenderComponentBuilder consoleApp = builder.newAppender("stderr",
- "Console");
- builder.add(consoleApp);
- Configurator.initialize(builder.build());
+ JLogger.LogLevel cachedLevel = getCachedLogLevel();
+ if (!Platform.isJS())
+ {
+ Log4j.init(cachedLevel);
+ }
// log output
- Logger laxis = LogManager.getLogger("org.apache.axis");
- log = LogManager.getLogger("jalview.bin.Jalview");
-
- Log4j.setLevel(laxis, Level.toLevel(
- Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
- // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- // Level.INFO.toString())));
- // we shouldn't need to do this
- Log4j.setRootLevel(Level.INFO);
-
- Log4j.setLevel(log, Level.toLevel(Cache
- .getDefault("logs.Jalview.level", Level.INFO.toString())));
- // laxis.addAppender(ap);
- // lcastor.addAppender(ap);
- // jalview.bin.Cache.log.addAppender(ap);
+ // is laxis used? Does getLogger do anything without a Logger object?
+ // Logger laxis = Log4j.getLogger("org.apache.axis", myLevel);
+ JLoggerLog4j.getLogger("org.apache.axis", cachedLevel);
+
+ // The main application logger
+ log = JLoggerLog4j.getLogger(JALVIEW_LOGGER_NAME, cachedLevel);
+ } catch (NoClassDefFoundError e)
+ {
+ System.err.println("Could not initialise the logger framework");
+ e.printStackTrace();
+ }
+
+ // Test message
+ if (log != null)
+ {
+ // Logging test message should got through the logger object
+ if (log.loggerExists())
+ log.debug(LOGGING_TEST_MESSAGE);
// Tell the user that debug is enabled
- log.debug(ChannelProperties.getProperty("app_name")
+ Cache.debug(ChannelProperties.getProperty("app_name")
+ " Debugging Output Follows.");
- } catch (Exception ex)
+ return true;
+ }
+ else
{
- System.err.println("Problems initializing the log4j system\n");
- ex.printStackTrace(System.err);
+ return false;
}
}
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ SiftsSettings.setSiftDownloadDirectory(Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
- jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+ Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
- jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
"https://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
- .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+ StructureImportSettings.setDefaultStructureFileFormat(
+ Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
- // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ // .setDefaultPDBFileParser(Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
String jnlpVersion = System.getProperty("jalview.version");
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- log.debug(
- "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
- Logger lvclient = LogManager.getLogger("uk.ac.vamsas");
- Log4j.setLevel(lvclient, Level.toLevel(Cache
- .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
-
- Log4j.addAppender(lvclient, log, "JalviewLogger");
+ JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
+ getCachedLogLevel("logs.Vamsas.Level"));
+ JLoggerLog4j.addAppender(lvclient, log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- log.debug("Vamsas Classes are not present");
+ debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- log.debug(
- "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
- Logger lgclient = LogManager.getLogger("groovy");
- Log4j.setLevel(lgclient, Level.toLevel(Cache
- .getDefault("logs.Groovy.Level", Level.INFO.toString())));
-
- Log4j.addAppender(lgclient, log, "JalviewLogger");
+ JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
+ getCachedLogLevel("logs.Groovy.Level"));
+ JLoggerLog4j.addAppender(lgclient, log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
} catch (Error e)
{
groovyJarsArePresent = 0;
- log.debug("Groovy Classes are not present", e);
+ debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- log.debug("Groovy Classes are not present");
+ debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
.loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log.debug(
- "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
{ String.class, String.class, String.class })
.newInstance(new Object[]
{ ChannelProperties.getProperty("app_name") + " Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
- + jalview.bin.Cache.getDefault("BUILD_DATE",
- "unknown")),
+ (vrs = Cache.getProperty("VERSION") + "_"
+ + Cache.getDefault("BUILD_DATE", "unknown")),
"UA-9060947-1" });
jgoogleanalyticstracker
.getMethod("trackAsynchronously", new Class[]
}
if (re != null || ex != null || err != null)
{
- if (log != null)
+ if (re != null)
{
- if (re != null)
- {
- log.debug("Caught runtime exception in googletracker init:",
- re);
- }
- if (ex != null)
- {
- log.warn(
- "Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs,
- ex);
- }
- if (err != null)
- {
- log.error(
- "Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs,
- err);
- }
+ debug("Caught runtime exception in googletracker init:", re);
}
- else
+ if (ex != null)
{
- if (re != null)
- {
- System.err.println(
- "Debug: Caught runtime exception in googletracker init:"
- + vrs);
- re.printStackTrace();
- }
- if (ex != null)
- {
- System.err.println(
- "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs);
- ex.printStackTrace();
- }
-
- if (err != null)
- {
- System.err.println(
- "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs);
- err.printStackTrace();
- }
+ warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs, ex);
+ }
+ if (err != null)
+ {
+ error("Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs, err);
}
}
else
{
- log.debug("Successfully initialised tracker.");
+ debug("Successfully initialised tracker.");
}
}
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- log.warn("Couldn't parse '" + colprop + "' as a colour for "
- + property);
+ warn("Couldn't parse '" + colprop + "' as a colour for " + property);
}
return (col == null) ? defcolour : col;
}
StringBuilder sb = new StringBuilder();
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Version: ");
- sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append(Cache.getDefault("VERSION", "TEST"));
sb.append("\n");
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Installation: ");
- sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append(Cache.getDefault("INSTALLATION", "unknown"));
sb.append("\n");
sb.append("Build Date: ");
- sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
sb.append("\n");
sb.append("Java version: ");
sb.append(System.getProperty("java.version"));
// Not displayed in release version ( determined by possible version number
// regex 9[9.]*9[.-_a9]* )
if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
- jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ Cache.getDefault("VERSION", "TEST")))
{
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdownappdir"), "\n", null);
{
// consider returning more human friendly info
// eg 'built from Source' or update channel
- return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ return Cache.getDefault("INSTALLATION", "unknown");
}
public static String getStackTraceString(Throwable t)
case Cache.PROXYTYPE_NONE:
if (!previousProxyType.equals(proxyType))
{
- Cache.log.info("Setting no proxy settings");
+ Cache.info("Setting no proxy settings");
Cache.setProxyProperties(null, null, null, null, null, null, null,
null, null);
}
case Cache.PROXYTYPE_CUSTOM:
// always re-set a custom proxy -- it might have changed, particularly
// password
- Cache.log.info("Setting custom proxy settings");
+ Cache.info("Setting custom proxy settings");
boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
Cache.getDefault("PROXY_PORT", null),
proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
break;
default: // system proxy settings by default
- Cache.log.info("Setting system proxy settings");
+ Cache.info("Setting system proxy settings");
Cache.resetProxyProperties();
}
}
}
}
- public final static int TRACE = 10;
+ public static void trace(String message)
+ {
+ if (initLogger())
+ {
+ log.trace(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+ }
+
+ public static void trace(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.trace(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+ }
+
+ public static void debug(String message)
+ {
+ if (initLogger())
+ {
+ log.debug(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void debug(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.debug(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
- public final static int DEBUG = 20;
+ public static void info(String message)
+ {
+ if (initLogger())
+ {
+ log.info(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
- public final static int INFO = 30;
+ }
- public final static int WARN = 40;
+ public static void info(String message, Throwable t)
+ {
+ if (initLogger())
+ {
+ log.info(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
- public final static int ERROR = 50;
+ }
- public static boolean println(int level, String message)
+ public static void warn(String message)
{
- if (Cache.log == null)
+ if (initLogger())
{
- if (level >= WARN)
- System.err.println(message);
- else if (level >= INFO)
- System.out.println(message);
- // not printing debug or trace messages
- return false;
+ log.warn(message, null);
}
- if (level >= ERROR)
+ else
{
- Cache.log.error(message);
+ System.out.println(message);
}
- else if (level >= WARN)
+
+ }
+
+ public static void warn(String message, Throwable t)
+ {
+ if (initLogger())
{
- Cache.log.warn(message);
+ log.warn(message, t);
}
- else if (level >= INFO)
+ else
{
- Cache.log.info(message);
+ System.out.println(message);
+ t.printStackTrace();
}
- else if (level >= DEBUG)
+
+ }
+
+ public static void error(String message)
+ {
+ if (initLogger())
{
- Cache.log.debug(message);
+ log.error(message, null);
}
else
{
- Cache.log.trace(message);
+ System.err.println(message);
}
- return true;
+
}
- public static void trace(String message)
+ public static void error(String message, Throwable t)
{
- println(TRACE, message);
+ if (initLogger())
+ {
+ log.error(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
}
- public static void debug(String message)
+ public static void fatal(String message)
{
- println(DEBUG, message);
+ if (initLogger())
+ {
+ log.fatal(message, null);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+
}
- public static void info(String message)
+ public static void fatal(String message, Throwable t)
{
- println(INFO, message);
+ if (initLogger())
+ {
+ log.fatal(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
}
- public static void warn(String message)
+ public static boolean isDebugEnabled()
{
- println(WARN, message);
+ return log == null ? false : log.isDebugEnabled();
}
- public static void error(String message)
+ public static boolean isTraceEnabled()
{
- println(ERROR, message);
+ return log == null ? false : log.isTraceEnabled();
}
/**
*/
package jalview.bin;
-import java.util.Locale;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
System.out.println("Launcher version: " + val);
}
+ try
+ {
+ Cache.initLogger();
+ } catch (NoClassDefFoundError error)
+ {
+ error.printStackTrace();
+ System.out.println("\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
+ System.exit(0);
+ }
+
// report Jalview version
Cache.loadBuildProperties(true);
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
- try
- {
- Cache.initLogger();
- } catch (NoClassDefFoundError error)
- {
- error.printStackTrace();
- System.out.println("\nEssential logging libraries not found."
- + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
- System.exit(0);
- }
desktop = null;
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(e.getMessage());
+ Cache.info("Cannot set Taskbar");
+ Cache.error(e.getMessage());
// e.printStackTrace();
} catch (Throwable t)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(t.getMessage());
+ Cache.info("Cannot set Taskbar");
+ Cache.error(t.getMessage());
// t.printStackTrace();
}
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
+ Cache.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
System.out.println("CMD questionnaire[-" + url
+ "] executed successfully!");
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug(
+ Cache.debug(
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
* @j2sIgnore
*/
{
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org",
- "https://www.jalview.org")
+ file = Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ "/examples/exampleFile_2_7.jvp");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
"http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
file.replace("http:", "https:");
lafSet = setCrossPlatformLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "system":
lafSet = setSystemLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "gtk":
lafSet = setGtkLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "metal":
lafSet = setMetalLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "nimbus":
lafSet = setNimbusLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "quaqua":
lafSet = setQuaquaLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "vaqua":
lafSet = setVaquaLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "mac":
lafSet = setMacLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Cache.error("Could not set requested laf=" + laf);
}
break;
case "none":
break;
default:
- Cache.log.error("Requested laf=" + laf + " not implemented");
+ Cache.error("Requested laf=" + laf + " not implemented");
}
if (!lafSet)
{
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Cache.error("Unexpected Look and Feel Exception");
+ Cache.error(ex.getMessage());
+ Cache.debug(Cache.getStackTraceString(ex));
}
return set;
}
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Cache.error("Unexpected Look and Feel Exception");
+ Cache.error(ex.getMessage());
+ Cache.debug(Cache.getStackTraceString(ex));
}
return set;
}
if (info.getName() != null && nameStartsWith
? info.getName().toLowerCase(Locale.ROOT)
.startsWith(name.toLowerCase(Locale.ROOT))
- : info.getName().toLowerCase(Locale.ROOT).equals(name.toLowerCase(Locale.ROOT)))
+ : info.getName().toLowerCase(Locale.ROOT)
+ .equals(name.toLowerCase(Locale.ROOT)))
{
className = info.getClassName();
break;
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Cache.error("Unexpected Look and Feel Exception");
+ Cache.error(ex.getMessage());
+ Cache.debug(Cache.getStackTraceString(ex));
}
return set;
}
@Override
public void run()
{
- Cache.log.debug(
- "Initialising googletracker for usage stats.");
+ Cache.debug("Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
- Cache.log.debug("Tracking enabled.");
+ Cache.debug("Tracking enabled.");
}
}, new Runnable()
{
@Override
public void run()
{
- Cache.log.debug("Not enabling Google Tracking.");
+ Cache.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);
chromosome, map);
} catch (NullPointerException | NumberFormatException e)
{
- Cache.log.error("Error looking up gene loci: " + e.getMessage());
+ Cache.error("Error looking up gene loci: " + e.getMessage());
e.printStackTrace();
}
return null;
if (upx.size() > 1)
{
- Cache.log.warn(
+ Cache.warn(
"Implementation issue - multiple uniprot acc on product sequence.");
}
}
}
else
{
- Cache.log.error("File not found: " + filePath);
+ Cache.error("File not found: " + filePath);
}
}
private String jmolScript(String script)
{
- Cache.log.debug(">>Jmol>> " + script);
+ Cache.debug(">>Jmol>> " + script);
String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
- Cache.log.debug("<<Jmol<< " + s);
+ Cache.debug("<<Jmol<< " + s);
return s;
}
int rc = conn.getResponseCode();
if (rc != HttpURLConnection.HTTP_OK)
{
- Cache.log.error(
+ Cache.error(
String.format("Error status from %s: %d", rpcUrl, rc));
return result;
}
} catch (SocketException e)
{
// thrown when 'quit' command is sent to PyMol
- Cache.log.warn(String.format("Request to %s returned %s", rpcUrl,
+ Cache.warn(String.format("Request to %s returned %s", rpcUrl,
e.toString()));
} catch (Exception e)
{
{
out.close();
}
- if (Cache.log.isTraceEnabled())
+ if (Cache.isTraceEnabled())
{
- Cache.log.trace("Sent: " + command.toString());
+ Cache.trace("Sent: " + command.toString());
if (result != null)
{
- Cache.log.trace("Received: " + result);
+ Cache.trace("Received: " + result);
}
}
}
this.pymolXmlRpcPort = getPortNumber();
if (pymolXmlRpcPort > 0)
{
- Cache.log.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
+ Cache.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
}
else
{
error += "Failed to read PyMOL XMLRPC port number";
- Cache.log.error(error);
+ Cache.error(error);
pymolProcess.destroy();
pymolProcess = null;
}
}
} catch (Exception e)
{
- Cache.log.error("Failed to get REST port number from " + responses
+ Cache.error("Failed to get REST port number from " + responses
+ ": " + e.getMessage());
// logger.error("Failed to get REST port number from " + responses + ": "
// + e.getMessage());
}
if (port == 0)
{
- Cache.log.error("Failed to start PyMOL with XMLRPC, response was: "
+ Cache.error("Failed to start PyMOL with XMLRPC, response was: "
+ responses);
}
- Cache.log.error("PyMOL started with XMLRPC on port " + port);
+ Cache.error("PyMOL started with XMLRPC on port " + port);
return port;
}
if (getResponse)
{
reply = lastReply;
- if (Cache.log.isDebugEnabled()) {
- Cache.log.debug(
+ if (Cache.isDebugEnabled()) {
+ Cache.debug(
"Response from command ('" + cmd + "') was:\n" + lastReply);
}
}
else
{
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug("Command executed: " + cmd);
+ Cache.debug("Command executed: " + cmd);
}
}
atomSpecs.add(spec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Failed to parse atomspec: " + atomSpec);
+ Cache.error("Failed to parse atomspec: " + atomSpec);
}
}
return atomSpecs;
spec = parseAtomSpec(atomSpec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Problem parsing atomspec " + atomSpec);
+ Cache.error("Problem parsing atomspec " + atomSpec);
continue;
}
}
}
long elapsed = System.currentTimeMillis() - now;
- Cache.log.info("Loaded Sequence Ontology from " + zipFile + " ("
+ Cache.info("Loaded Sequence Ontology from " + zipFile + " ("
+ elapsed + "ms)");
} catch (Exception e)
{
boolean oldTermIsObsolete = isObsolete(replaced);
if (newTermIsObsolete && !oldTermIsObsolete)
{
- Cache.log.debug("Ignoring " + term.getName()
+ Cache.debug("Ignoring " + term.getName()
+ " as obsolete and duplicated by "
+ replaced.getName());
term = replaced;
}
else if (!newTermIsObsolete && oldTermIsObsolete)
{
- Cache.log.debug("Ignoring " + replaced.getName()
+ Cache.debug("Ignoring " + replaced.getName()
+ " as obsolete and duplicated by " + term.getName());
}
else
{
- Cache.log.debug("Warning: " + term.getName()
+ Cache.debug("Warning: " + term.getName()
+ " has replaced " + replaced.getName()
+ " for lookup of '" + description + "'");
}
{
if (!termsNotFound.contains(term))
{
- Cache.log.error("SO term " + term + " invalid");
+ Cache.error("SO term " + term + " invalid");
termsNotFound.add(term);
}
}
@Override
public void actionPerformed(ActionEvent e)
{
- jalview.bin.Cache.setProperty(getAutosearchPreference(),
+ Cache.setProperty(getAutosearchPreference(),
Boolean.toString(btn_autosearch.isSelected()));
}
});
import java.util.Map;
import java.util.Objects;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
}
} catch (Exception mfe)
{
- jalview.bin.Cache.log.debug("Exception accessing urls", mfe);
+ Cache.debug("Exception accessing urls", mfe);
continue;
}
int colCounter = 0;
}
} catch (Exception x)
{
- Cache.log.warn(
+ Cache.warn(
"Couldn't retrieve 3d-beacons model for uniprot id"
+ searchTerm + " : " + tdbURL,
x);
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import jalview.util.Platform;
public void handleQuitRequestWith(
QuitEvent e, QuitResponse r)
{
- boolean confirmQuit = jalview.bin.Cache
+ boolean confirmQuit = Cache
.getDefault(
jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT,
true);
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = Cache.getDefault("SORT_ALIGNMENT",
"No sort");
if (sortby.equals("Id"))
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
*/
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
}
else
{
- Cache.log.error(MessageManager
+ Cache.error(MessageManager
.formatMessage("label.couldnt_save_file", new Object[]
{ lastFilenameSaved }));
}
BackupFiles backupfiles = null;
if (doBackup)
{
- Cache.log.trace(
+ Cache.trace(
"ALIGNFRAME making backupfiles object for " + file);
backupfiles = new BackupFiles(file);
}
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath()
: file;
- Cache.log.trace("ALIGNFRAME setting PrintWriter");
+ Cache.trace("ALIGNFRAME setting PrintWriter");
PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
if (backupfiles != null)
{
- Cache.log.trace("ALIGNFRAME about to write to temp file "
+ Cache.trace("ALIGNFRAME about to write to temp file "
+ backupfiles.getTempFilePath());
}
out.print(output);
- Cache.log.trace("ALIGNFRAME about to close file");
+ Cache.trace("ALIGNFRAME about to close file");
out.close();
- Cache.log.trace("ALIGNFRAME closed file");
+ Cache.trace("ALIGNFRAME closed file");
AlignFrame.this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
} catch (IOException e)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Cache.error(
"ALIGNFRAME Something happened writing the temp file");
- Cache.log.error(e.getMessage());
- Cache.log.debug(Cache.getStackTraceString(e));
+ Cache.error(e.getMessage());
+ Cache.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Cache.error(
"ALIGNFRAME Something unexpected happened writing the temp file");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Cache.error(ex.getMessage());
+ Cache.debug(Cache.getStackTraceString(ex));
}
if (doBackup)
{
backupfiles.setWriteSuccess(lastSaveSuccessful);
- Cache.log.debug("ALIGNFRAME writing temp file was "
+ Cache.debug("ALIGNFRAME writing temp file was "
+ (lastSaveSuccessful ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
- Cache.log.trace(
+ Cache.trace(
"ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
- Cache.log.debug(
+ Cache.debug(
"ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ (lastSaveSuccessful ? "" : "un")
+ "successfully");
public void associatedData_actionPerformed(ActionEvent e)
{
final JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
String tooltip = MessageManager
.getString("label.load_jalview_annotations");
public void run()
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
}
});
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Cache.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
if (originalSource != viewport)
{
- Cache.log.warn(
+ Cache.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.select_newick_like_tree_file"));
}
} catch (Exception e)
{
- Cache.log.debug(
+ Cache.debug(
"Exception during web service menu building process.",
e);
}
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log.warn(
+ Cache.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
+ Cache.error(
"Exception during translation. Please report this !", ex);
final String msg = MessageManager.getString(
"label.error_when_translating_sequences_submit_bug_report");
}
} catch (Exception x)
{
- Cache.log.debug(
+ Cache.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Cache.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Cache.debug("Setting viewport's view id : " + viewId);
}
init();
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Cache.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Cache.debug("Setting viewport's view id : " + viewId);
}
if (hiddenColumns != null)
// calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
if (needsUpdate)
{
- Cache.log.debug("trigger update for " + calcId);
+ Cache.debug("trigger update for " + calcId);
}
}
try
{
newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
// could not be validated and it is not clear if it is now being
// called. Log warning here in case it is called and unforeseen
// problems occur
- Cache.log.warn(
+ Cache.warn(
"Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
// scroll to start of panel
}
else
{
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.warn("Closing alignment panel which is already closed.");
+ Cache.warn("Closing alignment panel which is already closed.");
}
}
}
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Cache.debug("File locations are " + filesString);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ Cache.error("Couldn't open Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
new OOMWarning("When trying to add structures to the Jmol viewer!",
oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Cache.debug("File locations are " + filesString);
return;
} catch (Exception ex)
{
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ Cache.error("Couldn't add files to Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
try
{
- Cache.log.debug("Waiting around for jmb notify.");
+ Cache.debug("Waiting around for jmb notify.");
waitTotal += waitFor;
// Thread.sleep() throws an exception in JS
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
+ Cache.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
}
{
if (parent != null)
{
- Cache.log.debug("News window closed.");
+ Cache.debug("News window closed.");
jd = null;
parent.showNews(false);
}
public BlogReader(Desktop desktop)
{
- Cache.log.debug("Constructing news reader.");
+ Cache.debug("Constructing news reader.");
parent = desktop;
_channelModel = new ChannelListModel();
// Construct our jalview news channel
Channel chan = new Channel();
chan.setURL(
- jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
- jalview.bin.Cache.getDefault("www.jalview.org",
+ Cache.getDefault("JALVIEW_NEWS_RSS",
+ Cache.getDefault("www.jalview.org",
"https://www.jalview.org")
+ "/feeds/desktop/rss"));
loadLastM();
if (setvisible)
{
- Cache.log.debug("Will show jalview news automatically");
+ Cache.debug("Will show jalview news automatically");
showNews();
}
- Cache.log.debug("Completed construction of reader.");
+ Cache.debug("Completed construction of reader.");
}
MessageManager.getString("label.news_from_jalview"),
bounds.width, bounds.height);
jd.frame.setModalExclusionType(ModalExclusionType.NO_EXCLUDE);
- Cache.log.debug("Displaying news.");
+ Cache.debug("Displaying news.");
jd.waitForInput();
}
}
}
if (chan != null && chan.getItems() != null)
{
- Cache.log.debug("Scanning news items: newsnew=" + newsnew
+ Cache.debug("Scanning news items: newsnew=" + newsnew
+ " and lastDate is " + lastDate);
for (Item i : (List<Item>) chan.getItems())
{
{
String formatted = Cache
.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", lastDate);
- Cache.log.debug("Saved last read date as " + formatted);
+ Cache.debug("Saved last read date as " + formatted);
}
}
}
{
// this tests the detection of new news based on the last read date stored
// in jalview properties
- jalview.bin.Cache.loadProperties(null);
- jalview.bin.Cache.initLogger();
+ Cache.loadProperties(null);
+ Cache.initLogger();
// test will advance read date each time
Calendar today = Calendar.getInstance(),
lastread = Calendar.getInstance();
System.out.println("Set last date to " + formattedDate);
if (me.isNewsNew())
{
- Cache.log.debug("There is news to read.");
+ Cache.debug("There is news to read.");
}
else
{
- Cache.log.debug("There is no new news.");
+ Cache.debug("There is no new news.");
me.xf.setTitle("Testing : Last read is " + me.lastDate);
me.showNews();
me.xf.toFront();
}
- Cache.log.debug("Waiting for closure.");
+ Cache.debug("Waiting for closure.");
do
{
try
if (me.isNewsNew())
{
- Cache.log.debug("Still new news after reader displayed.");
+ Cache.debug("Still new news after reader displayed.");
}
if (lastread.getTime().before(me.lastDate))
{
- Cache.log.debug("The news was read.");
+ Cache.debug("The news was read.");
lastread.setTime(me.lastDate);
}
else
initChimera();
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Chimera viewer!", ex);
+ Cache.error("Couldn't open Chimera viewer!", ex);
}
}
int num = -1;
oomerror);
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Couldn't open " + pe.getFile() + " in Chimera viewer!",
ex);
} finally
{
- Cache.log.debug("File locations are " + files);
+ Cache.debug("File locations are " + files);
}
}
}
import java.io.PipedOutputStream;
import java.io.PrintStream;
+import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
-
-import org.apache.logging.log4j.Level;
+import javax.swing.border.Border;
+import javax.swing.text.DefaultCaret;
import jalview.bin.Cache;
+import jalview.log.JLoggerI.LogLevel;
+import jalview.log.JLoggerLog4j;
+import jalview.log.JalviewAppender;
import jalview.util.ChannelProperties;
-import jalview.util.Log4j;
import jalview.util.MessageManager;
+import jalview.util.Platform;
/**
* Simple Jalview Java Console. Version 1 - allows viewing of console output
private int MIN_HEIGHT = 250;
- private JComboBox<Level> logLevelCombo = new JComboBox<Level>();
+ private JComboBox<LogLevel> logLevelCombo = new JComboBox<LogLevel>();
- protected Level startingLogLevel = Level.INFO;
+ protected LogLevel startingLogLevel = LogLevel.INFO;
public Console()
{
// textArea = cpt.getTextArea();
textArea = new JTextArea();
textArea.setEditable(false);
+ // autoscroll
+ DefaultCaret caret = (DefaultCaret) textArea.getCaret();
+ caret.setUpdatePolicy(DefaultCaret.ALWAYS_UPDATE);
+ // toggle autoscroll by clicking on the text area
+ Border pausedBorder = BorderFactory.createMatteBorder(2, 2, 2, 2,
+ textArea.getForeground());
+ Border noBorder = BorderFactory.createEmptyBorder(2, 2, 2, 2);
+ JScrollPane scrollPane = new JScrollPane(textArea);
+ scrollPane.setBorder(noBorder);
+ textArea.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getButton() == MouseEvent.BUTTON1)
+ {
+ if (caret.getUpdatePolicy() == DefaultCaret.ALWAYS_UPDATE)
+ {
+ caret.setUpdatePolicy(DefaultCaret.NEVER_UPDATE);
+ scrollPane.setBorder(pausedBorder);
+ }
+ else
+ {
+ caret.setUpdatePolicy(DefaultCaret.ALWAYS_UPDATE);
+ textArea.setCaretPosition(textArea.getDocument().getLength());
+ scrollPane.setBorder(noBorder);
+ }
+ }
+ }
+ });
+
JButton clearButton = new JButton(
MessageManager.getString("action.clear"));
JButton copyToClipboardButton = new JButton(
JLabel logLevelLabel = new JLabel(
MessageManager.getString("label.log_level") + ":");
- // logLevelCombo.addItem(Level.ALL);
- logLevelCombo.addItem(Level.TRACE);
- logLevelCombo.addItem(Level.DEBUG);
- logLevelCombo.addItem(Level.INFO);
- logLevelCombo.addItem(Level.WARN);
- // logLevelCombo.addItem(Level.ERROR);
- // logLevelCombo.addItem(Level.FATAL);
- // logLevelCombo.addItem(Level.OFF);
+ // logLevelCombo.addItem(LogLevel.ALL);
+ logLevelCombo.addItem(LogLevel.TRACE);
+ logLevelCombo.addItem(LogLevel.DEBUG);
+ logLevelCombo.addItem(LogLevel.INFO);
+ logLevelCombo.addItem(LogLevel.WARN);
+ // logLevelCombo.addItem(LogLevel.ERROR);
+ // logLevelCombo.addItem(LogLevel.FATAL);
+ // logLevelCombo.addItem(LogLevel.ERROR);
+ // logLevelCombo.addItem(LogLevel.OFF);
// set startingLogLevel
- startingLogLevel = Cache.log == null ? Level.INFO
+ startingLogLevel = Cache.log == null ? LogLevel.INFO
: Cache.log.getLevel();
setChosenLogLevelCombo();
logLevelCombo.addActionListener(new ActionListener()
{
if (Cache.log != null)
{
- Log4j.setLevel(Cache.log,
- (Level) logLevelCombo.getSelectedItem());
+ Cache.log.setLevel((LogLevel) logLevelCombo.getSelectedItem());
}
}
// frame = cpt;
frame.getContentPane().setLayout(new BorderLayout());
- frame.getContentPane().add(new JScrollPane(textArea),
- BorderLayout.CENTER);
+ frame.getContentPane().add(scrollPane, BorderLayout.CENTER);
JPanel southPanel = new JPanel();
southPanel.setLayout(new GridBagLayout());
setChosenLogLevelCombo(startingLogLevel);
}
- private void setChosenLogLevelCombo(Level setLogLevel)
+ private void setChosenLogLevelCombo(LogLevel setLogLevel)
{
logLevelCombo.setSelectedItem(setLogLevel);
if (!logLevelCombo.getSelectedItem().equals(setLogLevel))
{
// setLogLevel not (yet) in list
- if (setLogLevel != null && setLogLevel instanceof Level)
+ if (setLogLevel != null && setLogLevel instanceof LogLevel)
{
// add new item to list (might be set via .jalview_properties)
boolean added = false;
for (int i = 0; i < logLevelCombo.getItemCount(); i++)
{
- Level l = (Level) logLevelCombo.getItemAt(i);
- if (l.isMoreSpecificThan(setLogLevel))
+ LogLevel l = (LogLevel) logLevelCombo.getItemAt(i);
+ if (l.compareTo(setLogLevel) >= 0)
{
logLevelCombo.insertItemAt(setLogLevel, i);
added = true;
}
else
{
- logLevelCombo.setSelectedItem(Level.INFO);
+ logLevelCombo.setSelectedItem(LogLevel.INFO);
}
}
}
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
// desktop.add(frame);
initConsole(false);
- JalviewAppender jappender = new JalviewAppender();
- JalviewAppender.setTextArea(textArea);
- Log4j.addAppenderToRootLogger(jappender);
+ LogLevel level = (LogLevel) logLevelCombo.getSelectedItem();
+ if (!Platform.isJS())
+ {
+ JalviewAppender jappender = new JalviewAppender(level);
+ JalviewAppender.setTextArea(textArea);
+ jappender.start();
+ if (Cache.log != null && Cache.log instanceof JLoggerLog4j)
+ {
+ JLoggerLog4j.addAppender(Cache.log, jappender);
+ }
+ }
}
public synchronized void stopConsole()
// reset log level to what it was before
if (Cache.log != null)
{
- Log4j.setLevel(Cache.log, startingLogLevel);
+ Cache.log.setLevel(startingLogLevel);
}
unredirectStreams();
new OOMWarning("whilst fetching crossreferences", e);
} catch (Throwable e)
{
- Cache.log.error("Error when finding crossreferences", e);
+ Cache.error("Error when finding crossreferences", e);
} finally
{
alignFrame.setProgressBar(MessageManager.formatMessage(
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GCutAndPasteHtmlTransfer;
// TODO: JAL-3048 JalviewFileChooser - Save option
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
// TODO: JAL-3048 JalviewFileChooser - Save option
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
try
{
af.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
awtAppClassNameField.setAccessible(true);
awtAppClassNameField.set(xToolkit, title);
} else {
- Cache.log.debug("XToolkit: awtAppClassName not found");
+ Cache.debug("XToolkit: awtAppClassName not found");
}
} catch (Exception e) {
Cache.debug("Error setting awtAppClassName");
new Thread(new Runnable() {
@Override
public void run() {
- Cache.log.debug("Filechooser init thread started.");
+ Cache.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
+ Cache.debug("Filechooser init thread finished.");
}
}).start();
// Add the service change listener
@Override
public void propertyChange(PropertyChangeEvent evt) {
- Cache.log.debug("Firing service changed event for " + evt.getNewValue());
+ Cache.debug("Firing service changed event for " + evt.getNewValue());
JalviewServicesChanged(evt);
}
});
new Thread(new Runnable() {
@Override
public void run() {
- Cache.log.debug("Starting news thread.");
+ Cache.debug("Starting news thread.");
jvnews = new BlogReader(me);
showNews.setVisible(true);
- Cache.log.debug("Completed news thread.");
+ Cache.debug("Completed news thread.");
}
}).start();
}
new Thread(new Runnable() {
@Override
public void run() {
- Cache.log.debug("Downloading data from identifiers.org");
+ Cache.debug("Downloading data from identifiers.org");
try {
UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation());
} catch (IOException e) {
- Cache.log.debug("Exception downloading identifiers.org data" + e.getMessage());
+ Cache.debug("Exception downloading identifiers.org data" + e.getMessage());
}
}
}).start();
}
void showNews(boolean visible) {
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ Cache.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
if (visible && !jvnews.isVisible()) {
new Thread(new Runnable() {
iy = (int) (iy * sh);
ih = (int) (ih * sh);
while (ix >= screenSize.width) {
- Cache.log.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ Cache.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height) {
- Cache.log.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ Cache.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- Cache.log.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ Cache.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ " height:" + ih);
}
// return dimensions for new instance
frame.requestFocus();
} catch (java.beans.PropertyVetoException ve) {
} catch (java.lang.ClassCastException cex) {
- Cache.log.warn(
+ Cache.warn(
"Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
}
}
private void storeLastKnownDimensions(String string, Rectangle jc) {
- Cache.log.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ Cache.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ " height:" + jc.height);
Cache.setProperty(string + "SCREEN_X", jc.x + "");
@Override
protected void garbageCollect_actionPerformed(ActionEvent e) {
// We simply collect the garbage
- Cache.log.debug("Collecting garbage...");
+ Cache.debug("Collecting garbage...");
System.gc();
- Cache.log.debug("Finished garbage collection.");
+ Cache.debug("Finished garbage collection.");
}
/*
} catch (OutOfMemoryError oom) {
new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom);
} catch (Exception ex) {
- Cache.log.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
+ Cache.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage("label.error_whilst_saving_current_state_to",
new Object[] { chosenFile.getName() }),
} catch (OutOfMemoryError oom) {
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex) {
- Cache.log.error("Problems whilst loading project from " + choice, ex);
+ Cache.error("Problems whilst loading project from " + choice, ex);
JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.error_whilst_loading_project_from", new Object[] { choice }),
MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE);
try {
openGroovyConsole();
} catch (Exception ex) {
- Cache.log.error("Groovy Shell Creation failed.", ex);
+ Cache.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
});
}
} else {
- Cache.log.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
+ Cache.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
}
}
}
Desktop.showUrl(url);
} catch (Exception x) {
if (url != null) {
- if (Cache.log != null) {
- Cache.log.error("Couldn't handle string " + url + " as a URL.");
- } else {
- System.err.println("Couldn't handle string " + url + " as a URL.");
- }
+ Cache.error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
try {
SwingUtilities.invokeAndWait(prompter);
} catch (Exception q) {
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ Cache.warn("Unexpected Exception in dialog thread.", q);
}
}
});
@Override
public void exportImage(Graphics g) throws Exception {
paintAll(g);
- Cache.log.info("Successfully written snapshot to file " + of.getAbsolutePath());
+ Cache.info("Successfully written snapshot to file " + of.getAbsolutePath());
}
};
String title = "View of desktop";
try {
urlFlavour = new DataFlavor("application/x-java-url; class=java.net.URL");
} catch (ClassNotFoundException cfe) {
- Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ Cache.debug("Couldn't instantiate the URL dataflavor.", cfe);
}
if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) {
if (url != null) {
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
+ Cache.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
return;
} else {
if (Platform.isAMacAndNotJS()) {
}
}
} catch (Throwable ex) {
- Cache.log.debug("URL drop handler failed.", ex);
+ Cache.debug("URL drop handler failed.", ex);
}
}
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) {
// Works on Windows and MacOSX
- Cache.log.debug("Drop handled as javaFileListFlavor");
+ Cache.debug("Drop handled as javaFileListFlavor");
for (Object file : (List) t.getTransferData(DataFlavor.javaFileListFlavor)) {
files.add(file);
protocols.add(DataSourceType.FILE);
boolean added = false;
String data = null;
if (t.isDataFlavorSupported(uriListFlavor)) {
- Cache.log.debug("Drop handled as uriListFlavor");
+ Cache.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
if (data == null) {
// fallback to text: workaround - on OSX where there's a JVM bug
- Cache.log.debug("standard URIListFlavor failed. Trying text");
+ Cache.debug("standard URIListFlavor failed. Trying text");
// try text fallback
DataFlavor textDf = new DataFlavor("text/plain;class=java.lang.String");
if (t.isDataFlavorSupported(textDf)) {
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
+ Cache.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
}
if (data != null) {
while (protocols.size() < files.size()) {
- Cache.log.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
+ Cache.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
for (java.util.StringTokenizer st = new java.util.StringTokenizer(data, "\r\n"); st.hasMoreTokens();) {
}
}
- if (Cache.log.isDebugEnabled()) {
+ if (Cache.isDebugEnabled()) {
if (data == null || !added) {
if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) {
- Cache.log.debug("Couldn't resolve drop data. Here are the supported flavors:");
+ Cache.debug("Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors()) {
- Cache.log.debug("Supported transfer dataflavor: " + fl.toString());
+ Cache.debug("Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
if (df != null) {
- Cache.log.debug("Retrieves: " + df);
+ Cache.debug("Retrieves: " + df);
} else {
- Cache.log.debug("Retrieved nothing");
+ Cache.debug("Retrieved nothing");
}
}
} else {
- Cache.log.debug("Couldn't resolve dataflavor for drop: " + t.toString());
+ Cache.debug("Couldn't resolve dataflavor for drop: " + t.toString());
}
}
}
}
if (Platform.isWindowsAndNotJS()) {
- Cache.log.debug("Scanning dropped content for Windows Link Files");
+ Cache.debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++) {
Object obj = files.get(f);
File lf = (obj instanceof File ? (File) obj : new File((String) obj));
// process link file to get a URL
- Cache.log.debug("Found potential link file: " + lf);
+ Cache.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
String fullname = wscfile.getRealFilename();
protocols.set(f, FormatAdapter.checkProtocol(fullname));
files.set(f, fullname);
- Cache.log.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
+ Cache.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
} catch (Exception ex) {
- Cache.log.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
+ Cache.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
}
}
}
attName = (String) attCombo.getSelectedItem();
} catch (Exception e)
{
- Cache.log.error("Problem casting Combo box entry to String");
+ Cache.error("Problem casting Combo box entry to String");
attName = attCombo.getSelectedItem().toString();
}
Condition cond = (Condition) condCombo.getSelectedItem();
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import java.awt.Component;
desktop = instance;
if (oomex != null)
{
- if (jalview.bin.Cache.log != null)
- {
- jalview.bin.Cache.log.error("Out of Memory when " + action,
+ Cache.error("Out of Memory when " + action,
oomex);
- }
- else
- {
- System.err.println("Out of Memory when " + action);
- oomex.printStackTrace();
- }
}
javax.swing.SwingUtilities.invokeLater(this);
System.gc();
// JAL-2647 disabled after load from project (until save to project done)
if (getPcaModel().getInputData() == null)
{
- Cache.log.info(
+ Cache.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
urlLink = new UrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ Cache.error("Exception for URLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Cache.error(urlLink.getInvalidMessage());
continue;
}
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+ Cache.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Cache.error(urlLink.getInvalidMessage());
continue;
}
final String label = urlLink.getLabel();
}
} catch (IllegalArgumentException e)
{
- Cache.log.error("Unknown structure viewer type: " + viewerType
+ Cache.error("Unknown structure viewer type: " + viewerType
+ ", defaulting to Jmol");
type = ViewerType.JMOL;
}
}
} catch (IllegalArgumentException x)
{
- Cache.log.error("Failed to set path - unknown viewer type",x);
+ Cache.error("Failed to set path - unknown viewer type",x);
}
}
}
proxyType.setSelected(customProxy.getModel(), true);
break;
default:
- Cache.log.warn(
+ Cache.warn(
"Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyTypeString);
}
if (index == -1)
{
// button no longer enabled if row is not selected
- Cache.log.debug("Edit with no row selected in linkUrlTable");
+ Cache.debug("Edit with no row selected in linkUrlTable");
return;
}
if (index == -1)
{
// button no longer enabled if row is not selected
- Cache.log.debug("Delete with no row selected in linkUrlTable");
+ Cache.debug("Delete with no row selected in linkUrlTable");
return;
}
else
* @param desktop
* - where the dialog box will be shown
* @param property
- * - boolean property in jalview.bin.Cache
+ * - boolean property in Cache
* @param dialogTitle
* - title of prompt box
* @param dialogText
return;
}
// First - check to see if wee have an old questionnaire/response id pair.
- String lastq = jalview.bin.Cache.getProperty(property);
+ String lastq = Cache.getProperty(property);
if (lastq == null)
{
raiseDialog();
- Cache.log.debug("Got user response.");
+ Cache.debug("Got user response.");
}
- lastq = jalview.bin.Cache.getProperty(property);
+ lastq = Cache.getProperty(property);
String extype = "";
Exception e = null;
if (lastq == null)
// report any exceptions
if (e != null)
{
- Cache.log.warn("Unexpected exception when executing the " + extype
+ Cache.warn("Unexpected exception when executing the " + extype
+ " runnable for property " + property, e);
}
}
*/
private void raiseDialog()
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Prompting user for " + dialogTitle
+ Cache.debug("Prompting user for " + dialogTitle
+ " for Cache property " + property);
}
try
JvOptionPane.QUESTION_MESSAGE);
// and finish parsing the result
- jalview.bin.Cache.log.debug("Got response : " + reply);
+ Cache.debug("Got response : " + reply);
if (reply == JvOptionPane.YES_OPTION)
{
- jalview.bin.Cache.setProperty(property, "true");
+ Cache.setProperty(property, "true");
}
else if (reply == JvOptionPane.NO_OPTION)
{
if (removeifunset)
{
- jalview.bin.Cache.removeProperty(property);
+ Cache.removeProperty(property);
}
else
{
- jalview.bin.Cache.setProperty(property, "false");
+ Cache.setProperty(property, "false");
}
}
else
{
- jalview.bin.Cache.log.debug("User cancelled setting " + property);
+ Cache.debug("User cancelled setting " + property);
return;
}
// verify the property is set for debugging
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("User set property to "
- + jalview.bin.Cache.getProperty(property));
+ Cache.debug("User set property to "
+ + Cache.getProperty(property));
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"Unexpected exception when prompting user for yes/no setting for property "
+ property,
e);
}
else
{
- Cache.log.error("Failed to launch PyMOL!");
+ Cache.error("Failed to launch PyMOL!");
}
return pymol != null;
}
// pdbId.replace('-', 0)
} catch (Exception x)
{
- Cache.log.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ Cache.error("Unxpected encoding exception for '"+pdbId+"'",x);
}
cmd.addParameter(pdbId);
initPymol();
} catch (Exception ex)
{
- Cache.log.error("Couldn't open PyMOL viewer!", ex);
+ Cache.error("Couldn't open PyMOL viewer!", ex);
}
}
int num = -1;
binding.stashFoundChains(pdb, pe.getFile());
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Couldn't open " + pe.getFile() + " in Chimera viewer!",
ex);
} finally
{
- // Cache.log.debug("File locations are " + files);
+ // Cache.debug("File locations are " + files);
}
}
}
boolean opened = binding.openSession(pymolSessionFile);
if (!opened)
{
- Cache.log.error(
+ Cache.error(
"An error occurred opening PyMOL session file "
+ pymolSessionFile);
}
}
else if (evt.getKeyChar() == 's')
{
- // Cache.log.warn("DEBUG: Rectangle selection");
+ // Cache.warn("DEBUG: Rectangle selection");
// todo not yet enabled as rectx2, recty2 are always -1
// need to set them in mouseDragged; JAL-1124
// if ((rectx2 != -1) && (recty2 != -1))
{
if (av.getAlignment() == null)
{
- Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ Cache.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ " ViewId=" + av.getViewId()
+ " 's alignment is NULL! returning immediately.");
return;
}
} catch (Exception e)
{
- Cache.log.info("Error retrieving " + accession + " from "
+ Cache.info("Error retrieving " + accession + " from "
+ proxy.getDbName(), e);
}
return success;
// StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(
MessageManager.formatMessage("label.select_pdb_file_for",
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Cache.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Cache.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
break;
default:
- Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
+ Cache.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
return viewer;
}
{
sp.append("'" + alignPanel.getViewName() + "' ");
}
- Cache.log.info("Couldn't align structures with the " + sp.toString()
+ Cache.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
return reply;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
{
// TODO: JAL-3048 save newick file for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_tree_as_newick"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
try
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
- jalview.bin.Cache.log.info(
+ Cache.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import java.io.BufferedReader;
{
if (url.indexOf("questionnaire.pl") == -1)
{
- jalview.bin.Cache.log.error("'" + url
+ Cache.error("'" + url
+ "' is an Invalid URL for the checkForQuestionnaire() method.\n"
+ "This argument is only for questionnaires derived from jalview's questionnaire.pl cgi interface.");
}
private boolean checkresponse(URL qurl) throws Exception
{
- jalview.bin.Cache.log.debug("Checking Response for : " + qurl);
+ Cache.debug("Checking Response for : " + qurl);
boolean prompt = false;
// see if we have already responsed to this questionnaire or get a new
// qid/rid pair
try
{
// First - check to see if wee have an old questionnaire/response id pair.
- String lastq = jalview.bin.Cache.getProperty("QUESTIONNAIRE");
+ String lastq = Cache.getProperty("QUESTIONNAIRE");
if (lastq == null)
{
prompt = checkresponse(new URL(url
if (qid != null && rid != null)
{
// Update our local property cache with latest qid and rid
- jalview.bin.Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
+ Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
}
if (prompt)
{
String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") + "qid="
+ qid + "&rid=" + rid;
- jalview.bin.Cache.log
- .info("Prompting user for questionnaire at " + qurl);
+ Cache.info("Prompting user for questionnaire at " + qurl);
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.getString("label.jalview_new_questionnaire"),
MessageManager.getString("label.jalview_user_survey"),
if (reply == JvOptionPane.YES_OPTION)
{
- jalview.bin.Cache.log.debug("Opening " + qurl);
+ Cache.debug("Opening " + qurl);
jalview.util.BrowserLauncher.openURL(qurl);
}
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .warn("When trying to access questionnaire URL " + url, e);
+ Cache.warn("When trying to access questionnaire URL " + url, e);
}
}
} catch (Exception e)
{
- jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",
+ Cache.error("Couldn't instantiate vamsas client !",
e);
return false;
}
}
} catch (Error e)
{
- Cache.log.warn(
+ Cache.warn(
"Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
e);
} catch (Exception e)
{
- Cache.log.warn(
+ Cache.warn(
"Probable VAMSAS client incompatibility - carrying on regardless",
e);
}
private ClientHandle getJalviewHandle()
{
return new ClientHandle("jalview.bin.Jalview",
- jalview.bin.Cache.getProperty("VERSION"));
+ Cache.getProperty("VERSION"));
}
/**
addStoreDocumentHandler();
startSession();
inInitialUpdate = true;
- Cache.log.debug(
+ Cache.debug(
"Jalview loading the Vamsas Session for the first time.");
dealWithDocumentUpdate(false); // we don't push an update out to the
inInitialUpdate = false;
// document yet.
- Cache.log.debug("... finished update for the first time.");
+ Cache.debug("... finished update for the first time.");
}
/**
}
} catch (Exception e)
{
- Cache.log.warn(
+ Cache.warn(
"Exception whilst refreshing jalview windows after a vamsas document update.",
e);
}
@Override
public void run()
{
- Cache.log.info("Jalview updating to the Vamsas Session.");
+ Cache.info("Jalview updating to the Vamsas Session.");
dealWithDocumentUpdate(true);
- Cache.log.info("Jalview finished updating to the Vamsas Session.");
+ Cache.info("Jalview finished updating to the Vamsas Session.");
}
});
{
throw new Error("Jalview not connected to Vamsas session");
}
- Cache.log.info("Jalview disconnecting from the Vamsas Session.");
+ Cache.info("Jalview disconnecting from the Vamsas Session.");
try
{
if (joinedSession)
boolean ourprompt = this.promptUser;
this.promptUser = promptUser;
vclient.finalizeClient();
- Cache.log.info("Jalview has left the session.");
+ Cache.info("Jalview has left the session.");
this.promptUser = ourprompt; // restore default value
}
else
{
- Cache.log.warn(
+ Cache.warn(
"JV Client leaving a session that's its not joined yet.");
}
joinedSession = false;
vobj2jv = null;
} catch (Exception e)
{
- Cache.log.error("Vamsas Session finalization threw exceptions!", e);
+ Cache.error("Vamsas Session finalization threw exceptions!", e);
}
}
public void updateJalview(IClientDocument cdoc)
{
- Cache.log.debug("Jalview updating from sesion document ..");
+ Cache.debug("Jalview updating from sesion document ..");
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
vds.updateToJalview();
} catch (Exception e)
{
- Cache.log.error("Failed to update Jalview from vamsas document.", e);
+ Cache.error("Failed to update Jalview from vamsas document.", e);
}
try
{
}
} catch (Exception e)
{
- Cache.log.error(
+ Cache.error(
"Exception when updating Jalview settings from Appdata.", e);
}
- Cache.log.debug(".. finished updating from sesion document.");
+ Cache.debug(".. finished updating from sesion document.");
}
} catch (Exception e)
{
errorsDuringUpdate = true;
- Cache.log.error("Exception synchronizing " + af.getTitle()
+ Cache.error("Exception synchronizing " + af.getTitle()
+ " "
+ (af.getViewport().getViewName() == null ? ""
: " view " + af.getViewport().getViewName())
}
} catch (Exception e)
{
- Cache.log.error("Exception synchronizing Views to Document :", e);
+ Cache.error("Exception synchronizing Views to Document :", e);
errorsDuringUpdate = true;
}
}
} catch (Exception e)
{
- Cache.log.error("Client Appdata Write exception", e);
+ Cache.error("Client Appdata Write exception", e);
errorsDuringAppUpdate = true;
}
vds.clearSkipList();
{
int storedviews = 0;
// called by update handler for document update.
- Cache.log.debug("Updating jalview from changed vamsas document.");
+ Cache.debug("Updating jalview from changed vamsas document.");
disableGui(true);
try
{
long time = System.currentTimeMillis();
IClientDocument cdoc = vclient.getClientDocument();
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug("Time taken to get ClientDocument = "
+ Cache.debug("Time taken to get ClientDocument = "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
if (fromJalview)
{
storedviews += updateVamsasDocument(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Time taken to update Vamsas Document from jalview\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
cdoc.setVamsasRoots(cdoc.getVamsasRoots());
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug("Time taken to set Document Roots\t\t= "
+ Cache.debug("Time taken to set Document Roots\t\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
else
{
updateJalview(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Time taken to update Jalview from vamsas document Roots\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
vclient.updateDocument(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug("Time taken to update Session Document\t= "
+ Cache.debug("Time taken to update Session Document\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
recover_objectMappingBackup();
storedviews = 0;
}
- Cache.log.debug("Finished updating from document change.");
+ Cache.debug("Finished updating from document change.");
disableGui(false);
return storedviews;
}
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- Cache.log.debug("Dealing with document update event.");
+ Cache.debug("Dealing with document update event.");
client.dealWithDocumentUpdate(false);
- Cache.log.debug("finished dealing with event.");
+ Cache.debug("finished dealing with event.");
}
});
- Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ Cache.debug("Added Jalview handler for vamsas document updates.");
}
private void addStoreDocumentHandler()
{
if (client.promptUser)
{
- Cache.log.debug(
+ Cache.debug(
"Asking user if the vamsas session should be stored.");
int reply = JvOptionPane.showInternalConfirmDialog(
Desktop.desktop,
if (reply == JvOptionPane.YES_OPTION)
{
- Cache.log.debug("Prompting for vamsas store filename.");
+ Cache.debug("Prompting for vamsas store filename.");
Desktop.instance.vamsasSave_actionPerformed(null);
- Cache.log
- .debug("Finished attempt at storing document.");
+ Cache.debug("Finished attempt at storing document.");
}
- Cache.log.debug(
+ Cache.debug(
"finished dealing with REQUESTTOCLOSE event.");
}
else
{
- Cache.log.debug(
+ Cache.debug(
"Ignoring store document request (promptUser==false)");
}
}
});
- Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ Cache.debug("Added Jalview handler for vamsas document updates.");
}
public void disableGui(boolean b)
} catch (Exception e)
{
// Complain to GUI
- Cache.log.error("Failed to join vamsas session.", e);
+ Cache.error("Failed to join vamsas session.", e);
vclient = null;
}
try
{
return;
}
- // if (Cache.log.isDebugEnabled())
+ // if (Cache.isDebugEnabled())
// {
- // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+"
+ // Cache.debug("Received MouseOverMessage "+mm.getVorbaID()+"
// "+mm.getPosition());
// }
Object jvobj = vobj2jv.get(mm.getVorbaID());
if (jvobj != null && jvobj instanceof SequenceI)
{
last = mstring;
- // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
+ // Cache.debug("Handling Mouse over "+mm.getVorbaID()+"
// bound to "+jvobj+" at "+mm.getPosition());
// position is character position in aligned sequence
ssm.mouseOverVamsasSequence((SequenceI) jvobj,
if (v != null)
{
// this should really be a trace message.
- // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ // Cache.debug("Mouse over " + v.getId() + " bound to "
// + seq + " at " + index);
last = seq;
i = index;
{
if (vobj2jv == null)
{
- Cache.log.warn(
+ Cache.warn(
"Selection listener still active for dead session.");
// not in a session.
return;
if (sm != null)
{
sm.validate(); // debug
- Cache.log.debug("Selection Message\n" + sm.getRawMessage());
+ Cache.debug("Selection Message\n" + sm.getRawMessage());
pm.sendMessage(sm);
}
}
ssm.addSelectionListener(selecter);
} catch (Exception e)
{
- Cache.log.error("Failed to init Vamsas Picking", e);
+ Cache.error("Failed to init Vamsas Picking", e);
}
}
}
if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug("Item state changed for " + setname
+ Cache.debug("Item state changed for " + setname
+ " (handling ? " + !settingDialog + ")");
}
if (settingDialog)
}
} catch (IOException e)
{
- Cache.log.info("Failed to parse parameter file " + pfile
+ Cache.info("Failed to parse parameter file " + pfile
+ " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
e);
}
{
if (filename != null && !((outfile = new File(filename)).canWrite()))
{
- Cache.log.warn("Can't write to " + filename
+ Cache.warn("Can't write to " + filename
+ " - Prompting for new file to write to.");
filename = null;
}
}
if (outfile != null)
{
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
+ String paramFiles = Cache.getDefault("WS_PARAM_FILES",
filename);
if (paramFiles.indexOf(filename) == -1)
{
parameterSet.setSourceFile(filename);
} catch (Exception e)
{
- Cache.log.error("Couldn't write parameter file to " + outfile, e);
+ Cache.error("Couldn't write parameter file to " + outfile, e);
}
}
}
/*
*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ * JalviewFileChooser chooser = new JalviewFileChooser(Cache
* .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
* "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
* jalview.io.JalviewFileView());
* int value = chooser.showOpenDialog(this);
*
* if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
- * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
+ * chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY",
+ * choice.getParent()); String defaultColours = Cache.getDefault(
* "USER_DEFINED_COLOURS", choice.getPath()); if
* (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
* defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
{
return;
}
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
+ String paramFiles = Cache.getDefault("WS_PARAM_FILES", "");
if (paramFiles.indexOf(filename) > -1)
{
String nparamFiles = new String();
nparamFiles = nparamFiles.concat("|").concat(fl);
}
}
- jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
+ Cache.setProperty("WS_PARAM_FILES", nparamFiles);
}
try
}
} catch (Exception e)
{
- Cache.log.error(
+ Cache.error(
"Exception when trying to delete webservice user preset: ",
e);
}
pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
} catch (Exception q)
{
- Cache.log.warn("Unknown filetype for 3D Beacons Model from: "
+ Cache.warn("Unknown filetype for 3D Beacons Model from: "
+ strucFormat + " - " + pdbIdStr + " - " + modelPage);
}
confirmDelete = Boolean.valueOf(st.nextToken());
} catch (Exception e)
{
- Cache.log.error("Error parsing backupfiles scheme '" + line + "'");
+ Cache.error("Error parsing backupfiles scheme '" + line + "'");
}
return new BackupFilesPresetEntry(suffix, digits, reverse, keepAll,
*/
package jalview.io;
+import jalview.bin.Cache;
import jalview.gui.AlignmentPanel;
import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
public static final String DEFAULT_DIR = System.getProperty("user.home")
+ File.separatorChar + ".biojs_templates" + File.separatorChar;
- public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+ public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
.getDefault("biojs_template_directory", DEFAULT_DIR);
- public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
+ public static final String BJS_TEMPLATE_GIT_REPO = Cache
.getDefault("biojs_template_git_repo",
"https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
int slashPos = line.indexOf('/');
if (slashPos == -1)
{
- Cache.log.error("Unexpected EMBL line ignored: " + line);
+ Cache.error("Unexpected EMBL line ignored: " + line);
line = nextLine();
continue;
}
data.codonStart = Integer.parseInt(featureValue.trim());
} catch (NumberFormatException e)
{
- Cache.log.error("Invalid codon_start in XML for " + this.accession
+ Cache.error("Invalid codon_start in XML for " + this.accession
+ ": " + e.getMessage());
}
}
}
else
{
- Cache.log.error("Ignoring CDS feature with no protein_id for "
+ Cache.error("Ignoring CDS feature with no protein_id for "
+ sourceDb + ":" + accession);
}
{
if (this.accession == null || this.sequenceString == null)
{
- Cache.log.error("Failed to parse data from EMBL");
+ Cache.error("Failed to parse data from EMBL");
return;
}
* workaround until we handle all 'location' formats fully
* e.g. X53828.1:60..1058 or <123..>289
*/
- Cache.log.error(String.format(
+ Cache.error(String.format(
"Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+ " - Making up the CDNA region of (%s:%s)... may be incorrect",
data.cdsLocation, sourceDb, this.accession));
if (peptideLength * 3 == completeCodonsLength)
{
// this might occur for CDS sequences where no features are marked
- Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
+ Cache.warn("Assuming no stop codon at end of cDNA fragment");
mappedDnaEnd = dna.getEnd();
}
else if ((peptideLength + 1) * 3 == completeCodonsLength)
{
- Cache.log.warn("Assuming stop codon at end of cDNA fragment");
+ Cache.warn("Assuming stop codon at end of cDNA fragment");
mappedDnaEnd = dna.getEnd() - 3;
}
return MappingUtils.rangeListToArray(ranges);
} catch (ParseException e)
{
- Cache.log.warn(
+ Cache.warn(
String.format("Not parsing inexact CDS location %s in ENA %s",
location, accession));
return new int[] {};
String[] tokens = line.split(WHITESPACE);
if (tokens.length < 2)
{
- Cache.log.error("Ignoring bad EMBL line for " + this.accession
+ Cache.error("Ignoring bad EMBL line for " + this.accession
+ ": " + line);
break;
}
this.length = Integer.valueOf(bits[0]);
} catch (NumberFormatException e)
{
- Cache.log.error("bad length read in flatfile, line: " + line);
+ Cache.error("bad length read in flatfile, line: " + line);
}
}
try
{
- alignFrame.setMaximum(jalview.bin.Cache
+ alignFrame.setMaximum(Cache
.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
{
if (!input.markSupported())
{
- Cache.log.error(
+ Cache.error(
"FileParse.izGzipStream: input stream must support mark/reset");
return false;
}
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
- annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
true);
- localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
true);
}
else
public boolean isEmbedData()
{
return Boolean.valueOf(
- jalview.bin.Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
}
@Override
*/
package jalview.io;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
{
value = r.stringMatched(1);
}
- // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+ // Cache.debug("from '" + field + "' matched '" + value +
// "'");
try
{
}
else
{
- // jalview.bin.Cache.log.debug(
+ // Cache.debug(
// "Ignoring non-Modeller description: invalid integer-like
// field '" + field + "'");
type = -1; /* invalid field! - throw the FieldSet away */
*/
package jalview.io;
-import java.util.Locale;
-
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import jalview.util.Format;
import jalview.util.MessageManager;
-// import org.apache.log4j.*;
-
/**
* This class is supposed to parse a Stockholm format file into Jalview There
* are TODOs in this class: we do not know what the database source and version
{
private static final String ANNOTATION = "annotation";
-// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
-//
-// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+ // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ //
+ // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
public static final Regex DETECT_BRACKETS = new Regex(
"(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
- // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using
+ // NOT_RNASS first.
public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
// use the following regex to decide an annotations (whole) line is NOT an RNA
Regex openparen = new Regex("(<|\\[)", "(");
Regex closeparen = new Regex("(>|\\])", ")");
-// // Detect if file is RNA by looking for bracket types
-// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ // // Detect if file is RNA by looking for bracket types
+ // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
if (dbr != null)
{
// we could get very clever here - but for now - just try to
- // guess accession type from type of sequence, source of alignment plus
+ // guess accession type from type of sequence, source of alignment
+ // plus
// structure
// of accession
guessDatabaseFor(seqO, dbr, dbsource);
treeName = an.stringMatched(2);
treeString = new StringBuffer();
}
- // TODO: JAL-3532 - this is where GF comments and database references are lost
- // suggest overriding this method for Stockholm files to catch and properly
+ // TODO: JAL-3532 - this is where GF comments and database
+ // references are lost
+ // suggest overriding this method for Stockholm files to catch and
+ // properly
// process CC, DR etc into multivalued properties
setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
}
}
if (dbsource == null)
{
- // make up an origin based on whether the sequence looks like it is nucleotide
+ // make up an origin based on whether the sequence looks like it is
+ // nucleotide
// or protein
dbsource = (seqO.isProtein()) ? "PFAM" : "RFAM";
}
return ref.getSource().toString() + " ; "
+ ref.getAccessionId().toString();
}
+
@Override
public String print(SequenceI[] s, boolean jvSuffix)
{
Vobject obj = getjv2vObj(seqsetidobj);
if (obj != null && !(obj instanceof Alignment))
{
- Cache.log.warn(
+ Cache.warn(
"IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+ seqsetidobj + " to object " + obj);
}
}
else
{
- Cache.log.warn("Unexpected mapping for Jalview String Object ID "
+ Cache.warn("Unexpected mapping for Jalview String Object ID "
+ seqsetidobj + " to another jalview dataset object "
+ seqsetidobj);
}
}
}
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log.debug(
+ Cache.debug(
"Registering new object and returning null for getvObj2jv");
return null;
}
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Cache.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
: "unregisterable")
+ " object " + vobj);
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
+ Cache.debug(
"Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
new Exception(MessageManager.getString(
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Cache.debug(
"Warning? Overwriting existing jalview object binding for "
+ jvobj,
new Exception("Overwriting jalview object binding."));
}
/*
- * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
* +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
* already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
* bindjvvobj")); }
*/
// we just update the hash's regardless!
- Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+ Cache.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
DataSet dataset = null;
if (jds == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Cache.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
jds = jal.getDataset();
}
if (dataset == null)
{
- Cache.log.warn("Creating new vamsas dataset for alignment view "
+ Cache.warn("Creating new vamsas dataset for alignment view "
+ av.getSequenceSetId());
// we create a new dataset on the default vamsas root.
root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
if (aa[i].groupRef != null)
{
// TODO: store any group associated annotation references
- Cache.log.warn(
+ Cache.warn(
"Group associated sequence annotation is not stored in VAMSAS document.");
continue;
}
// LOCK METHODS)
{
// verify annotation - update (perhaps)
- Cache.log.info(
+ Cache.info(
"update alignment sequence annotation. not yet implemented.");
}
else
{
// verify annotation - update (perhaps)
- Cache.log.info(
+ Cache.info(
"updated alignment sequence annotation added.");
}
}
}
if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
{
- Cache.log.warn(
+ Cache.warn(
"Serious Implementation error - Unbound dataset sequence in alignment: "
+ jvalsq.getDatasetSequence());
}
alseq.setDescription(valseq.getDescription());
modal = true;
}
- if (modal && Cache.log.isDebugEnabled())
+ if (modal && Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Updating apparently edited sequence " + alseq.getName());
}
}
}
else
{
- Cache.log.error(
+ Cache.error(
"Invalid dataset sequence id (null) for alignment sequence "
+ valseq.getVorbaId());
}
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log.debug(
+ Cache.debug(
"Returning client input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getClientInputStream());
}
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log.debug(
+ Cache.debug(
"Returning user input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getUserInputStream());
}
// TODO implement this : af.getNumberOfViews
String seqsetidobj = av.getSequenceSetId();
views = Desktop.getViewports(seqsetidobj);
- Cache.log
- .debug("Found " + (views == null ? " no " : "" + views.length)
+ Cache.debug("Found " + (views == null ? " no " : "" + views.length)
+ " views for '" + av.getSequenceSetId() + "'");
if (views.length > 1)
{
} catch (Exception e)
{
// TODO raise GUI warning if user requests it.
- jalview.bin.Cache.log.error(
+ Cache.error(
"Couldn't update jalview client application data. Giving up - local settings probably lost.",
e);
}
}
else
{
- jalview.bin.Cache.log.error(
+ Cache.error(
"Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
}
}
int jremain = 0;
if (jdataset == null)
{
- Cache.log.debug("Initialising new jalview dataset fields");
+ Cache.debug("Initialising new jalview dataset fields");
newds = true;
dsseqs = new Vector();
}
else
{
- Cache.log.debug("Update jalview dataset from vamsas.");
+ Cache.debug("Update jalview dataset from vamsas.");
jremain = jdataset.getHeight();
dsseqs = jdataset.getSequences();
}
dsseqs.set(i, null);
}
jdataset = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas dataset imported into jalview.");
+ Cache.debug("New vamsas dataset imported into jalview.");
bindjvvobj(jdataset, dataset);
}
// ////////
// annotations
if (dsSeq == null)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"Couldn't resolve jalview sequenceI for dataset object reference "
+ ((Vobject) dataset
.getDataSetAnnotations(dsa)
// JBPNote: we could just add them to all alignments but
// that may complicate cross references in the jalview
// datamodel
- Cache.log.warn(
+ Cache.warn(
"Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
}
}
}
else
{
- Cache.log.warn(
+ Cache.warn(
"Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
}
}
// OBJECT LOCK
// METHODS)
{
- Cache.log.info(
+ Cache.info(
"UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
// TODO: should at least replace with new one - otherwise
// things will break
dsseqs.set(i, null);
}
jal = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas alignment imported into jalview "
+ Cache.debug("New vamsas alignment imported into jalview "
+ alignment.getVorbaId().getId());
jal.setDataset(jdataset);
}
// jan.update(getjAlignmentAnnotation(jal, an[a])); // update
// from another annotation object in place.
- Cache.log.debug(
+ Cache.debug(
"update from vamsas alignment annotation to existing jalview alignment annotation.");
if (an[j].getModifiable() == null) // TODO: USE VAMSAS
// LIBRARY OBJECT LOCK
{
// TODO: user defined annotation is totally mutable... - so
// load it up or throw away if locally edited.
- Cache.log.info(
+ Cache.info(
"NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
}
// TODO: compare annotation element rows
AlignFrame alignFrame;
if (av == null)
{
- Cache.log.debug("New alignframe for alignment "
+ Cache.debug("New alignframe for alignment "
+ alignment.getVorbaId());
// ///////////////////////////////
// construct alignment view
}
// TODO: automatically create meaningful title for a vamsas
// alignment using its provenance.
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
title = title + "(" + alignment.getVorbaId() + ")";
vstree.UpdateSequenceTreeMap(tp);
} catch (RuntimeException e)
{
- Cache.log.warn("update of labels failed.", e);
+ Cache.warn("update of labels failed.", e);
}
}
else
{
- Cache.log.warn("Cannot create tree for tree " + t
+ Cache.warn("Cannot create tree for tree " + t
+ " in document ("
+ alignment.getTree(t).getVorbaId());
}
if (anot[row][pos] != null)
{
// only time this should happen is if the After flag is set.
- Cache.log.debug("Ignoring duplicate annotation site at " + pos);
+ Cache.debug("Ignoring duplicate annotation site at " + pos);
continue;
}
if (anot[1 - row][pos] != null)
else if (glyphs[g].getDict().equals(
uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
- Cache.log.debug("ignoring hydrophobicity glyph marker.");
+ Cache.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
char c = (dc = glyphs[g].getContent()).charAt(0);
// dc may get overwritten - but we still set the colour.
}
else
{
- Cache.log.debug(
+ Cache.debug(
"IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ glyphs[g].getDict());
}
AeContent[HASVALS] = true;
if (ae[aa].getValueCount() > 1)
{
- Cache.log.warn(
+ Cache.warn(
"ignoring additional " + (ae[aa].getValueCount() - 1)
+ " values in annotation element.");
}
}
else
{
- Cache.log.warn("Ignoring out of bound annotation element " + aa
+ Cache.warn("Ignoring out of bound annotation element " + aa
+ " in " + annotation.getVorbaId().getId());
}
}
val = Float.valueOf(props[p].getContent());
} catch (Exception e)
{
- Cache.log.warn("Failed to parse threshold property");
+ Cache.warn("Failed to parse threshold property");
}
if (val != null)
{
}
if (parsedRangeAnnotation == null)
{
- Cache.log.debug(
+ Cache.debug(
"Inserting empty annotation row elements for a whole-alignment annotation.");
}
else
{
if (parsedRangeAnnotation[3] != null)
{
- Cache.log.warn("Ignoring 'After' annotation row in "
+ Cache.warn("Ignoring 'After' annotation row in "
+ annotation.getVorbaId());
}
jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
}
if (annotation.getLinkCount() > 0)
{
- Cache.log.warn("Ignoring " + annotation.getLinkCount()
+ Cache.warn("Ignoring " + annotation.getLinkCount()
+ "links added to AlignmentAnnotation.");
}
if (annotation.getModifiable() == null
}
} catch (Exception e)
{
- Cache.log.info(
+ Cache.info(
"UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
}
return jan;
DataSet dataset = null;
if (jal.getDataset() == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Cache.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
}
dataset = (DataSet) ((Alignment) getjv2vObj(
if (dataset == null)
{
dataset = (DataSet) getjv2vObj(jal.getDataset());
- Cache.log.error(
+ Cache.error(
"Can't find the correct dataset for the alignment in this view. Creating new one.");
}
}
else
{
- Cache.log.warn(
+ Cache.warn(
"NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
+ dmps[smp].getDisplayId(true) + " to "
+ mps[smp].getTo().getName());
import java.util.IdentityHashMap;
import java.util.Vector;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import jalview.bin.Cache;
import jalview.io.VamsasAppDatastore;
+import jalview.log.JLoggerLog4j;
import jalview.util.MessageManager;
import uk.ac.vamsas.client.IClientDocument;
import uk.ac.vamsas.client.Vobject;
/**
* shared log instance
*/
- protected static Logger log = LogManager.getLogger(DatastoreItem.class);
+ protected static JLoggerLog4j log = JLoggerLog4j
+ .getLogger(DatastoreItem.class.getCanonicalName());
/**
* note: this is taken verbatim from jalview.io.VamsasAppDatastore
{
return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
}
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log.debug(
+ Cache.debug(
"Registering new object and returning null for getvObj2jv");
return null;
}
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Cache.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
: "unregisterable")
+ " object " + vobj);
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
+ Cache.debug(
"Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
new Exception(MessageManager.getString(
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Cache.debug(
"Warning? Overwriting existing jalview object binding for "
+ jvobj,
new Exception(MessageManager.getString(
"exception.overwriting_jalview_id_binding")));
}
/*
- * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
* +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
* already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
* bindjvvobj")); }
*/
// we just update the hash's regardless!
- Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+ Cache.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
{
if (this.jvobj != null && this.vobj != null)
{
- Cache.log.debug("updating dsobj registry. ("
- + this.getClass().getName() + ")");
+ Cache.debug("updating dsobj registry. (" + this.getClass().getName()
+ + ")");
}
this.jvobj = jvobj;
this.vobj = vobj;
import java.util.Iterator;
import java.util.Map;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import jalview.log.JLoggerLog4j;
public class DatastoreRegistry implements AutoCloseable
{
- protected static Logger log = LogManager
- .getLogger(DatastoreRegistry.class);
+ protected static JLoggerLog4j log = JLoggerLog4j
+ .getLogger(DatastoreRegistry.class.getCanonicalName());
/**
* map between Datastore objects and the objects they are handling- used to
*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
}
else
{
- jalview.bin.Cache.log.debug(
+ Cache.debug(
"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
- .debug("Ignoring additional mappings on DbRef: "
+ Cache.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
{
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
- jalview.bin.Cache.log
- .debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ Cache.debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ vobj.getSource() + " " + vobj.getVorbaId());
// TODO Auto-generated method stub
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
- .debug("Ignoring additional mappings on DbRef: "
+ Cache.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
}
else
{
- jalview.bin.Cache.log.debug(
+ Cache.debug(
"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
import jalview.io.VamsasAppDatastore;
import jalview.util.MessageManager;
{
if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
{
- jalview.bin.Cache.log
- .warn("using default mapping length of 1:1 for map "
+ Cache.warn("using default mapping length of 1:1 for map "
+ (map.isRegistered() ? map.getVorbaId().toString()
: ("<no Id registered> " + map.toString())));
}
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
if (dsa.getSeqRefCount() != 1)
{
- Cache.log.warn("Not binding " + dsa.getVorbaId()
+ Cache.warn("Not binding " + dsa.getVorbaId()
+ " to Sequence Feature - has multiple dataset sequence references.");
return;
}
if (dsa.getSeqRefCount() != 1)
{
replaceJvObjMapping(feature, null);
- Cache.log.warn(
+ Cache.warn(
"Binding of annotation to jalview feature has changed. Removing binding and recreating.");
doSync(); // re-verify bindings.
}
getDSAnnotationFromJalview(dsa, feature);
if (oldref != dsa.hashCode())
{
- Cache.log
- .debug("Updated dataset sequence annotation from feature.");
+ Cache.debug("Updated dataset sequence annotation from feature.");
addProvenance(dsa.getProvenance(), "modified");
}
}
{
// conflicting update from document - we cannot map this feature anymore.
replaceJvObjMapping(feature, null);
- Cache.log.warn("annotation (" + dsa.getVorbaId()
+ Cache.warn("annotation (" + dsa.getVorbaId()
+ " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
// - consider deleting the feature ?
dsSeq.deleteFeature(feature);
vSeg.setInclusive(true);
if (dsa.getSegCount() > 1)
{
- Cache.log.debug(
+ Cache.debug(
"About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
}
if (from != null && sequenceMapping.getLoc() != from)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ Cache.warn("Probable IMPLEMENTATION ERROR: " + from
+ " doesn't match the local mapping sequence.");
}
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+ Cache.warn("Probable IMPLEMENTATION ERROR: " + ds
+ " doesn't match the parent of the bound sequence mapping object.");
}
}
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
if (!dnaToProt)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug(
+ Cache.debug(
"Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
// SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
+ Cache.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
}
private void update(SequenceMapping sequenceMapping,
jalview.datamodel.Mapping mjvmapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Update DBRef Mapping from Jalview");
+ Cache.error("Not implemented: Update DBRef Mapping from Jalview");
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log.error(
+ Cache.error(
"Not implemented: Jalview Update Sequence DBRef Mapping");
}
}
if (sdloc == null || sdmap == null)
{
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ Cache.info("Ignoring non sequence-sequence mapping");
return;
}
mobj = this.getvObj2jv(sdloc);
if (from == null || to == null)
{
- jalview.bin.Cache.log.error(
+ Cache.error(
"Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
}
{
if (from.getDBRefs() == null && to.getDBRefs() == null)
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ Cache.debug("Not matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
return;
}
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ Cache.debug("Matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
List<DBRefEntry> fdb = from.getDBRefs();
boolean fmpnnl = (fmp != null);
// if (fmpnnl && fmp.getTo()!=null)
// {
- // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // Cache.debug("Not overwriting existing To reference in
// "+fe);
// continue;
// }
}
} catch (Exception e)
{
- Cache.log.warn("Problems parsing treefile '"
+ Cache.warn("Problems parsing treefile '"
+ tree.getNewick(0).getContent() + "'", e);
}
}
@Override
public void conflict()
{
- Cache.log.info(
+ Cache.info(
"Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
}
* idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
* getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
* title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
- * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
+ * (Exception e) { Cache.warn("Problems parsing treefile '" +
* tree.getNewick(0).getContent() + "'", e); }
*/
log.debug("Update the local tree in jalview from the document.");
*/
private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
{
- Cache.log.debug("Making Tree provenance for " + tp.getTitle());
+ Cache.debug("Making Tree provenance for " + tp.getTitle());
Provenance prov = new Provenance();
prov.addEntry(new Entry());
prov.getEntry(0).setAction("imported " + tp.getTitle());
vInput.addSeg(visSeg);
}
}
- Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
+ Cache.debug("Finished Tree provenance for " + tp.getTitle());
return prov;
}
}
if (alsq.size() < sequences.length)
{
- Cache.log.warn(
+ Cache.warn(
"Not recovered all alignment sequences for given set of input sequence CIGARS");
}
return alsq;
if (tp.getTree() == null)
{
- Cache.log.warn(
+ Cache.warn(
"Not updating SequenceTreeMap for " + tree.getVorbaId());
return;
}
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Cache.log.warn(
+ Cache.warn(
"Ignoring additional input spec in provenance entry "
+ tp.getEntry(pe).toString());
}
// bidirection alignments yet.
if (to < se[1])
{
- Cache.log.warn("Ignoring invalid segment in InputData spec.");
+ Cache.warn("Ignoring invalid segment in InputData spec.");
}
else
{
return new Object[] { new AlignmentView(view), jal };
}
}
- Cache.log.debug(
+ Cache.debug(
"Returning null for input data recovery from provenance.");
return null;
}
return true;
} catch (Exception e)
{
- Cache.log.debug("Failed to parse newick tree string", e);
+ Cache.debug("Failed to parse newick tree string", e);
}
return false;
}
VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
if (headerLine == null)
{
- Cache.log.error("VCF reference header not found");
+ Cache.error("VCF reference header not found");
return null;
}
String ref = headerLine.getValue();
}
else
{
- Cache.log.error("VCF reference not found: " + ref);
+ Cache.error("VCF reference not found: " + ref);
}
return seq;
{
if (reference == null)
{
- Cache.log.error("No VCF ##reference found, defaulting to "
+ Cache.error("No VCF ##reference found, defaulting to "
+ DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
}
GeneLociI seqCoords = seq.getGeneLoci();
if (seqCoords == null)
{
- Cache.log.warn(String.format(
+ Cache.warn(String.format(
"Can't query VCF for %s as chromosome coordinates not known",
seq.getName()));
return null;
// returned with the Ensembl sequence; todo: support aliases?
if (!vcfSpecies.equalsIgnoreCase(species))
{
- Cache.log.warn("No VCF loaded to " + seq.getName()
+ Cache.warn("No VCF loaded to " + seq.getName()
+ " as species not matched");
return null;
}
vcfAssembly);
if (newRange == null)
{
- Cache.log.error(
+ Cache.error(
String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
chromosome, seqRef, range[0], range[1],
vcfAssembly));
*/
String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
- Cache.log.error(msg);
+ Cache.error(msg);
}
}
VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(infoId);
if (infoHeader == null)
{
- Cache.log.error("Field " + infoId + " has no INFO header");
+ Cache.error("Field " + infoId + " has no INFO header");
return false;
}
VCFHeaderLineType infoType = infoHeader.getType();
if (!badData.contains(token))
{
badData.add(token);
- Cache.log.error(String.format("Invalid VCF data at %s:%d %s=%s",
+ Cache.error(String.format("Invalid VCF data at %s:%d %s=%s",
variant.getContig(), variant.getStart(), infoId, value));
}
}
if (seq != last || i != index)
{
// this should really be a trace message.
- // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ // Cache.debug("Mouse over " + v.getId() + " bound to "
// + seq + " at " + index);
last = seq;
i = index;
+++ /dev/null
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public abstract class Appender
-{
- public abstract void append(LoggingEvent loggingEvent);
-
-}
+++ /dev/null
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public class ConsoleAppender
-{
-
- private String name;
-
- private Layout layout;
-
-
- public ConsoleAppender()
- {
- }
-
- public ConsoleAppender(Layout layout, String name)
- {
- this.layout = layout;
- this.name = name;
- }
-
- public void setLayout(Layout layout)
- {
- this.layout = layout;
- }
-
- public void setName(String name)
- {
- this.name = name;
- }
-
- public void append(LoggingEvent event)
- {
-
- System.out
- .println(event.getLevel() + ": " + event.getRenderedMessage());
-
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j;
-
-import org.apache.logging.log4j.core.layout.PatternLayout;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-import jalview.javascript.log4j.spi.OptionHandler;
-//import org.apache.log4j.TTCCLayout;
-
-public abstract class Layout implements OptionHandler
-{
-
- // Note that the line.separator property can be looked up even by
- // applets.
- public final static String LINE_SEP = System
- .getProperty("line.separator");
-
- public final static int LINE_SEP_LEN = LINE_SEP.length();
-
- /**
- * Implement this method to create your own layout format.
- */
- abstract public String format(LoggingEvent event);
-
- /**
- * Returns the content type output by this layout. The base class returns
- * "text/plain".
- */
- public String getContentType()
- {
- return "text/plain";
- }
-
- /**
- * Returns the header for the layout format. The base class returns
- * <code>null</code>.
- */
- public String getHeader()
- {
- return null;
- }
-
- /**
- * Returns the footer for the layout format. The base class returns
- * <code>null</code>.
- */
- public String getFooter()
- {
- return null;
- }
-
- /**
- * If the layout handles the throwable object contained within
- * {@link LoggingEvent}, then the layout should return <code>false</code>.
- * Otherwise, if the layout ignores throwable object, then the layout should
- * return <code>true</code>. If ignoresThrowable is true, the appender is
- * responsible for rendering the throwable.
- * <p>
- * The {@link SimpleLayout}, {@link TTCCLayout}, {@link PatternLayout} all
- * return <code>true</code>. The {@link org.apache.log4j.xml.XMLLayout}
- * returns <code>false</code>.
- *
- * @since 0.8.4
- */
- abstract public boolean ignoresThrowable();
-
-}
+++ /dev/null
-package jalview.javascript.log4j;
-
-import java.util.Locale;
-
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.ObjectStreamException;
-import java.io.Serializable;
-
-/**
- * Defines the minimum set of levels recognized by the system, that is
- * <code>OFF</code>, <code>FATAL</code>, <code>ERROR</code>, <code>WARN</code>,
- * <code>INFO</code>, <code>DEBUG</code> and <code>ALL</code>.
- *
- * <p>
- * The <code>Level</code> class may be subclassed to define a larger level set.
- * </p>
- *
- * @author Ceki Gülcü
- */
-public class Level extends Priority implements Serializable
-{
-
- private static final String ALL_NAME = "ALL";
-
- private static final String TRACE_NAME = "TRACE";
-
- private static final String DEBUG_NAME = "DEBUG";
-
- private static final String INFO_NAME = "INFO";
-
- private static final String WARN_NAME = "WARN";
-
- private static final String ERROR_NAME = "ERROR";
-
- private static final String FATAL_NAME = "FATAL";
-
- private static final String OFF_NAME = "OFF";
-
- /**
- * TRACE level integer value.
- *
- * @since 1.2.12
- */
- public static final int TRACE_INT = 5000;
-
- /**
- * The <code>OFF</code> has the highest possible rank and is intended to turn
- * off logging.
- */
- final static public Level OFF = new Level(OFF_INT, OFF_NAME, 0);
-
- /**
- * The <code>FATAL</code> level designates very severe error events that will
- * presumably lead the application to abort.
- */
- final static public Level FATAL = new Level(FATAL_INT, FATAL_NAME, 0);
-
- /**
- * The <code>ERROR</code> level designates error events that might still allow
- * the application to continue running.
- */
- final static public Level ERROR = new Level(ERROR_INT, ERROR_NAME, 3);
-
- /**
- * The <code>WARN</code> level designates potentially harmful situations.
- */
- final static public Level WARN = new Level(WARN_INT, WARN_NAME, 4);
-
- /**
- * The <code>INFO</code> level designates informational messages that
- * highlight the progress of the application at coarse-grained level.
- */
- final static public Level INFO = new Level(INFO_INT, INFO_NAME, 6);
-
- /**
- * The <code>DEBUG</code> Level designates fine-grained informational events
- * that are most useful to debug an application.
- */
- final static public Level DEBUG = new Level(DEBUG_INT, DEBUG_NAME, 7);
-
- /**
- * The <code>TRACE</code> Level designates finer-grained informational events
- * than the <code>DEBUG</code level.
- *
- * @since 1.2.12
- */
- public static final Level TRACE = new Level(TRACE_INT, TRACE_NAME, 7);
-
- /**
- * The <code>ALL</code> has the lowest possible rank and is intended to turn
- * on all logging.
- */
- final static public Level ALL = new Level(ALL_INT, ALL_NAME, 7);
-
- /**
- * Serialization version id.
- */
- static final long serialVersionUID = 3491141966387921974L;
-
- /**
- * Instantiate a Level object.
- */
- protected Level(int level, String levelStr, int syslogEquivalent)
- {
- super(level, levelStr, syslogEquivalent);
- }
-
- /**
- * Convert the string passed as argument to a level. If the conversion fails,
- * then this method returns {@link #DEBUG}.
- */
- public static Level toLevel(String sArg)
- {
- return toLevel(sArg, Level.DEBUG);
- }
-
- /**
- * Convert an integer passed as argument to a level. If the conversion fails,
- * then this method returns {@link #DEBUG}.
- */
- public static Level toLevel(int val)
- {
- return toLevel(val, Level.DEBUG);
- }
-
- /**
- * Convert an integer passed as argument to a level. If the conversion fails,
- * then this method returns the specified default.
- */
- public static Level toLevel(int val, Level defaultLevel)
- {
- switch (val)
- {
- case ALL_INT:
- return ALL;
- case DEBUG_INT:
- return Level.DEBUG;
- case INFO_INT:
- return Level.INFO;
- case WARN_INT:
- return Level.WARN;
- case ERROR_INT:
- return Level.ERROR;
- case FATAL_INT:
- return Level.FATAL;
- case OFF_INT:
- return OFF;
- case TRACE_INT:
- return Level.TRACE;
- default:
- return defaultLevel;
- }
- }
-
- /**
- * Convert the string passed as argument to a level. If the conversion fails,
- * then this method returns the value of <code>defaultLevel</code>.
- */
- public static Level toLevel(String sArg, Level defaultLevel)
- {
- if (sArg == null)
- {
- return defaultLevel;
- }
- String s = sArg.toUpperCase(Locale.ROOT);
-
- if (s.equals(ALL_NAME))
- {
- return Level.ALL;
- }
- if (s.equals(DEBUG_NAME))
- {
- return Level.DEBUG;
- }
- if (s.equals(INFO_NAME))
- {
- return Level.INFO;
- }
- if (s.equals(WARN_NAME))
- {
- return Level.WARN;
- }
- if (s.equals(ERROR_NAME))
- {
- return Level.ERROR;
- }
- if (s.equals(FATAL_NAME))
- {
- return Level.FATAL;
- }
- if (s.equals(OFF_NAME))
- {
- return Level.OFF;
- }
- if (s.equals(TRACE_NAME))
- {
- return Level.TRACE;
- }
- //
- // For Turkish i problem, see bug 40937
- //
- if (s.equals("\u0130NFO"))
- {
- return Level.INFO;
- }
- return defaultLevel;
- }
-
- /**
- * Custom deserialization of Level.
- *
- * @param s
- * serialization stream.
- * @throws IOException
- * if IO exception.
- * @throws ClassNotFoundException
- * if class not found.
- */
- private void readObject(final ObjectInputStream s)
- throws IOException, ClassNotFoundException
- {
- s.defaultReadObject();
- level = s.readInt();
- syslogEquivalent = s.readInt();
- levelStr = s.readUTF();
- if (levelStr == null)
- {
- levelStr = "";
- }
- }
-
- /**
- * Serialize level.
- *
- * @param s
- * serialization stream.
- * @throws IOException
- * if exception during serialization.
- */
- private void writeObject(final ObjectOutputStream s) throws IOException
- {
- s.defaultWriteObject();
- s.writeInt(level);
- s.writeInt(syslogEquivalent);
- s.writeUTF(levelStr);
- }
-
- /**
- * Resolved deserialized level to one of the stock instances. May be overriden
- * in classes derived from Level.
- *
- * @return resolved object.
- * @throws ObjectStreamException
- * if exception during resolution.
- */
- private Object readResolve() throws ObjectStreamException
- {
- //
- // if the deserizalized object is exactly an instance of Level
- //
- if (getClass() == Level.class)
- {
- return toLevel(level);
- }
- //
- // extension of Level can't substitute stock item
- //
- return this;
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-import java.util.Hashtable;
-import java.util.Map;
-
-public class Logger
-{
-
- private static Map<String, Logger> registry;
-
- private String name;
-
- private Level level;
-
- private boolean enabled = true;
-
- private boolean isEnabled;
-
- private Appender appender;
-
- private Logger(String name)
- {
- this.name = name;
- }
-
- public static Logger getLogger(String name)
- {
- if (registry == null)
- {
- registry = new Hashtable<>();
- getLogger("root");
- }
- Logger logger = registry.get(name);
- if (logger == null)
- {
- registry.put(name, logger = new Logger(name));
- logger.setLevel(Level.INFO);
- }
- return logger;
- }
-
- public static Logger getRootLogger()
- {
- return getLogger("root");
- }
-
- public void setLevel(Level l)
- {
- this.level = l;
- }
-
- public void addAppender(Appender appender)
- {
- this.appender = appender;
- }
-
- public boolean isDebugEnabled()
- {
- return isEnabled;
- }
-
- public void debug(Object o)
- {
- debug(o, null);
- }
-
- public void debug(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- case Priority.INFO_INT:
- case Priority.DEBUG_INT:
- log(o, e);
- break;
- }
- }
-
- public void info(Object o)
- {
- info(o, null);
- }
-
- public void info(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- case Priority.INFO_INT:
- log(o, e);
- break;
- }
-
- }
-
- public void warn(Object o)
- {
- warn(o, null);
- }
-
- public void warn(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- log(o, e);
- break;
- }
-
- }
-
- public void error(Object o)
- {
- error(o, null);
- }
-
- public void error(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- log(o, e);
- break;
- }
-
- }
-
- private void log(Object s, Throwable e)
- {
- switch (level.level)
- {
- case Priority.ERROR_INT:
- if (appender == null)
- {
- System.err.println(s);
- return;
- }
- break;
- case Priority.WARN_INT:
- if (appender == null)
- {
- System.err.println(s);
- return;
- }
- break;
- case Priority.INFO_INT:
- if (appender == null)
- {
- System.out.println(s);
- return;
- }
- break;
- case Priority.DEBUG_INT:
- if (appender == null)
- {
- System.out.println(s);
- return;
- }
- break;
- }
- e.printStackTrace();
- appender.append(new LoggingEvent(this, s.toString(), level));
- }
-
-}
+++ /dev/null
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// Contributors: Kitching Simon <Simon.Kitching@orange.ch>
-
-package jalview.javascript.log4j;
-
-/**
- <font color="#AA4444">Refrain from using this class directly, use
- the {@link Level} class instead</font>.
-
- @author Ceki Gülcü */
-public class Priority {
-
- transient int level;
- transient String levelStr;
- transient int syslogEquivalent;
-
- public final static int OFF_INT = Integer.MAX_VALUE;
- public final static int FATAL_INT = 50000;
- public final static int ERROR_INT = 40000;
- public final static int WARN_INT = 30000;
- public final static int INFO_INT = 20000;
- public final static int DEBUG_INT = 10000;
- //public final static int FINE_INT = DEBUG_INT;
- public final static int ALL_INT = Integer.MIN_VALUE;
-
- // too twisted for J2S -- Level class initializer initializes Priority, which
- // creates a
- // new Level before Priority is indicated to be a superclass of Level.
- /**
- * @deprecated Use {@link Level#FATAL} instead.
- */
- @Deprecated
- final static public Priority FATAL = null;// new Level(FATAL_INT, "FATAL", 0);
-
- /**
- * @deprecated Use {@link Level#ERROR} instead.
- */
- @Deprecated
- final static public Priority ERROR = null;// new Level(ERROR_INT, "ERROR", 3);
-
- /**
- * @deprecated Use {@link Level#WARN} instead.
- */
- @Deprecated
- final static public Priority WARN = null;// new Level(WARN_INT, "WARN", 4);
-
- /**
- * @deprecated Use {@link Level#INFO} instead.
- */
- @Deprecated
- final static public Priority INFO = null;// new Level(INFO_INT, "INFO", 6);
-
- /**
- * @deprecated Use {@link Level#DEBUG} instead.
- */
- @Deprecated
- final static public Priority DEBUG = null;// new Level(DEBUG_INT, "DEBUG", 7);
-
- /**
- * Default constructor for deserialization.
- */
- protected Priority() {
- level = DEBUG_INT;
- levelStr = "DEBUG";
- syslogEquivalent = 7;
- }
-
- /**
- Instantiate a level object.
- */
- protected
- Priority(int level, String levelStr, int syslogEquivalent) {
- this.level = level;
- this.levelStr = levelStr;
- this.syslogEquivalent = syslogEquivalent;
- }
-
- /**
- Two priorities are equal if their level fields are equal.
- @since 1.2
- */
- @Override
- public
- boolean equals(Object o) {
- if(o instanceof Priority) {
- Priority r = (Priority) o;
- return (this.level == r.level);
- } else {
- return false;
- }
- }
-
- /**
- Return the syslog equivalent of this priority as an integer.
- */
- public
- final
- int getSyslogEquivalent() {
- return syslogEquivalent;
- }
-
-
-
- /**
- Returns <code>true</code> if this level has a higher or equal
- level than the level passed as argument, <code>false</code>
- otherwise.
-
- <p>You should think twice before overriding the default
- implementation of <code>isGreaterOrEqual</code> method.
-
- */
- public
- boolean isGreaterOrEqual(Priority r) {
- return level >= r.level;
- }
-
- // /**
- // Return all possible priorities as an array of Level objects in
- // descending order.
- //
- // @deprecated This method will be removed with no replacement.
- // */
- // public
- // static
- // Priority[] getAllPossiblePriorities() {
- // return new Priority[] {Priority.FATAL, Priority.ERROR, Level.WARN,
- // Priority.INFO, Priority.DEBUG};
- // }
-
-
- /**
- Returns the string representation of this priority.
- */
- @Override
- final
- public
- String toString() {
- return levelStr;
- }
-
- /**
- Returns the integer representation of this level.
- */
- public
- final
- int toInt() {
- return level;
- }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(String)} method instead.
- // */
- // public
- // static
- // Priority toPriority(String sArg) {
- // return Level.toLevel(sArg);
- // }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(int)} method instead.
- // */
- // public
- // static
- // Priority toPriority(int val) {
- // return toPriority(val, Priority.DEBUG);
- // }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(int, Level)} method
- // instead.
- // */
- // public
- // static
- // Priority toPriority(int val, Priority defaultPriority) {
- // return Level.toLevel(val, (Level) defaultPriority);
- // }
- //
- // /**
- // * @deprecated Please use the {@link Level#toLevel(String, Level)} method
- // instead.
- // */
- // public
- // static
- // Priority toPriority(String sArg, Priority defaultPriority) {
- // return Level.toLevel(sArg, (Level) defaultPriority);
- // }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public class SimpleLayout extends Layout
-{
-
- StringBuffer sbuf = new StringBuffer(128);
-
- @Override
- public void activateOptions()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public String format(LoggingEvent event)
- {
-
- sbuf.setLength(0);
- sbuf.append(event.getLevel().toString());
- sbuf.append(" - ");
- sbuf.append(event.getRenderedMessage());
- sbuf.append(LINE_SEP);
- return sbuf.toString();
- }
- @Override
- public boolean ignoresThrowable()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
-}
+++ /dev/null
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package jalview.javascript.log4j;
-
-public abstract class WriterAppender extends Appender
-{
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j.spi;
-
-import jalview.javascript.log4j.Logger;
-
-public class LoggingEvent
-{
-
- private Object level;
-
- private String msg;
-
- private Logger logger;
-
- public LoggingEvent(Logger logger, String level, Object message)
- {
- this.logger = logger;
- this.level = level;
- this.msg = message.toString();
-
- }
-
- public Object getLevel()
- {
- return level;
- }
-
- public String getRenderedMessage()
- {
- return msg;
- }
-}
+++ /dev/null
-package jalview.javascript.log4j.spi;
-
-public interface OptionHandler
-{
-
- void activateOptions();
-
-}
});
seqLimits.setText(
MessageManager.getString("label.show_sequence_limits"));
- seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
@Override
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem
- .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ .setState(Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
autoCalculate.setState(
- jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
- .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ .setState(Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
@Override
}
else
{
- Cache.log.error(
+ Cache.error(
"Preset '" + value + "' [key:" + key + "] not implemented");
}
.getSelectedItem();
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Problem casting Combo entry to IntKeyStringValueEntry.");
e = null;
}
e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
continue;
}
i = ((Integer) s.getValue()).intValue();
} catch (Exception e)
{
- Cache.log.error(
+ Cache.error(
"Exception casting the initial value of s.getValue()");
}
}
i = (Integer) s.getValue();
} catch (Exception e)
{
- Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
+ Cache.error("Failed casting (Integer) JSpinner s.getValue()");
}
return i;
}
*/
package jalview.jbgui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
wsMenuRefreshButs.add(resetWs, null);
wsMenuRefreshButs.add(progressBar, null);
myBorderlayout.setHgap(3);
- if (jalview.bin.Cache.getDefault("ENABLE_RSBS_EDITOR", false))
+ if (Cache.getDefault("ENABLE_RSBS_EDITOR", false))
{
JTabbedPane listPanels = new JTabbedPane();
listPanels.addTab("JABAWS Servers", wsListPanel);
--- /dev/null
+package jalview.log;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import jalview.bin.Cache;
+import jalview.util.Platform;
+
+public abstract class JLogger implements JLoggerI
+{
+ protected String name;
+
+ protected LogLevel level;
+
+ private Object logger = null;
+
+ private static Map<String, JLogger> registry = new HashMap<>();
+
+ // implement these abstract methods
+ protected abstract void loggerSetup();
+
+ public abstract boolean loggerExists();
+
+ protected abstract void loggerSetLevel(LogLevel level);
+
+ protected abstract void loggerLogMessage(LogLevel level, String message,
+ Throwable t);
+
+ public static LogLevel toLevel(String levelString)
+ {
+ try
+ {
+ return LogLevel.valueOf(levelString);
+ } catch (IllegalArgumentException e)
+ {
+ Cache.error("Could not parse LogLevel '" + levelString + "'", e);
+ return LogLevel.INFO;
+ }
+ }
+
+ public static JLogger getLogger(String name)
+ {
+ return getLogger(name, LogLevel.INFO);
+ }
+
+ public static JLogger getLogger(String name, LogLevel loglevel)
+ {
+ return registry.containsKey(name) ? (JLogger) registry.get(name) : null;
+ }
+
+ protected JLogger()
+ {
+ }
+
+ protected JLogger(String name, LogLevel level)
+ {
+ this.name = name;
+ this.level = level;
+ this.loggerSetup();
+ this.registryStore();
+ }
+
+ protected void registryStore()
+ {
+ registry.put(this.name, this);
+ }
+
+ protected static boolean registryContainsKey(String name)
+ {
+ return registry.containsKey(name);
+ }
+
+ protected static JLogger registryGet(String name)
+ {
+ return registry.get(name);
+ }
+
+ public LogLevel getLevel()
+ {
+ return this.level;
+ }
+
+ public void setLevel(LogLevel level)
+ {
+ this.level = level;
+ if (loggerExists())
+ loggerSetLevel(level);
+ }
+
+ private boolean println(LogLevel level, String message, Throwable t)
+ {
+ if (!loggerExists() || Platform.isJS())
+ {
+ String logLine = String.format("%s: %s", level.toString(), message);
+ System.out.println(logLine);
+ if (t != null)
+ {
+ if (level.compareTo(LogLevel.DEBUG) <= 0)
+ t.printStackTrace(System.err);
+ else
+ System.err.println(t.getMessage());
+ }
+ return false;
+ }
+ else
+ {
+ loggerLogMessage(level, message, t);
+ return true;
+ }
+ }
+
+ public void trace(String message)
+ {
+ trace(message, null);
+ }
+
+ public void trace(String message, Throwable t)
+ {
+ println(LogLevel.TRACE, message, t);
+ }
+
+ public void debug(String message)
+ {
+ debug(message, null);
+ }
+
+ public void debug(String message, Throwable t)
+ {
+ println(LogLevel.DEBUG, message, t);
+ }
+
+ public void info(String message)
+ {
+ info(message, null);
+ }
+
+ public void info(String message, Throwable t)
+ {
+ println(LogLevel.INFO, message, t);
+ }
+
+ public void warn(String message)
+ {
+ warn(message, null);
+ }
+
+ public void warn(String message, Throwable t)
+ {
+ println(LogLevel.WARN, message, t);
+ }
+
+ public void error(String message)
+ {
+ error(message, null);
+ }
+
+ public void error(String message, Throwable t)
+ {
+ println(LogLevel.ERROR, message, t);
+ }
+
+ public void fatal(String message)
+ {
+ fatal(message, null);
+ }
+
+ public void fatal(String message, Throwable t)
+ {
+ println(LogLevel.FATAL, message, t);
+ }
+
+ public boolean isDebugEnabled()
+ {
+ return level.compareTo(LogLevel.DEBUG) <= 0;
+ }
+
+ public boolean isTraceEnabled()
+ {
+ return level.compareTo(LogLevel.TRACE) <= 0;
+ }
+}
--- /dev/null
+package jalview.log;
+
+public interface JLoggerI
+{
+ public enum LogLevel
+ {
+ ALL, TRACE, DEBUG, INFO, WARN, ERROR, FATAL
+ }
+
+ public LogLevel getLevel();
+
+ public void setLevel(LogLevel level);
+
+ public void trace(String message);
+
+ public void trace(String message, Throwable t);
+
+ public void debug(String message);
+
+ public void debug(String message, Throwable t);
+
+ public void info(String message);
+
+ public void info(String message, Throwable t);
+
+ public void warn(String message);
+
+ public void warn(String message, Throwable t);
+
+ public void error(String message);
+
+ public void error(String message, Throwable t);
+
+ public void fatal(String message);
+
+ public void fatal(String message, Throwable t);
+
+ public boolean isDebugEnabled();
+
+ public boolean isTraceEnabled();
+}
--- /dev/null
+package jalview.log;
+
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.Appender;
+
+import jalview.util.Log4j;
+import jalview.util.Platform;
+
+public class JLoggerLog4j extends JLogger implements JLoggerI
+{
+ private Logger logger = null;
+
+ public static JLoggerLog4j getLogger(String name)
+ {
+ return getLogger(name, LogLevel.INFO);
+ }
+
+ public static JLoggerLog4j getLogger(String name, LogLevel loglevel)
+ {
+ return registryContainsKey(name) ? (JLoggerLog4j) registryGet(name)
+ : new JLoggerLog4j(name, loglevel);
+ }
+
+ private JLoggerLog4j(String name, LogLevel level)
+ {
+ // super(name, level);
+ this.name = name;
+ this.level = level;
+ this.loggerSetup();
+ this.registryStore();
+ }
+
+ @Override
+ protected void loggerSetup()
+ {
+ if (!Platform.isJS())
+ this.logger = Log4j.isInit() ? Log4j.getLogger(this.name, this.level)
+ : null;
+ }
+
+ @Override
+ public boolean loggerExists()
+ {
+ return logger != null;
+ }
+
+ @Override
+ protected void loggerSetLevel(JLoggerI.LogLevel level)
+ {
+ if (loggerExists())
+ {
+ Log4j.setLevel(logger, level);
+ }
+ }
+
+ @Override
+ protected void loggerLogMessage(LogLevel level, String message,
+ Throwable t)
+ {
+ if (!loggerExists())
+ return;
+ if (t != null)
+ {
+ switch (level)
+ {
+ case FATAL:
+ logger.fatal(message, t);
+ break;
+ case ERROR:
+ logger.error(message, t);
+ break;
+ case WARN:
+ logger.warn(message, t);
+ break;
+ case INFO:
+ logger.info(message, t);
+ break;
+ case DEBUG:
+ logger.debug(message, t);
+ break;
+ case TRACE:
+ logger.trace(message, t);
+ break;
+ case ALL:
+ logger.trace(message, t);
+ break;
+ }
+ }
+ else
+ {
+ switch (level)
+ {
+ case FATAL:
+ logger.fatal(message);
+ break;
+ case ERROR:
+ logger.error(message);
+ break;
+ case WARN:
+ logger.warn(message);
+ break;
+ case INFO:
+ logger.info(message);
+ break;
+ case DEBUG:
+ logger.debug(message);
+ break;
+ case TRACE:
+ logger.trace(message);
+ break;
+ case ALL:
+ logger.trace(message);
+ break;
+ }
+ }
+ }
+
+ private Logger getLoggerObject()
+ {
+ return this.logger;
+ }
+
+ public synchronized static void addAppender(JLoggerLog4j l1,
+ Appender appender)
+ {
+ if (!Platform.isJS())
+ Log4j.addAppender(l1.getLoggerObject(), appender);
+ }
+
+ public synchronized static void addAppender(JLoggerLog4j l1,
+ JLoggerLog4j l2, String name)
+ {
+ if (!Platform.isJS())
+ Log4j.addAppender(l1.getLoggerObject(), l2.getLoggerObject(), name);
+ }
+
+}
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.gui;
+package jalview.log;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import javax.swing.JTextArea;
import javax.swing.SwingUtilities;
+import org.apache.logging.log4j.Level;
import org.apache.logging.log4j.core.Filter;
import org.apache.logging.log4j.core.Layout;
import org.apache.logging.log4j.core.LogEvent;
import org.apache.logging.log4j.core.appender.AbstractAppender;
-import org.apache.logging.log4j.core.layout.PatternLayout;
+import org.apache.logging.log4j.core.config.Property;
+
+import jalview.log.JLoggerI.LogLevel;
+import jalview.util.Log4j;
/**
* From http://textareaappender.zcage.com/ the means to capture the logs, too.
*/
public class JalviewAppender extends AbstractAppender
{
+ public final static String NAME = "JalviewAppender";
- private final static Layout simpleLayout;
-
- static
+ public JalviewAppender()
{
- // SimpleLayout pattern found from
- // https://logging.apache.org/log4j/log4j-2.12.4/manual/migration.html
- simpleLayout = PatternLayout.newBuilder().withPattern("%level - %m%n")
- .build();
+ this(LogLevel.INFO);
}
- protected JalviewAppender()
+ public JalviewAppender(LogLevel loglevel)
{
- this("JalviewAppender", null, simpleLayout);
+ super(NAME,
+ Log4j.getThresholdFilter(loglevel == null ? Level.INFO
+ : Log4j.log4jLevel(loglevel)),
+ Log4j.getSimpleLayout(), false, new Property[0]);
}
protected JalviewAppender(String name, Filter filter,
- Layout<? extends Serializable> layout)
+ Layout<? extends Serializable> layout, boolean ignoreExceptions,
+ Property[] properties)
{
- super(name, filter, layout);
+ super(name, filter, layout, ignoreExceptions, properties);
// TODO Auto-generated constructor stub
}
*/
public void append(LogEvent logEvent)
{
- final String message = new String(simpleLayout.toByteArray(logEvent),
- StandardCharsets.UTF_8);
+ final String message = new String(
+ this.getLayout().toByteArray(logEvent), StandardCharsets.UTF_8);
// Append formatted message to textarea using the Swing Thread.
SwingUtilities.invokeLater(new Runnable()
} catch (Exception e)
{
- Cache.log.error("Couln't write Jalview state to " + statefile, e);
+ Cache.error("Couln't write Jalview state to " + statefile, e);
// TODO: inform user of the problem - they need to know if their data was
// not saved !
if (errorMessage == null)
System.err.println("error writing date: " + e.toString());
}
object.setVersion(
- jalview.bin.Cache.getDefault("VERSION", "Development Build"));
+ Cache.getDefault("VERSION", "Development Build"));
/**
* rjal is full height alignment, jal is actual alignment with full metadata
}
else
{
- Cache.log.error(
+ Cache.error(
"Failed to save viewer state for " + viewerType);
}
}
.getHiddenColumns();
if (hidden == null)
{
- warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ Cache.warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
else
{
object.getPcaViewer().add(viewer);
} catch (Throwable t)
{
- Cache.log.error("Error saving PCA: " + t.getMessage());
+ Cache.error("Error saving PCA: " + t.getMessage());
}
}
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- Cache.log.warn(
+ Cache.warn(
"Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ pdbentry.getFile());
}
calcIdParam.getParameters().replace("|\\n|", "\n"));
} catch (IOException x)
{
- warn("Couldn't parse parameter data for "
+ Cache.warn("Couldn't parse parameter data for "
+ calcIdParam.getCalcId(), x);
return false;
}
}
else
{
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ Cache.warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
return false;
}
}
return id.toString();
}
// give up and warn that something has gone wrong
- warn("Cannot find ID for object in external mapping : " + jvobj);
+ Cache.warn("Cannot find ID for object in external mapping : " + jvobj);
}
return altCode;
}
mp.setDseqFor(jmpid);
if (!seqRefIds.containsKey(jmpid))
{
- jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ Cache.debug("creatign new DseqFor ID");
seqRefIds.put(jmpid, ps);
}
else
{
- jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ Cache.debug("reusing DseqFor ID");
}
// mp.setMappingChoice(mpc);
}
else
{
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Cache.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
- warn("There was a problem recovering stored Newick tree: \n"
+ Cache.warn("There was a problem recovering stored Newick tree: \n"
+ tree.getNewick());
continue;
}
else
{
errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
- warn(errorMessage);
+ Cache.warn(errorMessage);
}
}
}
} catch (IllegalArgumentException | NullPointerException e)
{
// TODO JAL-3619 show error dialog / offer an alternative viewer
- Cache.log.error("Invalid structure viewer type: " + type);
+ Cache.error("Invalid structure viewer type: " + type);
}
}
}
else
{
- warn("Couldn't recover parameters for "
+ Cache.warn("Couldn't recover parameters for "
+ calcIdParam.getCalcId());
}
}
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- if (Cache.log != null && Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Skipping seuqence set id " + id);
- }
+ Cache.debug("Skipping seuqence set id " + id);
return true;
}
return false;
{
if (ds != null && ds != seqSetDS)
{
- warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ Cache.warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ " - CDS/Protein crossreference data may be lost");
if (xtant_ds != null)
{
// This can only happen if the unique sequence set ID was bound to a
// dataset that did not contain any of the sequences in the view
// currently being restored.
- warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
+ Cache.warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
}
}
ds = seqSetDS;
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
- debug("Created new dataset " + vamsasSet.getDatasetId()
+ Cache.debug("Created new dataset " + vamsasSet.getDatasetId()
+ " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
if (prevDS != null && prevDS != ds)
{
- warn("Dataset sequence appears in many datasets: "
+ Cache.warn("Dataset sequence appears in many datasets: "
+ restoredSeq.getDsseqid());
// TODO: try to merge!
}
{
if (dataset.getDataset() != null)
{
- warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ Cache.warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
}
String datasetId = makeHashCode(dataset, null);
if (datasetId == null)
seqRefIds.put(sqid, djs);
}
- jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ Cache.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
}
private Hashtable jvids2vobj;
- private void warn(String msg)
- {
- warn(msg, null);
- }
-
- private void warn(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.warn(msg, e);
- }
- else
- {
- Cache.log.warn(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
- private void debug(String string)
- {
- debug(string, null);
- }
-
- private void debug(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.debug(msg, e);
- }
- else
- {
- Cache.log.debug(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
/**
* set the object to ID mapping tables used to write/recover objects and XML
* ID strings for the jalview project. If external tables are provided then
if (!jvann.annotationId.equals(anid))
{
// TODO verify that this is the correct behaviour
- this.warn("Overriding Annotation ID for " + anid
+ Cache.warn("Overriding Annotation ID for " + anid
+ " from different id : " + jvann.annotationId);
jvann.annotationId = anid;
}
}
else
{
- Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Cache.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
}
else
{
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Cache.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
}
} catch (Exception ex)
{
- Cache.log.error("Error loading PCA: " + ex.toString());
+ Cache.error("Error loading PCA: " + ex.toString());
}
}
});
} catch (InvocationTargetException | InterruptedException ex)
{
- warn("Unexpected error when opening " + viewerType
+ Cache.warn("Unexpected error when opening " + viewerType
+ " structure viewer", ex);
}
}
}
} catch (IOException e)
{
- Cache.log.error("Error restoring Jmol session: " + e.toString());
+ Cache.error("Error restoring Jmol session: " + e.toString());
}
return null;
}
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ Cache.warn("Couldn't parse out graduated feature color.", e);
}
NoValueColour noCol = colourModel.getNoValueColour();
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- Cache.log.error("SIFTS mapping failed", e);
- Cache.log.error("Falling back on Needleman & Wunsch alignment");
+ Cache.error("SIFTS mapping failed", e);
+ Cache.error("Falling back on Needleman & Wunsch alignment");
siftsClient = null;
}
} catch (SiftsException e)
{
// fall back to NW alignment
- Cache.log.error(e.getMessage());
+ Cache.error(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
saveSession(f);
} catch (IOException e)
{
- Cache.log.error(String.format("Error saving %s session: %s", prefix,
+ Cache.error(String.format("Error saving %s session: %s", prefix,
e.toString()));
}
dataProvider.setUrlData(data);
} catch (IllegalArgumentException ex)
{
- Cache.log.error(ex.getMessage());
+ Cache.error(ex.getMessage());
}
}
});
*/
package jalview.util;
+import jalview.bin.Cache;
+
import java.io.File;
import java.io.IOException;
import java.lang.reflect.Constructor;
case OTHER:
default:
- browser = jalview.bin.Cache.getDefault("DEFAULT_BROWSER", "firefox");
+ browser = Cache.getDefault("DEFAULT_BROWSER", "firefox");
break;
}
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.Appender;
+import org.apache.logging.log4j.core.Filter;
+import org.apache.logging.log4j.core.Layout;
import org.apache.logging.log4j.core.LoggerContext;
+import org.apache.logging.log4j.core.appender.ConsoleAppender;
import org.apache.logging.log4j.core.config.Configuration;
+import org.apache.logging.log4j.core.config.ConfigurationFactory;
+import org.apache.logging.log4j.core.config.Configurator;
import org.apache.logging.log4j.core.config.LoggerConfig;
+import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
+import org.apache.logging.log4j.core.config.builder.api.FilterComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.LayoutComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
+import org.apache.logging.log4j.core.filter.ThresholdFilter;
+import org.apache.logging.log4j.core.layout.PatternLayout;
+
+import jalview.log.JLogger;
+import jalview.log.JalviewAppender;
public class Log4j
{
+
+ public final static String SIMPLE_PATTERN = "%level - %m%n";
+
+ private static boolean init = false;
+
+ public static boolean isInit()
+ {
+ return init;
+ }
+
+ public static Level log4jLevel(JLogger.LogLevel loglevel)
+ {
+ return Level.toLevel(loglevel.toString());
+ }
+
+ public static void init(JLogger.LogLevel myLevel)
+ {
+ init(log4jLevel(myLevel));
+ }
+
+ public static void init(Level myLevel)
+ {
+ if (init)
+ return;
+ try
+ {
+ // configure the root logger to stderr
+ ConfigurationBuilder<BuiltConfiguration> configBuilder = Log4j
+ .getConfigurationBuilder();
+
+ configBuilder.setStatusLevel(Level.WARN);
+
+ String consoleLoggerName = "STDERR";
+ AppenderComponentBuilder appenderBuilder = configBuilder
+ .newAppender(consoleLoggerName, "Console");
+ appenderBuilder.addAttribute("target",
+ ConsoleAppender.Target.SYSTEM_ERR);
+ appenderBuilder.add(Log4j.getSimpleLayoutBuilder());
+ appenderBuilder.add(Log4j.getThresholdFilterBuilder());
+ configBuilder.add(appenderBuilder);
+
+ configBuilder.add(configBuilder.newRootLogger(myLevel)
+ .add(configBuilder.newAppenderRef(consoleLoggerName)));
+
+ Configurator.initialize(configBuilder.build());
+
+ init = true;
+ } catch (Exception e)
+ {
+ System.err.println("Problems initializing the log4j system\n");
+ e.printStackTrace(System.err);
+ }
+ }
+
+ public static Logger getLogger(String name)
+ {
+ return getLogger(name, Level.INFO);
+ }
+
+ public static Logger getLogger(String name, JLogger.LogLevel loglevel)
+ {
+ return getLogger(name, log4jLevel(loglevel));
+ }
+
+ public static Logger getLogger(String name, Level level)
+ {
+ Logger logger = LogManager.getLogger(name);
+ Log4j.setLevel(logger, level);
+ return logger;
+ }
+
+ public static ConfigurationBuilder<BuiltConfiguration> getConfigurationBuilder()
+ {
+ return ConfigurationFactory.newConfigurationBuilder();
+ }
+
+ public static Layout getSimpleLayout()
+ {
+ return PatternLayout.newBuilder().withPattern(SIMPLE_PATTERN).build();
+ }
+
+ public static LayoutComponentBuilder getSimpleLayoutBuilder()
+ {
+ return getConfigurationBuilder().newLayout("PatternLayout")
+ .addAttribute("pattern", Log4j.SIMPLE_PATTERN);
+ }
+
+ public static Filter getThresholdFilter(Level level)
+ {
+ return ThresholdFilter.createFilter(level, Filter.Result.ACCEPT,
+ Filter.Result.NEUTRAL);
+ }
+
+ public static FilterComponentBuilder getThresholdFilterBuilder()
+ {
+ return getConfigurationBuilder().newFilter("ThresholdFilter",
+ Filter.Result.ACCEPT, Filter.Result.NEUTRAL);
+ }
+
+ public static void setLevel(Logger logger, JLogger.LogLevel loglevel)
+ {
+ setLevel(logger, log4jLevel(loglevel));
+ }
+
public static void setLevel(Logger logger, Level level)
{
- LoggerContext context = (LoggerContext) LogManager.getContext(false);
- Configuration config = context.getConfiguration();
- LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName());
- loggerConfig.setLevel(level);
+ if (!Platform.isJS())
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName());
+ loggerConfig.setLevel(level);
+
+ Map<String, Appender> appenders = config.getAppenders();
+
+ Appender jappender = config.getAppender(JalviewAppender.NAME);
+
+ context.updateLoggers();
+ }
+ }
+
+ public static void setRootLevel(JLogger.LogLevel loglevel)
+ {
+ setRootLevel(log4jLevel(loglevel));
}
public static void setRootLevel(Level level)
setLevel(LogManager.getRootLogger(), level);
}
+ public static Appender getAppender(String name)
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ Map<String, Appender> appenders = config.getAppenders();
+ return appenders.get(name);
+ }
+
public static void addAppender(Logger logger, Logger logger2,
String name2)
{
.getAppenders();
Appender appender = logger2AppendersMap.get(name2);
addAppender(logger, appender);
+ context.updateLoggers();
}
public static void addAppender(Logger logger, Appender appender)
{
+ if (appender == null)
+ return;
LoggerContext context = (LoggerContext) LogManager.getContext(false);
Configuration config = context.getConfiguration();
LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName());
+ if (loggerConfig == null)
+ return;
+
+ Level level = loggerConfig.getLevel();
+
+ config.addAppender(appender);
loggerConfig.addAppender(appender, null, null);
+
+ context.updateLoggers();
}
public static void addAppenderToRootLogger(Appender appender)
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- Cache.log.error("Invalid format for fromRange "
+ Cache.error("Invalid format for fromRange "
+ Arrays.toString(range) + " may cause errors");
}
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- Cache.log.error("Invalid format for toRange "
+ Cache.error("Invalid format for toRange "
+ Arrays.toString(range) + " may cause errors");
}
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
action = action.getUndoAction();
}
// TODO write this
- Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
+ Cache.error("MappingUtils.mapCutOrPaste not yet implemented");
}
/**
{
if (range.length % 2 != 0)
{
- Cache.log.error(
+ Cache.error(
"Error unbalance start/end ranges: " + ranges.toString());
return 0;
}
/*
* not coded for [start1, end1, start2, end2, ...]
*/
- Cache.log.error(
+ Cache.error(
"MappingUtils.removeEndPositions doesn't handle multiple ranges");
return;
}
/*
* not coded for a reverse strand range (end < start)
*/
- Cache.log.error(
+ Cache.error(
"MappingUtils.removeEndPositions doesn't handle reverse strand");
return;
}
import java.util.ResourceBundle.Control;
import java.util.Set;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import jalview.log.JLoggerLog4j;
/**
*
{
private static ResourceBundle rb;
- // BH 2018 switched to org.apache.llog4j.Logger
- private static Logger log = LogManager
+ private static JLoggerLog4j log = JLoggerLog4j
.getLogger(MessageManager.class.getCanonicalName());
private static Locale loc;
throw (new Exception(
"Timed out when communicating with server\nTry again later.\n"));
}
- jalview.bin.Cache.log.debug("Job " + j + " Result state "
+ Cache.debug("Job " + j + " Result state "
+ jobs[j].getState() + "(ServerError="
+ jobs[j].isServerError() + ")");
} catch (Exception ex)
.formatMessage("info.server_exception", new Object[]
{ WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ Cache.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
// todo: could limit trace to cause if this is a SOAPFaultException.
ex.printStackTrace();
if (jobs[j].allowedServerExceptions > 0)
{
jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
+ Cache.debug("Sleeping after a server exception.");
try
{
Thread.sleep(5000);
}
else
{
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ Cache.warn("Dropping job " + j + " " + jobs[j].jobId);
jobs[j].subjobComplete = true;
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_SERVERERROR);
jobs[j].clearResponse(); // may contain out of date result data
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_ERROR);
- Cache.log.error("Out of memory when retrieving Job " + j
+ Cache.error("Out of memory when retrieving Job " + j
+ " id:" + WsUrl + "/" + jobs[j].jobId, er);
new jalview.gui.OOMWarning(
"retrieving result for " + WebServiceName, er);
Thread.sleep(5000);
} catch (InterruptedException e)
{
- Cache.log.debug("Interrupted sleep waiting for next job poll.",
+ Cache.debug("Interrupted sleep waiting for next job poll.",
e);
}
// System.out.println("I'm alive "+alTitle);
}
else
{
- Cache.log.debug(
+ Cache.debug(
"WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(
AlignmentI retrieved = null;
try
{
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug("Querying " + dbsource.getDbName()
+ Cache.debug("Querying " + dbsource.getDbName()
+ " with : '" + queryString.toString() + "'");
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
if (al == null)
{
- Cache.log.error(
+ Cache.error(
"No record found for '" + dbName + ":" + query + "'");
}
}
return listToArray(ranges);
} catch (ParseException e)
{
- Cache.log.warn(
+ Cache.warn(
String.format("Not parsing inexact CDS location %s in ENA %s",
location, accession));
return new int[] {};
// TODO: trap HTTP 404 exceptions and return null
String xfamUrl = getURL(queries);
- if (Cache.log != null)
- {
- Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
- }
+ Cache.debug("XFAM URL for retrieval is: " + xfamUrl);
AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
DataSourceType.URL, FileFormat.Stockholm);
*/
package jalview.ws.jws1;
+import jalview.bin.Cache;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
// timeout
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
+ Cache.error(
"Serious! Service location failed\nfor URL :" + WsURL + "\n",
ex);
static private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
- String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
+ String RootServiceURLs = Cache.getDefault("DISCOVERY_URLS",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
try
}
else
{
- jalview.bin.Cache.log
- .info("Ignoring duplicate url in DISCOVERY_URLS list");
+ Cache.info("Ignoring duplicate url in DISCOVERY_URLS list");
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .warn("Problem whilst trying to make a URL from '"
+ Cache.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"This was probably due to a malformed comma separated list"
+ " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ", ex);
+ Cache.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"Error parsing comma separated list of urls in DISCOVERY_URLS.",
ex);
}
*/
static public void doDiscovery()
{
- jalview.bin.Cache.log
- .debug("(Re)-Initialising the discovery URL list.");
+ Cache.debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = jalview.bin.Cache
+ reallyDiscoverServices = Cache
.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
}
else
{
- jalview.bin.Cache.log.debug("Setting default services");
+ Cache.debug("Setting default services");
services = new Hashtable<>();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
ServiceHandles shs = null;
try
{
- jalview.bin.Cache.log.debug("Discovering services using " + location);
+ Cache.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
} catch (org.apache.axis.AxisFault f)
{
}
else
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Axis Fault", f);
+ Cache.warn("No Discovery service at " + location);
+ Cache.debug("Axis Fault", f);
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
+ Cache.warn("No Discovery service at " + location);
+ Cache.debug("Discovery Service General Exception", e);
}
if ((shs != null) && shs.getServices().length > 0)
{
{
if (!cat.contains(sh[i]))
{
- jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+ Cache.debug("A " + sh[i].getAbstractName()
+ " service called " + sh[i].getName() + " exists at "
+ sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log.debug(
+ Cache.debug(
"Adding new discovery service at " + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .debug("Ignoring bad discovery service URL "
+ Cache.debug("Ignoring bad discovery service URL "
+ sh[i].getEndpointURL(), e);
}
}
int s_url = 0;
if (ServiceURLList == null)
{
- jalview.bin.Cache.log
- .debug("No service endpoints to use for service discovery.");
+ Cache.debug("No service endpoints to use for service discovery.");
return;
}
while (s_url < ServiceURLList.size())
}
else
{
- jalview.bin.Cache.log.warn("No services at "
+ Cache.warn("No services at "
+ (ServiceURLList.get(s_url))
+ " - check DISCOVERY_URLS property in .jalview_properties");
}
Jpred server = locateWebService();
if (server == null)
{
- Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+ Cache.warn("Couldn't find a Jpred webservice to invoke!");
return;
}
SeqCigar[] msf = null;
JpredResult result = (JpredResult) this.result;
- Cache.log.debug("Parsing output from JNet job.");
+ Cache.debug("Parsing output from JNet job.");
// JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
// "File");
JPredFile prediction = new JPredFile(result.getPredfile(),
DataSourceType.PASTE);
SequenceI[] preds = prediction.getSeqsAsArray();
- Cache.log.debug("Got prediction profile.");
+ Cache.debug("Got prediction profile.");
if ((this.msa != null) && (result.getAligfile() != null))
{
- Cache.log.debug("Getting associated alignment.");
+ Cache.debug("Getting associated alignment.");
// we ignore the returned alignment if we only predicted on a single
// sequence
FileFormatI format = new IdentifyFile()
{
job.setSubmitted(true);
job.setSubjobComplete(false);
- Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+ Cache.info(WsUrl + " Job Id '" + job.getJobId() + "'");
}
}
else
"JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+ e.getMessage() + "\n");
- jalview.bin.Cache.log.warn("Server Exception", e);
+ Cache.warn("Server Exception", e);
}
else
{
"info.failed_to_submit_prediction", new String[]
{ e.getMessage(), wsInfo.getProgressText() }));
- jalview.bin.Cache.log
- .debug("Failed Submission of job " + j.getJobnum(), e);
+ Cache.debug("Failed Submission of job " + j.getJobnum(), e);
}
j.setAllowedServerExceptions(-1);
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Unexpected exception when processing results for " + altitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
msa = (j.msa != null) ? true : msa;
try
{
- jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ Cache.debug("Parsing output of job " + jn);
jobres = j.getResultSet();
- jalview.bin.Cache.log.debug("Finished parsing output.");
+ Cache.debug("Finished parsing output.");
if (jobs.length == 1)
{
res = jobres;
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .error("JNet Client: JPred Annotation Parse Error", e);
+ Cache.error("JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(j.getJobnum(),
}
else
{
- Cache.log.info("Append results onto existing alignment.");
+ Cache.info("Append results onto existing alignment.");
}
}
}
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Cache.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
&& jobs[j].hasResults())
{
results++;
- // if (Cache.log.isDebugEnabled())
+ // if (Cache.isDebugEnabled())
// {
// System.out.println("Job lob for job
// "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
*/
package jalview.ws.jws1;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
.getSupportedDatabases();
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"Database list request failed, so disabling SeqSearch Service client "
+ sh.getName() + " at " + sh.getEndpointURL(),
e);
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Cache.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
scores = scoremanager.getAnnotationForSequence(seqId);
} catch (Exception q)
{
- Cache.log
- .info("Couldn't recover disorder prediction for sequence "
+ Cache.info("Couldn't recover disorder prediction for sequence "
+ seq.getName() + "(Prediction name was " + seqId
+ ")"
+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
}
if (collectAnnotationResultsFor(rslt))
{
- jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ Cache.debug("Updating result annotation from Job "
+ rslt + " at " + service.getUri());
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
else
{
jws2Discoverer.addInvalidServiceUrl(jwsserver);
- Cache.log.warn("Ignoring invalid Jws2 service url " + jwsserver);
+ Cache.warn("Ignoring invalid Jws2 service url " + jwsserver);
}
} catch (Exception e)
{
e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
+ Cache.warn("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsserver);
} catch (Error e)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
+ Cache.error("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
running = false;
if (service != null
&& !fave.getService().hosturl.equals(service.hosturl))
{
- Cache.log.debug("Changing AACon service to " + service.hosturl
+ Cache.debug("Changing AACon service to " + service.hosturl
+ " from " + fave.getService().hosturl);
fave.setService(service);
}
if (!service.serviceType.toString()
.equals(compbio.ws.client.Services.AAConWS.toString()))
{
- Cache.log.warn(
+ Cache.warn(
"Ignoring invalid preferred service for AACon calculations (service type was "
+ service.serviceType + ")");
service = null;
{
try
{
- Cache.log.debug(
+ Cache.debug(
"Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
}
}
aborted = false;
- Cache.log.debug("Old discovery thread has finished.");
+ Cache.debug("Old discovery thread has finished.");
}
running = true;
}
if (aborted)
{
- Cache.log.debug(
+ Cache.debug(
"Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
}
else
{
- Cache.log.warn("Ignoring duplicate url " + url + " in "
+ Cache.warn("Ignoring duplicate url " + url + " in "
+ JWS2HOSTURLS + " list");
}
} catch (MalformedURLException ex)
{
- Cache.log.warn("Problem whilst trying to make a URL from '"
+ Cache.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- Cache.log.warn(
+ Cache.warn(
"This was probably due to a malformed comma separated list"
+ " in the " + JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
- Cache.log.debug("Exception was ", ex);
+ Cache.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- Cache.log.warn("Error parsing comma separated list of urls in "
+ Cache.warn("Error parsing comma separated list of urls in "
+ JWS2HOSTURLS + " preference.", ex);
}
return urls;
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Cache.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
- Cache.log.debug(
+ Cache.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
} catch (Exception e)
{
- Cache.log.warn(
+ Cache.warn(
"Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
}
} while (nunchanged > 0 && nexcept > 0);
- if (Cache.log.isDebugEnabled())
+ if (Cache.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
+ msjob.getJobId() + " on server " + WsUrl);
{
// job has failed for some reason - probably due to invalid
// parameters
- Cache.log.debug(
+ Cache.debug(
"Results not available for finished job - marking as broken job.",
e);
msjob.jobProgress.append(
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
- Cache.log.error("Couldn't get Alignment for job.", e);
+ Cache.error("Couldn't get Alignment for job.", e);
// TODO: Increment count and retry ?
msjob.setjobStatus(JobStatus.UNDEFINED);
}
} catch (Exception ex)
{
- Cache.log.error(
+ Cache.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
{
error = true;
errormessage = "Couldn't parse message from web service.";
- Cache.log.warn("Failed to parse MIME multipart content", me);
+ Cache.warn("Failed to parse MIME multipart content", me);
en.consumeContent();
}
return new ParsePackedSet().getAlignment(ds,
: en.getContentEncoding().getValue();
if (en.getContentType() != null)
{
- Cache.log.debug("Result Type: " + en.getContentType().toString());
+ Cache.debug("Result Type: " + en.getContentType().toString());
}
else
{
- Cache.log.debug("No Result Type Specified.");
+ Cache.debug("No Result Type Specified.");
}
if (enc == null || enc.length() < 1)
{
- Cache.log.debug("Assuming 'Default' Result Encoding.");
+ Cache.debug("Assuming 'Default' Result Encoding.");
}
else
{
- Cache.log.debug("Result Encoded as : " + enc);
+ Cache.debug("Result Encoded as : " + enc);
}
// attempt to identify file and construct an appropriate DataSource
// identifier for it.
: new InputStreamReader(en.getContent());
} catch (UnsupportedEncodingException e)
{
- Cache.log.error("Can't handle encoding '" + enc
+ Cache.error("Can't handle encoding '" + enc
+ "' for response from webservice.", e);
en.consumeContent();
error = true;
{
for (RestServiceDescription descr : RestServiceDescription
.parseDescriptions(
- jalview.bin.Cache.getDefault(RSBS_SERVICES,
+ Cache.getDefault(RSBS_SERVICES,
makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
+ "</a><br>See Console output for details.";
rj.setAllowedServerExceptions(0);// unrecoverable;
rj.error = true;
- Cache.log.fatal("Unexpected REST Job " + getStage(stg)
+ Cache.fatal("Unexpected REST Job " + getStage(stg)
+ "exception for URL " + rj.rsd.postUrl);
throw (he);
} catch (IOException e)
+ "Job. <br>Problematic url was <a href=\""
+ request.getURI() + "\">" + request.getURI()
+ "</a><br>See Console output for details.";
- Cache.log.warn("IO Exception for REST Job " + getStage(stg)
+ Cache.warn("IO Exception for REST Job " + getStage(stg)
+ "exception for URL " + rj.rsd.postUrl);
throw (e);
{
case 200:
rj.running = false;
- Cache.log.debug("Processing result set.");
+ Cache.debug("Processing result set.");
processResultSet(rj, response, request);
break;
case 202:
{
if (loc.length > 1)
{
- Cache.log.warn("Ignoring additional " + (loc.length - 1)
+ Cache.warn("Ignoring additional " + (loc.length - 1)
+ " location(s) provided in response header ( next one is '"
+ loc[1].getValue() + "' )");
}
default:
// Some other response. Probably need to pop up the content in a window.
// TODO: deal with all other HTTP response codes from server.
- Cache.log.warn("Unhandled response status when " + getStage(stg)
+ Cache.warn("Unhandled response status when " + getStage(stg)
+ "for " + postUrl + ": " + response.getStatusLine());
rj.error = true;
rj.setAllowedServerExceptions(0);
+ "</a><br/>Filtered response content below:<br/>");
} catch (IOException e)
{
- Cache.log.debug("IOException when consuming unhandled response",
+ Cache.debug("IOException when consuming unhandled response",
e);
}
;
{
job.setSubjobComplete(true);
job.setAllowedServerExceptions(-1);
- Cache.log.error("Exception when trying to start Rest Job.", ex);
+ Cache.error("Exception when trying to start Rest Job.", ex);
}
}
{
// crazy users will see this message
// TODO: finish this! and remove the message below!
- Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
+ Cache.warn("Rest job result parser is currently INCOMPLETE!");
int validres = 0;
for (RestJob rj : (RestJob[]) jobs)
{
String ln = null;
try
{
- Cache.log.debug("Parsing data for job " + rj.getJobId());
+ Cache.debug("Parsing data for job " + rj.getJobId());
rj.parseResultSet();
if (rj.hasResults())
{
validres++;
}
- Cache.log.debug("Finished parsing data for job " + rj.getJobId());
+ Cache.debug("Finished parsing data for job " + rj.getJobId());
} catch (Error ex)
{
- Cache.log.warn(
+ Cache.warn(
"Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} catch (Exception ex)
{
- Cache.log.warn(
+ Cache.warn(
"Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} finally
{
// TODO: decide if multiple multiple alignments returned by
// non-vseparable services are allowed.
- Cache.log.warn(
+ Cache.warn(
"dealing with multiple alignment products returned by non-vertically separable service.");
}
// recover reference to last alignment created for this rest frame
}
else
{
- Cache.log.warn(
+ Cache.warn(
"Couldn't resolve original sequence for new sequence.");
}
}
grass = groupNames.get(alan[nrj][an].groupRef.getName());
if (grass == null)
{
- Cache.log.error(
+ Cache.error(
"Couldn't relocate group referemce for group "
+ alan[nrj][an].groupRef.getName());
}
{
// TODO: process each newick file, lifting over sequence refs to
// current alignment, if necessary.
- Cache.log.error(
+ Cache.error(
"Tree recovery from restjob not yet implemented.");
}
}
return true;
}
}
- Cache.log.warn("isFetchable doesn't know about '" + source + "'");
+ Cache.warn("isFetchable doesn't know about '" + source + "'");
return false;
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import static org.testng.Assert.assertNotNull;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.concurrent.TimeUnit;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ScanResult;
+import jalview.bin.Cache;
+
+public class Log4jTest
+{
+ private static final int TIMEOUT = 10;
+
+ private static class Worker extends Thread
+ {
+ private final Process process;
+
+ private BufferedReader outputReader;
+
+ private BufferedReader errorReader;
+
+ private boolean exited;
+
+ private Worker(Process process)
+ {
+ this.process = process;
+ }
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ exited = process.waitFor(TIMEOUT, TimeUnit.SECONDS);
+ } catch (InterruptedException ignore)
+ {
+ return;
+ }
+ this.interrupt();
+ this.process.destroy();
+ }
+
+ public BufferedReader getOutputReader()
+ {
+ return outputReader;
+ }
+
+ public void setOutputReader(BufferedReader outputReader)
+ {
+ this.outputReader = outputReader;
+ }
+
+ public BufferedReader getErrorReader()
+ {
+ return errorReader;
+ }
+
+ public void setErrorReader(BufferedReader errorReader)
+ {
+ this.errorReader = errorReader;
+ }
+ }
+
+ private static ClassGraph scanner = null;
+
+ private static String classpath = null;
+
+ private static String java_exe = null;
+
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
+ {
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
+ java_exe = System.getProperty("java.home") + File.separator + "bin"
+ + File.separator + "java";
+
+ }
+ while (classpath == null)
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+ return classpath;
+ }
+
+ private Worker getJalviewDesktopRunner(String appArgs)
+ {
+ String classpath = getClassPath();
+ String cmd = java_exe + " " + " -classpath " + classpath + " "
+ + " jalview.bin.Jalview " + " "
+ + "-props test/jalview/util/log4jTestProps.jvprops " + appArgs;
+ Process proc = null;
+ Worker worker = null;
+ try
+ {
+ proc = Runtime.getRuntime().exec(cmd);
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
+ if (proc != null)
+ {
+ BufferedReader outputReader = new BufferedReader(
+ new InputStreamReader(proc.getInputStream()));
+ BufferedReader errorReader = new BufferedReader(
+ new InputStreamReader(proc.getErrorStream()));
+ worker = new Worker(proc);
+ worker.start();
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
+ return worker;
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public void initialize()
+ {
+ new Log4jTest();
+ }
+
+ @Test(groups = { "Functional" })
+ public void testLog4j()
+ {
+ String appArgs = " -open examples/uniref50.fa -nosplash -nonews -noquestionnaire -nousagestats -nowebservicediscovery";
+
+ Worker worker = getJalviewDesktopRunner(appArgs);
+ assertNotNull(worker, "worker is null");
+
+ String ln = null;
+ int count = 0;
+ boolean logTestFound = false;
+ try
+ {
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ if (++count > 500)
+ {
+ break;
+ }
+ if (ln.contains(Cache.LOGGING_TEST_MESSAGE))
+ {
+ logTestFound = true;
+ break;
+ }
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ if (worker != null && worker.exited == false)
+ {
+ worker.interrupt();
+ worker.process.destroy();
+ }
+ if (!logTestFound)
+ {
+ Assert.fail("Did not find Log4j Test message line '"
+ + Cache.LOGGING_TEST_MESSAGE + "'");
+ }
+ }
+
+}
--- /dev/null
+#---JalviewX Properties File---
+# HiDPI screen
+SCREENGEOMETRY_WIDTH=3840
+SCREENGEOMETRY_HEIGHT=2160
+SCREEN_WIDTH=3000
+SCREEN_HEIGHT=2000
+USAGESTATS=false
+STARTUP_FILE=examples/uniref50.fa
+SHOW_STARTUP_FILE=false
+FONT_STYLE=plain
+FONT_SIZE=10
+ANTI_ALIAS=false
+SHOW_JAVA_CONSOLE=false
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
git://source.jalview.org / jalview.git / commitdiff