Package com.biomatters.geneious.publicapi.utilities

Class Logs

  • public class Logs
extends java.lang.Object
    This is a convenience class for logging that is easier to use, but isn't as flexible or powerful as java.util.logging.

    Advantages of using a java.util.logging.Logger over using Logs:

    1.) The minimum severity of a log statement for it to be logged can be adjusted without changing the code and recompiling, i.e. it can even be adjusted in the distribution version.

    2.) The logging level can be adjusted on a per-package (and even per-class) basis, so e.g. developer #1 can get all logs for Collaboration but nothing else on stdout, while developer #2 gets his logs printed to a file and only sees Collaboration logs if they are severe.

    Advantages of Logs over java.util.logging.Logger:

    1) You don't have to put private final Logger logger = Logger.getLogger(getClass().getName()) at the top of every class you want to put a log line in.

    2) Logs will automatically be recorded and appear in the Geneious Crash System (Talkback)

    Since:
    API 4.202220 (Geneious 2022.2.0)

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.util.logging.Logger SHARED  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static long duration​(long start, long logIfDurationGreaterThan, java.lang.String message)
      Best used in conjunction with start().
      static void fine​(java.lang.String message)
      Logs a message at Level.FINE
      static void fine​(java.lang.String format, java.lang.Object... arguments)
      Logs the String formatted with String.format(String, Object...) to Level.FINE Logs.
      static void info​(java.lang.String message)
      Logs a message to the Level.INFO log.
      static void info​(java.lang.String format, java.lang.Object... arguments)
      Logs the String formatted with String.format(String, Object...) to Level.INFO Logs.
      static void infoButNotToStandardOut​(java.lang.String message)
      Logs a message to the Level.INFO log without attempting to print to standard out.
      static void log​(java.lang.String message, java.util.logging.Level level)
      Adds a message to the history of the specified level.
      static void severe​(java.lang.String message)
      Logs a message about something that should never happen under normal Geneious usage, and which has caused an irrecoverable crash.
      static void severe​(java.lang.String format, java.lang.Object... arguments)
      Logs a message about something that should never happen under normal Geneious usage, and which has caused an irrecoverable crash.
      static long start()
      Best used in conjunction with duration(long, long, String).
      static void warning​(java.lang.String message)
      Logs a message about something that shouldn't happen under normal Geneious usage, but Geneious was able to recover without crashing (e.g.
      static void warning​(java.lang.String format, java.lang.Object... arguments)
      Logs a message about something that shouldn't happen under normal Geneious usage, but Geneious was able to recover without crashing (e.g.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • SHARED

        public static final java.util.logging.Logger SHARED

    • Method Detail

      • fine

        public static void fine​(java.lang.String format,
                        java.lang.Object... arguments)
        Logs the String formatted with String.format(String, Object...) to Level.FINE Logs. Note that logging to fine will not print the message to console by default.
        Parameters:
        format - The format string
        arguments - The arguments referenced by the format specifiers in the format string.
        Since:
        API 4.202220 (Geneious 2022.2.0)
        See Also:
        String.format(String, Object...)

      • fine

        public static void fine​(java.lang.String message)
        Logs a message at Level.FINE
        Parameters:
        message - The message to log
        Since:
        API 4.202220 (Geneious 2022.2.0)

      • info

        public static void info​(java.lang.String format,
                        java.lang.Object... arguments)
        Logs the String formatted with String.format(String, Object...) to Level.INFO Logs.
        Parameters:
        format - The format string
        arguments - The arguments referenced by the format specifiers in the format string.
        Since:
        API 4.202220 (Geneious 2022.2.0)
        See Also:
        String.format(String, Object...)

      • info

        public static void info​(java.lang.String message)
        Logs a message to the Level.INFO log. This should be used to log messages which may be helpful when debugging but are not necessary in production builds.
        Parameters:
        message - The message to log
        Since:
        API 4.202220 (Geneious 2022.2.0)

      • infoButNotToStandardOut

        public static void infoButNotToStandardOut​(java.lang.String message)
        Logs a message to the Level.INFO log without attempting to print to standard out. This should be used to log messages which may be helpful when debugging but are not necessary in production builds.
        Parameters:
        message - The message to log
        Since:
        API 4.202220 (Geneious 2022.2.0)

      • warning

        public static void warning​(java.lang.String format,
                           java.lang.Object... arguments)
        Logs a message about something that shouldn't happen under normal Geneious usage, but Geneious was able to recover without crashing (e.g. failure to load documents, failure to save a document, data that looks corrupt, user continuing to use Geneious with options they've been warned might cause Geneious to hang etc.). These messages will be printed during normal Command Line runs of Geneious.

        Logs the String formatted with String.format(String, Object...) to Level.WARNING Logs. Note that logging to warning will print the message to standard out by default.

        Parameters:
        format - The format string
        arguments - The arguments referenced by the format specifiers in the format string.
        Since:
        API 4.202220 (Geneious 2022.2.0)
        See Also:
        String.format(String, Object...)

      • warning

        public static void warning​(java.lang.String message)
        Logs a message about something that shouldn't happen under normal Geneious usage, but Geneious was able to recover without crashing (e.g. failure to load documents, failure to save a document, data that looks corrupt, user continuing to use Geneious with options they've been warned might cause Geneious to hang etc.). These messages will be printed during normal Command Line runs of Geneious.
        Parameters:
        message - The message to log
        Since:
        API 4.202220 (Geneious 2022.2.0)

      • severe

        public static void severe​(java.lang.String format,
                          java.lang.Object... arguments)
        Logs a message about something that should never happen under normal Geneious usage, and which has caused an irrecoverable crash.

        Logs the String formatted with String.format(String, Object...) to Level.SEVERE Logs. Note that logging to severe will print the message to standard out by default.

        Parameters:
        format - The format string
        arguments - The arguments referenced by the format specifiers in the format string.
        Since:
        API 4.202220 (Geneious 2022.2.0)
        See Also:
        String.format(String, Object...)

      • severe

        public static void severe​(java.lang.String message)
        Logs a message about something that should never happen under normal Geneious usage, and which has caused an irrecoverable crash.
        Parameters:
        message - The message to log
        Since:
        API 4.202220 (Geneious 2022.2.0)

      • log

        public static void log​(java.lang.String message,
                       java.util.logging.Level level)
        Adds a message to the history of the specified level. Messages will not be printed to standard out at any level.
        Parameters:
        message - The message to log
        level - The Log Level to log the message at
        Since:
        API 4.202220 (Geneious 2022.2.0)

      • duration

        public static long duration​(long start,
                            long logIfDurationGreaterThan,
                            java.lang.String message)
        Best used in conjunction with start(). This method will log a message only if the time since start() was called is more than logIfDurationGreaterThan milliseconds.

        For example: 

        
  long start = Logs.start();
  // ...Do something...
  Logs.duration(start, 100, "Do Something took longer than 100ms");
        Parameters:
        start - time operation started is returned by start()
        logIfDurationGreaterThan - in milliseconds
        message - a message to be displayed
        Returns:
        the duration in milliseconds
        Since:
        API 4.202220 (Geneious 2022.2.0)

      • start

        public static long start()
        Best used in conjunction with duration(long, long, String). This returns the current nano time, for use with the duration method.

        For example: 

        
  long start = Logs.start();
  // ...Do something...
  Logs.duration(start, 100, "Do Something took longer than 100ms");
        Returns:
        The current nano time
        Since:
        API 4.202220 (Geneious 2022.2.0)
        See Also:
        duration(long, long, String)