Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / bin / Console.java

diff --git a/src/jalview/bin/Console.java b/src/jalview/bin/Console.java
index b868e7b..1b230ec 100644 (file)
--- a/src/jalview/bin/Console.java
+++ b/src/jalview/bin/Console.java
@@ -20,6 +20,7 @@
  */
 package jalview.bin;
 
+import java.io.PrintStream;
 import java.util.Locale;
 
 import jalview.log.JLogger;
@@ -43,8 +44,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -57,7 +58,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
 
   }
@@ -70,8 +71,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
   }
 
@@ -83,7 +84,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
 
   }
@@ -96,8 +97,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -110,7 +111,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
 
   }
@@ -123,7 +124,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
   }
 
@@ -135,8 +136,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -149,7 +150,7 @@ public class Console
     }
     else
     {
-      System.err.println(message);
+      jalview.bin.Console.errPrintln(message);
     }
 
   }
@@ -162,8 +163,8 @@ public class Console
     }
     else
     {
-      System.err.println(message);
-      t.printStackTrace(System.err);
+      jalview.bin.Console.errPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -176,7 +177,7 @@ public class Console
     }
     else
     {
-      System.err.println(message);
+      jalview.bin.Console.errPrintln(message);
     }
 
   }
@@ -189,8 +190,8 @@ public class Console
     }
     else
     {
-      System.err.println(message);
-      t.printStackTrace(System.err);
+      jalview.bin.Console.errPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -220,6 +221,11 @@ public class Console
     return JLogger.toLevel(level);
   }
 
+  public static JLogger getLogger()
+  {
+    return log;
+  }
+
   public static boolean initLogger()
   {
     return initLogger(null);
@@ -236,14 +242,21 @@ public class Console
       JLogger.LogLevel logLevel = JLogger.LogLevel.INFO;
 
       if (JLogger.isLevel(providedLogLevel))
+      {
         logLevel = Console.getLogLevel(providedLogLevel);
+      }
       else
+      {
         logLevel = getCachedLogLevel();
+      }
 
       if (!Platform.isJS())
       {
-        System.err
-                .println("Setting initial log level to " + logLevel.name());
+        if (!Jalview.quiet())
+        {
+          jalview.bin.Console.errPrintln(
+                  "Setting initial log level to " + logLevel.name());
+        }
         Log4j.init(logLevel);
       }
       // log output
@@ -255,8 +268,9 @@ public class Console
       log = JLoggerLog4j.getLogger(Cache.JALVIEW_LOGGER_NAME, logLevel);
     } catch (NoClassDefFoundError e)
     {
-      System.err.println("Could not initialise the logger framework");
-      e.printStackTrace();
+      jalview.bin.Console
+              .errPrintln("Could not initialise the logger framework");
+      Console.printStackTrace(e);
     }
 
     // Test message
@@ -294,6 +308,96 @@ public class Console
     }
   }
 
+  public static void outPrint()
+  {
+    outPrint("");
+  }
+
+  public static void outPrintln()
+  {
+    outPrintln("");
+  }
+
+  public static void outPrint(Object message)
+  {
+    outPrintMessage(message, false, false);
+  }
+
+  public static void outPrint(Object message, boolean forceStdout)
+  {
+    outPrintMessage(message, false, forceStdout);
+  }
+
+  public static void outPrintln(Object message)
+  {
+    outPrintMessage(message, true, false);
+  }
+
+  public static PrintStream outputStream(boolean forceStdout)
+  {
+    // send message to stderr if an output file to stdout is expected
+    if (!forceStdout && Jalview.getInstance() != null
+            && Jalview.getInstance().getBootstrapArgs() != null
+            && Jalview.getInstance().getBootstrapArgs().outputToStdout())
+    {
+      return System.err;
+    }
+    else
+    {
+      return System.out;
+    }
+  }
+
+  public static void outPrintMessage(Object message, boolean newline,
+          boolean forceStdout)
+  {
+    PrintStream ps = outputStream(forceStdout);
+    if (newline)
+    {
+      ps.println(message);
+    }
+    else
+    {
+      ps.print(message);
+    }
+  }
+
+  public static void errPrint()
+  {
+    errPrint("");
+  }
+
+  public static void errPrintln()
+  {
+    errPrintln("");
+  }
+
+  public static void errPrint(Object message)
+  {
+    System.err.print(message);
+  }
+
+  public static void errPrintln(Object message)
+  {
+    System.err.println(message);
+  }
+
+  public static void debugPrintStackTrace(Throwable t)
+  {
+    if (!isDebugEnabled())
+    {
+      return;
+    }
+    // send message to stderr if output to stdout is expected
+    printStackTrace(t);
+  }
+
+  public static void printStackTrace(Throwable t)
+  {
+    // send message to stderr if output to stdout is expected
+    t.printStackTrace(System.err);
+  }
+
   public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
 
-}
+}
\ No newline at end of file