From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 11 Sep 2023 23:21:10 +0000 (+0100)
Subject: Merge branch 'improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_pro... 
X-Git-Tag: Release_2_11_4_0~174^2~30
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0798a7c77a9f2193cc7179215d28197c7a443e16;p=jalview.git

Merge branch 'improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed' into bug/JAL-4277_dirname_substitution_always_absolute
---

0798a7c77a9f2193cc7179215d28197c7a443e16
diff --cc src/jalview/bin/Commands.java
index cd72e60,d910819..e6c7b54
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@@ -140,28 -139,11 +141,30 @@@ public class Command
        }
  
      }
 +
 +    // report errors
 +    StringBuilder sb = new StringBuilder();
 +    for (String error : errors)
 +    {
 +      sb.append("- " + error);
 +      sb.append("\n");
 +    }
 +    if (Platform.isHeadless())
 +    {
 +      Console.debug("All errors from command line argument commands:\n"
 +              + sb.toString());
 +    }
 +    else
 +    {
 +      // scrollable dialog box
 +
 +    }
 +
      if (argParser.getBoolean(Arg.QUIT))
      {
-       Jalview.exit("Exiting due to " + Arg.QUIT.argString(), 0);
+       Jalview.getInstance().exit(
+               "Exiting due to " + Arg.QUIT.argString() + " argument.",
+               ExitCode.OK);
        return true;
      }
      // carry on with jalview.bin.Jalview