From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 16 Feb 2023 13:14:11 +0000 (+0000)
Subject: Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
X-Git-Tag: Release_2_11_3_0~18^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0de37d1a047209510bab82225109ae2a47931f79;p=jalview.git

Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects

 Conflicts:
	src/jalview/bin/Jalview.java
---

0de37d1a047209510bab82225109ae2a47931f79
diff --cc src/jalview/bin/Jalview.java
index 0ec9889,e259cc2..a988a09
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@@ -324,13 -299,23 +325,25 @@@ public class Jalvie
      // report Jalview version
      Cache.loadBuildProperties(true);
  
+     // old ArgsParser
      ArgsParser aparser = new ArgsParser(args);
 +
      boolean headless = false;
  
+     try
+     {
+       Console.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);
+     }
+ 
      String usrPropsFile = aparser.getValue("props");
 -    Cache.loadProperties(usrPropsFile); // must do this before
 +    Cache.loadProperties(usrPropsFile); // must do this
 +                                        // before
      if (usrPropsFile != null)
      {
        System.out.println(