From ad837aac2287d355277129f51bb5aa1cedf7cf67 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 7 Jul 2020 20:35:39 +0100
Subject: [PATCH] JAL-3628 System.out/err -> Cache.log.info/error

---
 src/jalview/bin/Jalview.java |   30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5df9ace..ead9b9f 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -297,7 +297,8 @@ public class Jalview
 
     desktop = null;
 
-    // property laf = "crossplatform", "system", "gtk", "metal" or "mac"
+    // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
+    // "mac"
     // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
     // try Quaqua/Vaqua.
     String lafProp = System.getProperty("laf");
@@ -318,62 +319,63 @@ public class Jalview
       lafSet = setCrossPlatformLookAndFeel();
       if (!lafSet)
       {
-        System.err.println("Could not set requested laf=" + laf);
+        Cache.log.error("Could not set requested laf=" + laf);
       }
       break;
     case "system":
       lafSet = setSystemLookAndFeel();
       if (!lafSet)
       {
-        System.err.println("Could not set requested laf=" + laf);
+        Cache.log.error("Could not set requested laf=" + laf);
       }
       break;
     case "gtk":
       lafSet = setGtkLookAndFeel();
     {
-      System.err.println("Could not set requested laf=" + laf);
+      Cache.log.error("Could not set requested laf=" + laf);
     }
       break;
     case "metal":
       lafSet = setMetalLookAndFeel();
     {
-      System.err.println("Could not set requested laf=" + laf);
+      Cache.log.error("Could not set requested laf=" + laf);
     }
       break;
     case "nimbus":
       lafSet = setNimbusLookAndFeel();
     {
-      System.err.println("Could not set requested laf=" + laf);
+      Cache.log.error("Could not set requested laf=" + laf);
     }
       break;
     case "quaqua":
       lafSet = setQuaquaLookAndFeel();
     {
-      System.err.println("Could not set requested laf=" + laf);
+      Cache.log.error("Could not set requested laf=" + laf);
     }
       break;
     case "vaqua":
       lafSet = setVaquaLookAndFeel();
     {
-      System.err.println("Could not set requested laf=" + laf);
+      Cache.log.error("Could not set requested laf=" + laf);
     }
       break;
     case "mac":
       lafSet = setMacLookAndFeel();
       if (!lafSet)
       {
-        System.err.println("Could not set requested laf=" + laf);
+        Cache.log.error("Could not set requested laf=" + laf);
       }
       break;
     case "none":
       break;
     default:
-      System.err.println("Requested laf=" + laf + " not implemented");
+      Cache.log.error("Requested laf=" + laf + " not implemented");
     }
     if (!lafSet)
     {
       setSystemLookAndFeel();
-      if (Platform.isLinux()) {
+      if (Platform.isLinux())
+      {
         setMetalLookAndFeel();
       }
       if (Platform.isAMac())
@@ -401,11 +403,13 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        System.out.println("Cannot set Taskbar");
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(e.getMessage());
         // e.printStackTrace();
       } catch (Throwable t)
       {
-        System.out.println("Cannot set Taskbar");
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(t.getMessage());
         // t.printStackTrace();
       }
 
-- 
1.7.10.2