From d14d7360a1855481eadb19536b86253bbc8eccdc Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 24 Mar 2023 00:19:42 +0000
Subject: [PATCH] JAL-629 Test tidyup

---
 src/jalview/bin/argparser/Arg.java         |   32 ++++++++++++++--------------
 src/jalview/gui/Desktop.java               |    3 ---
 src/jalview/io/FileLoader.java             |    2 --
 test/jalview/bin/ArgParserTest.java        |    1 -
 test/jalview/bin/CommandsTest.java         |    3 ---
 test/jalview/gui/QuitHandlerTest.java      |    2 ++
 test/jalview/project/Jalview2xmlTests.java |    2 --
 7 files changed, 18 insertions(+), 27 deletions(-)

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 092f5d2..6b70ab7 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -95,6 +95,22 @@ public enum Arg
 
   private boolean defaultBoolValue = false;
 
+  private Arg()
+  {
+    this(new String[0]);
+  }
+
+  private Arg(String... names)
+  {
+    int length = (names == null || names.length == 0
+            || (names.length == 1 && names[0] == null)) ? 1
+                    : names.length + 1;
+    this.argNames = new String[length];
+    this.argNames[0] = this.getName();
+    if (length > 1)
+      System.arraycopy(names, 0, this.argNames, 1, names.length);
+  }
+
   public String toLongString()
   {
     StringBuilder sb = new StringBuilder();
@@ -118,22 +134,6 @@ public enum Arg
     return sb.toString();
   }
 
-  private Arg()
-  {
-    this(new String[0]);
-  }
-
-  private Arg(String... names)
-  {
-    int length = (names == null || names.length == 0
-            || (names.length == 1 && names[0] == null)) ? 1
-                    : names.length + 1;
-    this.argNames = new String[length];
-    this.argNames[0] = this.getName();
-    if (length > 1)
-      System.arraycopy(names, 0, this.argNames, 1, names.length);
-  }
-
   public String[] getNames()
   {
     return argNames;
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 20543af..981a060 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2033,9 +2033,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
     for (AlignFrame af : frames)
     {
-      System.out.println("###### frames=" + frames);
-      System.out.println("###### af=" + af);
-      System.out.println("###### af.alignPanels=" + af.alignPanels);
       for (AlignmentPanel ap : af.alignPanels)
       {
         if (alignmentId == null
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3b4cc31..971aba3 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -288,8 +288,6 @@ public class FileLoader implements Runnable
   @Override
   public void run()
   {
-    System.out.println("######## Starting FileLoader.run()");
-    System.out.println("######## loading file " + file);
     String title = protocol == DataSourceType.PASTE
             ? "Copied From Clipboard"
             : file;
diff --git a/test/jalview/bin/ArgParserTest.java b/test/jalview/bin/ArgParserTest.java
index d0a11fa..e93f36f 100644
--- a/test/jalview/bin/ArgParserTest.java
+++ b/test/jalview/bin/ArgParserTest.java
@@ -20,7 +20,6 @@ public class ArgParserTest
   @AfterClass(alwaysRun = true)
   public static void resetProps()
   {
-    // Cache.applicationProperties.clear();
     Cache.loadProperties("test/jalview/testProps.jvprops");
   }
 
diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 9458044..41588e6 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -28,7 +28,6 @@ public class CommandsTest
   @AfterClass(alwaysRun = true)
   public static void resetProps()
   {
-    // Cache.applicationProperties.clear();
     Cache.loadProperties("test/jalview/testProps.jvprops");
   }
 
@@ -65,8 +64,6 @@ public class CommandsTest
                       + "' was not found in opened alignment files: "
                       + cmdLine);
     }
-
-    System.out.println("##### GOT TO END");
   }
 
   public static boolean lookForSequenceName(String sequenceName)
diff --git a/test/jalview/gui/QuitHandlerTest.java b/test/jalview/gui/QuitHandlerTest.java
index 299b0d1..42df90e 100644
--- a/test/jalview/gui/QuitHandlerTest.java
+++ b/test/jalview/gui/QuitHandlerTest.java
@@ -70,6 +70,8 @@ public class QuitHandlerTest
       Desktop.instance.closeAll_actionPerformed(null);
     // reset debug delay
     Jalview2XML.setDebugDelaySave(20);
+    // load normal testprops
+    Cache.loadProperties("test/jalview/testProps.jvprops");
   }
 
   @BeforeMethod(alwaysRun = true)
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 094e0ea..13df735 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -287,8 +287,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     int origCount = Desktop.getAlignFrames() == null ? 0
             : Desktop.getAlignFrames().length;
-    System.out
-            .println("###### Calling FileLoader().LoadFileWaitTillLoaded");
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
-- 
1.7.10.2