From 7485177a17e47a8107ed99c87e57e4b82e014fe1 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 20 Dec 2023 00:08:56 +0000
Subject: [PATCH] JAL-4290 fixed tests

---
 test/jalview/bin/CommandsTest.java |   50 +++++++++++++++++++-----------------
 1 file changed, 27 insertions(+), 23 deletions(-)

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 80354f9..c34a7fa 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -185,10 +185,10 @@ public class CommandsTest
           throws IOException
   {
     cleanupFiles(filenames);
-    String[] args = (cmdLine + "").split("\\s+");
+    String[] args = (cmdLine).split("\\s+");
     try
     {
-      callJalviewMain(args);
+      callJalviewMain(args, true);
       Commands cmds = Jalview.getInstance().getCommands();
       Assert.assertNotNull(cmds);
       verifyIncreasingSize(cmdLine, filenames);
@@ -454,56 +454,60 @@ public class CommandsTest
     return new Object[][] {
         //
         /*
+                */
         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
-                + "--structureimage=" + testfiles + "/structureimage1.png "
+                + "--structureimage=" + testfiles
+                + "/structureimage0-1.png "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage2.png --scale=1.5 "
+                + "/structureimage0-2.png --scale=1.5 "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage3.png --scale=2.0 ",
+                + "/structureimage0-3.png --scale=2.0 ",
             new String[]
-            { testfiles + "/structureimage1.png",
-                testfiles + "/structureimage2.png",
-                testfiles + "/structureimage3.png" } },
+            { testfiles + "/structureimage0-1.png",
+                testfiles + "/structureimage0-2.png",
+                testfiles + "/structureimage0-3.png" } },
         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
-                + "--structureimage=" + testfiles + "/structureimage1.png "
+                + "--structureimage=" + testfiles
+                + "/structureimage1-1.png "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage2.png --scale=1.5 "
+                + "/structureimage1-2.png --scale=1.5 "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage3.png --scale=2.0 ",
+                + "/structureimage1-3.png --scale=2.0 ",
             new String[]
-            { testfiles + "/structureimage1.png",
-                testfiles + "/structureimage2.png",
-                testfiles + "/structureimage3.png" } },
-                */
+            { testfiles + "/structureimage1-1.png",
+                testfiles + "/structureimage1-2.png",
+                testfiles + "/structureimage1-3.png" } },
         { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "
                 + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
                 + "--structureimage " + testfiles
-                + "/1gaq.png --structure examples/3W5V.pdb "
+                + "/structureimage2-1gaq.png --structure examples/3W5V.pdb "
                 + "--seqid \"3W5V|A\" --structureimage " + testfiles
-                + "/3w5v.png --overwrite",
+                + "/structureimage2-3w5v.png --overwrite",
 
             new String[]
-            { testfiles + "/1gaq.png", testfiles + "/3w5v.png" } },
-        /*
+            { testfiles + "/structureimage2-3w5v.png",
+                testfiles + "/structureimage2-1gaq.png", } },
         { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "
                 + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
                 + "--structureimage " + testfiles
-                + "/1gaq.png --structure examples/3W5V.pdb "
+                + "/structureimage3-1gaq.png --structure examples/3W5V.pdb "
                 + "--seqid \"3W5V|A\" --structureimage " + testfiles
-                + "/3w5v.png --overwrite",
-        
+                + "/structureimage3-3w5v.png --overwrite",
+
             new String[]
-            { testfiles + "/1gaq.png", testfiles + "/3w5v.png" } }
+            { testfiles + "/structureimage3-3w5v.png",
+                testfiles + "/structureimage3-1gaq.png", } }
+        /*
                 */
         //
     };
-- 
1.7.10.2