JAL-4277 Corrected choice of all or last opened linkedIds. Better wildcard syntactic...

[jalview.git] / test / jalview / bin / CommandsTest.java

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 73a0241..36522c4 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -50,11 +50,15 @@ public class CommandsTest
   {
     Desktop.closeDesktop();
   }
-  
-  public static void callJalviewMain(String[] args) {
-    if (Jalview.getInstance()!=null) {
+
+  public static void callJalviewMain(String[] args)
+  {
+    if (Jalview.getInstance() != null)
+    {
       Jalview.getInstance().doMain(args);
-    } else {
+    }
+    else
+    {
       Jalview.main(args);
     }
   }
@@ -121,7 +125,10 @@ public class CommandsTest
     }
   }
 
-  @Test(groups = {"Functional","testTask1"}, dataProvider = "structureImageOutputFiles")
+  @Test(
+    groups =
+    { "Functional", "testTask1" },
+    dataProvider = "structureImageOutputFiles")
   public void structureImageOutputTest(String cmdLine, String[] filenames)
           throws IOException
   {
@@ -164,28 +171,30 @@ public class CommandsTest
   {
     cleanupFiles(filenames);
     String[] args = (cmdLine + " --gui").split("\\s+");
-    try {
-    callJalviewMain(args);
-    Commands cmds = Jalview.getInstance().getCommands();
-    Assert.assertNotNull(cmds);
-    File lastFile = null;
-    for (String filename : filenames)
+    try
     {
-      File file = new File(filename);
-      Assert.assertTrue(file.exists(), "File '" + filename
-              + "' was not created by '" + cmdLine + "'");
-      Assert.assertTrue(file.isFile(), "File '" + filename
-              + "' is not a file from '" + cmdLine + "'");
-      Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
-              + "' has no content from '" + cmdLine + "'");
-      // make sure the successive output files get bigger!
-      if (lastFile != null)
-        Assert.assertTrue(
-                Files.size(file.toPath()) > Files.size(lastFile.toPath()));
-    }
+      callJalviewMain(args);
+      Commands cmds = Jalview.getInstance().getCommands();
+      Assert.assertNotNull(cmds);
+      File lastFile = null;
+      for (String filename : filenames)
+      {
+        File file = new File(filename);
+        Assert.assertTrue(file.exists(), "File '" + filename
+                + "' was not created by '" + cmdLine + "'");
+        Assert.assertTrue(file.isFile(), "File '" + filename
+                + "' is not a file from '" + cmdLine + "'");
+        Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+                + "' has no content from '" + cmdLine + "'");
+        // make sure the successive output files get bigger!
+        if (lastFile != null)
+          Assert.assertTrue(Files.size(file.toPath()) > Files
+                  .size(lastFile.toPath()));
+      }
     } catch (Exception x)
     {
-      Assert.fail("Unexpected exception during argFilesGlobAndSubstitutions",
+      Assert.fail(
+              "Unexpected exception during argFilesGlobAndSubstitutions",
               x);
     } finally
     {
@@ -214,7 +223,6 @@ public class CommandsTest
             { testfiles + "/structureimage1.png",
                 testfiles + "/structureimage2.png",
                 testfiles + "/structureimage3.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 "
@@ -230,6 +238,7 @@ public class CommandsTest
             { testfiles + "/structureimage1.png",
                 testfiles + "/structureimage2.png",
                 testfiles + "/structureimage3.png" } },
+        /*
                 */
         //
     };
@@ -355,8 +364,6 @@ public class CommandsTest
   {
     return new Object[][] {
         //
-        /*
-         */
         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/test1.stk",
@@ -399,7 +406,7 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
             null },
-        { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/test1.stk",
                 "test/jalview/bin/argparser/testfiles/test2.stk",
@@ -414,7 +421,7 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
             null },
-        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
@@ -429,7 +436,20 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
-        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/test1.stk",
+                "test/jalview/bin/argparser/testfiles/test2.stk",
+                "test/jalview/bin/argparser/testfiles/test3.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
@@ -444,7 +464,7 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
-        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
@@ -459,7 +479,7 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
-        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",