X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=66250d8cbbe6918ffaea0d89281aab8637bba9ef;hb=0798a7c77a9f2193cc7179215d28197c7a443e16;hp=fe40682d82111e81fcdd9491ef0fad08d1a5e9c0;hpb=c932f0e85a8852824cdd8ce790af68682732c85c;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index fe40682..66250d8 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -331,6 +331,8 @@ public class CommandsTest
     }
   }
 
+  private final String deleteDir = "test/deleteAfter";
+
   @Test(
     groups = "Functional",
     dataProvider = "allLinkedIdsData",
@@ -357,6 +359,12 @@ public class CommandsTest
                 "File " + nonfilename + " exists when it shouldn't!");
       }
     }
+
+    File deleteDirF = new File(deleteDir);
+    if (deleteDirF.exists())
+    {
+      deleteDirF.delete();
+    }
   }
 
   @DataProvider(name = "allLinkedIdsData")
@@ -364,8 +372,6 @@ 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",
@@ -408,7 +414,7 @@ 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",
@@ -423,7 +429,7 @@ 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",
@@ -438,7 +444,20 @@ 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",
@@ -453,7 +472,7 @@ 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",
@@ -468,7 +487,7 @@ 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",
@@ -495,6 +514,81 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
+        // --mkdirs
+        { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
+                + deleteDir
+                + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
+                + deleteDir
+                + "/{dirname}/{basename}.aln --close --all --mkdirs",
+            new String[]
+            { deleteDir
+                    + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
+            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/dir2/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/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",
+                "test/jalview/bin/argparser/testfiles/test1.aln",
+                "test/jalview/bin/argparser/testfiles/test2.aln",
+                "test/jalview/bin/argparser/testfiles/test3.aln",
+                "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test1.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test2.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test3.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test1.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test2.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test3.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
         //
     };
   }