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JAL-1551 spotlessApply
[jalview.git] / test / jalview / bin / CommandsTest.java
diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index fda047c..20ccd11 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -24,10 +24,6 @@ public class CommandsTest
 {
   private static final String testfiles = "test/jalview/bin/argparser/testfiles";
 
-  private static final String png1 = testfiles + "/dir1/test1.png";
-
-  private static final String png2 = testfiles + "/dir2/test1.png";
-
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
@@ -83,7 +79,8 @@ public class CommandsTest
     Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
             "Overall command parse and operation is false");
 
-    Assert.assertEquals(Desktop.getAlignFrames().length, numFrames);
+    Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+            "Wrong number of AlignFrames");
 
     if (sequences != null)
     {
@@ -140,6 +137,7 @@ public class CommandsTest
   public Object[][] argfileOutputFiles()
   {
     return new Object[][] {
+        //
         { "--argfile=" + testfiles + "/**/*.txt", new String[]
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
             testfiles + "/dir3/subdir/test0.png" } },
@@ -147,14 +145,17 @@ public class CommandsTest
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
         { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
-        { "--initsubstitutions --open examples/uniref50.fa --image "
+        { "--initsubstitutions --append examples/uniref50.fa --image "
                 + testfiles + "/{basename}.png",
             new String[]
             { testfiles + "/uniref50.png" } },
-        { "--open examples/uniref50.fa --image " + testfiles
-                + "/{basename}.png",
+        { "--append examples/uniref50.fa --nosubstitutions --image "
+                + testfiles + "/{basename}.png",
             new String[]
-            { testfiles + "/{basename}.png" } } };
+            { testfiles + "/{basename}.png" } }
+        //
+    };
+
   }
 
   @DataProvider(name = "cmdLines")
@@ -166,24 +167,28 @@ public class CommandsTest
     String[] t2 = new String[] { "TEST2" };
     String[] t3 = new String[] { "TEST3" };
     return new Object[][] {
-        { "--open=examples/uniref50.fa", true, 1, someUniref50Seqs },
-        { "--open examples/uniref50.fa", true, 1, someUniref50Seqs },
-        { "--open=examples/uniref50*.fa", true, 1, someUniref50Seqs },
+        /*
+        */
+        { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
+        { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
+        { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
         // NOTE we cannot use shell expansion in tests, so list all files!
-        { "--open examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+        { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+            someUniref50Seqs },
+        { "--append=[new]examples/uniref50*.fa", true, 2,
             someUniref50Seqs },
-        { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
-        { "--opennew=examples/uniref50*.fa", true, 2, someUniref50Seqs },
+        { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
         { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
             ArrayUtils.concatArrays(t1, t3) },
-        { "--argfile=" + testfiles + "/argfile*.txt", true, 4,
+        { "--argfile=" + testfiles + "/argfile*.txt", true, 5,
             ArrayUtils.concatArrays(t1, t2, t3) },
         { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
             ArrayUtils.concatArrays(t1, t2) } };
+
   }
 
   public static boolean lookForSequenceName(String sequenceName)
@@ -214,4 +219,172 @@ public class CommandsTest
     }
   }
 
+  @Test(
+    groups = "Functional",
+    dataProvider = "allLinkedIdsData",
+    singleThreaded = true)
+  public void allLinkedIdsTest(String cmdLine, String[] filenames,
+          String[] nonfilenames)
+  {
+    String[] args = cmdLine.split("\\s+");
+    Jalview.main(args);
+    Commands cmds = Jalview.getInstance().getCommands();
+    Assert.assertNotNull(cmds);
+    for (String filename : filenames)
+    {
+      Assert.assertTrue(new File(filename).exists(),
+              "File '" + filename + "' was not created");
+    }
+    cleanupFiles(filenames);
+    if (nonfilenames != null)
+    {
+      for (String nonfilename : nonfilenames)
+      {
+        File nonfile = new File(nonfilename);
+        Assert.assertFalse(nonfile.exists(),
+                "File " + nonfilename + " exists when it shouldn't!");
+      }
+    }
+  }
+
+  @DataProvider(name = "allLinkedIdsData")
+  public Object[][] allLinkedIdsData()
+  {
+    return new Object[][] {
+        //
+        /*
+         */
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/test1.stk",
+                "test/jalview/bin/argparser/testfiles/test2.stk",
+                "test/jalview/bin/argparser/testfiles/test3.stk", },
+            null },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/test1.png",
+                "test/jalview/bin/argparser/testfiles/test2.png",
+                "test/jalview/bin/argparser/testfiles/test3.png", },
+            null },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/test1.stk",
+                "test/jalview/bin/argparser/testfiles/test2.stk",
+                "test/jalview/bin/argparser/testfiles/test3.stk", },
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.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", }, },
+        { "--open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
+            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/dir1/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.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", },
+            null },
+        { "--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",
+                "test/jalview/bin/argparser/testfiles/test3.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.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", },
+            null },
+        { "--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/dir1/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.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", },
+            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", }, },
+        { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.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/dir1/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.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", }, },
+        { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.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/dir1/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.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", }, },
+        { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
+                "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
+                "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", }, },
+        //
+    };
+  }
+
 }