JAL-1499 tweak output format for Description

[jalview.git] / test / jalview / io / MegaFileTest.java

diff --git a/test/jalview/io/MegaFileTest.java b/test/jalview/io/MegaFileTest.java
index 5caa50e..fef8337 100644 (file)
--- a/test/jalview/io/MegaFileTest.java
+++ b/test/jalview/io/MegaFileTest.java
@@ -419,7 +419,58 @@ public class MegaFileTest
     //@formatter:off
     String expected = 
          "#MEGA\n!Title Data with description;\n" +
-         "!Description     Line one of description\n" +
+         "!Description\n" +
+         "    Line one of description\n" +
+         "    Line two of description;\n" +
+         "!Format\n" +
+         "    DataType=DNA CodeTable=Standard\n" +
+         "    NSeqs=2 NSites=12\n" +
+         "    Indel=- Identical=. Missing=?;\n\n" +
+         "#U455   CGC GTA\n" +
+         "#CPZANT ATC GGG\n\n" +
+         "#U455   CGA TTT\n" +
+         "#CPZANT CAA TGC\n";
+    //@formatter:on
+    assertEquals("Roundtrip didn't match", expected,
+            formatted);
+  }
+
+  /**
+   * Test reading a MEGA file to an alignment then writing it out in MEGA
+   * format. Verify the output is (functionally) the same as the input.
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testRoundTrip_multilineFormatWithComments()
+          throws IOException
+  {
+    AppletFormatAdapter fa = new AppletFormatAdapter();
+    //@formatter:off
+    AlignmentI al = fa.readFile("#MEGA\n"
+    + "!Title Data with description;\n"
+    + "[ this comment should be ignored\n"
+    + "including [this nested comment]\n"
+    + "]\n"
+    + "!Format \n"
+    + "DataType=DNA CodeTable=Standard\n"
+    + "indel=- Missing=? MatchChar=.;\n\n"
+    + "!Description\n" 
+    + "    Line one of description\n"
+    + "    Line two of description;\n\n"
+    + "#U455   CGC GTA\n" 
+    + "#CPZANT ATC GGG\n\n"
+    + "#U455   CGA TTT\n" 
+    + "#CPZANT CAA TGC\n",
+            AppletFormatAdapter.PASTE, "MEGA");
+    //@formatter:on
+    MegaFile output = new MegaFile();
+    String formatted = output.print(al);
+    //@formatter:off
+    String expected = 
+         "#MEGA\n!Title Data with description;\n" +
+         "!Description\n" +
+         "    Line one of description\n" +
          "    Line two of description;\n" +
          "!Format\n" +
          "    DataType=DNA CodeTable=Standard\n" +