JAL-1499 tests with gaps; NSites = width

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

diff --git a/test/jalview/io/MegaFileTest.java b/test/jalview/io/MegaFileTest.java
index 477f982..d868dcb 100644 (file)
--- a/test/jalview/io/MegaFileTest.java
+++ b/test/jalview/io/MegaFileTest.java
@@ -72,7 +72,7 @@ public class MegaFileTest
           + "#CPZANT  MNOPQR\n\n"
           + "#U456   KLMNOP\n";
 
-  // the 'fancy' format, different header format, bases in triplet groups
+  // interleaved with description, bases/gaps in triplet groups
   private static final String INTERLEAVED_WITH_DESCRIPTION = 
           "#MEGA\n"
           + "!Title Data with description;\n"
@@ -80,10 +80,10 @@ public class MegaFileTest
           + "!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";
+          + "#U455   C-- GTA\n" 
+          + "#CPZANT ATC -G-\n\n"
+          + "#U455   CGA --T\n" 
+          + "#CPZANT CA- -GC\n";
 
   //@formatter:on
 
@@ -358,9 +358,9 @@ public class MegaFileTest
     assertEquals("Second sequence id wrong", "CPZANT", seqs.get(1)
             .getName());
     // check sequence data
-    assertEquals("First sequence data wrong", "CGCGTACGATTT", seqs.get(0)
+    assertEquals("First sequence data wrong", "C--GTACGA--T", seqs.get(0)
             .getSequenceAsString());
-    assertEquals("Second sequence data wrong", "ATCGGGCAATGC", seqs.get(1)
+    assertEquals("Second sequence data wrong", "ATC-G-CA--GC", seqs.get(1)
             .getSequenceAsString());
     assertTrue("File format is not flagged as interleaved",
             testee.isInterleaved());
@@ -431,12 +431,12 @@ public class MegaFileTest
          "    Line two of description;\n" +
          "!Format\n" +
          "    DataType=DNA CodeTable=Standard\n" +
-         "    NSeqs=2 NSites=12\n" +
+         "    NSeqs=2 NSites=12\n" + // NSites includes gaps
          "    Indel=- Identical=. Missing=?;\n\n" +
-         "#U455   CGC GTA [6]\n" +
-         "#CPZANT ATC GGG [6]\n\n" +
-         "#U455   CGA TTT [12]\n" +
-         "#CPZANT CAA TGC [12]\n";
+         "#U455   C-- GTA [6]\n" +
+         "#CPZANT ATC -G- [6]\n\n" +
+         "#U455   CGA --T [12]\n" +
+         "#CPZANT CA- -GC [12]\n";
     //@formatter:on
     assertEquals("Roundtrip didn't match", expected,
             formatted);
@@ -603,4 +603,7 @@ public class MegaFileTest
     assertTrue("File format is not flagged as interleaved",
             testee.isInterleaved());
   }
+
+  //@formatter:on
+
 }