JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / test / jalview / analysis / TestAlignSeq.java

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 2845d91..43ebd63 100644 (file)
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -22,14 +22,16 @@ package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import java.io.PrintStream;
 
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import java.io.PrintStream;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 /**
  * Test the alignment -> Mapping routines
  * 
@@ -44,7 +46,7 @@ public class TestAlignSeq
   /**
    * @throws java.lang.Exception
    */
-  @BeforeMethod
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
     s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
@@ -57,14 +59,13 @@ public class TestAlignSeq
 
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   /**
    * simple test that mapping from alignment corresponds identical positions.
    */
   public void testGetMappingForS1()
   {
-    AlignSeq as = AlignSeq
-            .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
     System.out.println("s1: " + as.getAStr1());
     System.out.println("s2: " + as.getAStr2());
 
@@ -84,7 +85,7 @@ public class TestAlignSeq
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testExtractGaps()
   {
     assertNull(AlignSeq.extractGaps(null, null));
@@ -94,7 +95,7 @@ public class TestAlignSeq
     assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testPrintAlignment()
   {
     AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
@@ -118,7 +119,7 @@ public class TestAlignSeq
     String expected = "Score = 320\nLength of alignment = 10\nSequence Seq1 :  3 - 18 (Sequence length = 14)\nSequence Seq1 :  1 - 10 (Sequence length = 10)\n\n"
             + "Seq1 SDFAQQQRRR\n"
             + "     |||||||   \n"
-            + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
+            + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n";
     assertEquals(expected, baos.toString());
   }
 }