/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import java.io.PrintStream;
-
-import org.junit.Before;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
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
*
/**
* @throws java.lang.Exception
*/
- @Before
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
}
- @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());
}
}
- @Test
+ @Test(groups = { "Functional" })
public void testExtractGaps()
{
assertNull(AlignSeq.extractGaps(null, null));
assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
}
- @Test
+ @Test(groups = { "Functional" })
public void testPrintAlignment()
{
AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);