JAL-1270 JUnit to TestNG refactoring

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

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index edf7f20..df4b660 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -20,7 +20,8 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.*;
+import org.testng.annotations.Test;
+import org.testng.AssertJUnit;
 import jalview.io.TCoffeeScoreFile.Block;
 import jalview.io.TCoffeeScoreFile.Header;
 
@@ -31,7 +32,6 @@ import java.util.List;
 
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.junit.Test;
 import org.xml.sax.SAXException;
 
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
@@ -54,23 +54,23 @@ public class TCoffeeScoreFileTest
 
     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
             AppletFormatAdapter.FILE);
-    assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
+    AssertJUnit.assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
 
     Header header = scoreFile.header;
-    assertNotNull(header);
-    assertEquals(
+    AssertJUnit.assertNotNull(header);
+    AssertJUnit.assertEquals(
             "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
             header.head);
-    assertEquals(90, header.score);
-    assertEquals(89, header.getScoreFor("1PHT"));
-    assertEquals(90, header.getScoreFor("1BB9"));
-    assertEquals(94, header.getScoreFor("1UHC"));
-    assertEquals(94, header.getScoreFor("1YCS"));
-    assertEquals(93, header.getScoreFor("1OOT"));
-    assertEquals(94, header.getScoreFor("1ABO"));
-    assertEquals(94, header.getScoreFor("1FYN"));
-    assertEquals(94, header.getScoreFor("1QCF"));
-    assertEquals(90, header.getScoreFor("cons"));
+    AssertJUnit.assertEquals(90, header.score);
+    AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
+    AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
+    AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
+    AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
+    AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
+    AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
+    AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
+    AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
+    AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
   }
 
   @Test
@@ -80,10 +80,10 @@ public class TCoffeeScoreFileTest
     {
       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
               FormatAdapter.FILE);
-      assertFalse(result.isValid());
+      AssertJUnit.assertFalse(result.isValid());
     } catch (IOException x)
     {
-      assertTrue("File not found exception thrown",
+      AssertJUnit.assertTrue("File not found exception thrown",
               x instanceof FileNotFoundException);
     }
   }
@@ -93,9 +93,9 @@ public class TCoffeeScoreFileTest
   {
     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
             FormatAdapter.FILE);
-    assertTrue(result.isValid());
-    assertEquals(8, result.getHeight());
-    assertEquals(83, result.getWidth());
+    AssertJUnit.assertTrue(result.isValid());
+    AssertJUnit.assertEquals(8, result.getHeight());
+    AssertJUnit.assertEquals(83, result.getWidth());
   }
 
   @Test
@@ -116,24 +116,24 @@ public class TCoffeeScoreFileTest
     FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
     Block block = TCoffeeScoreFile.readBlock(source, 0);
 
-    assertNotNull(block);
-    assertEquals("999999999999999999999999998762112222543211112134",
+    AssertJUnit.assertNotNull(block);
+    AssertJUnit.assertEquals("999999999999999999999999998762112222543211112134",
             block.getScoresFor("1PHT"));
-    assertEquals("99999999999999999999999999987-------4322----2234",
+    AssertJUnit.assertEquals("99999999999999999999999999987-------4322----2234",
             block.getScoresFor("1BB9"));
-    assertEquals("99999999999999999999999999987-------5321----2246",
+    AssertJUnit.assertEquals("99999999999999999999999999987-------5321----2246",
             block.getScoresFor("1UHC"));
-    assertEquals("99999999999999999999999999986-------4321----1-35",
+    AssertJUnit.assertEquals("99999999999999999999999999986-------4321----1-35",
             block.getScoresFor("1YCS"));
-    assertEquals("999999999999999999999999999861-------3------1135",
+    AssertJUnit.assertEquals("999999999999999999999999999861-------3------1135",
             block.getScoresFor("1OOT"));
-    assertEquals("99999999999999999999999999986-------422-------34",
+    AssertJUnit.assertEquals("99999999999999999999999999986-------422-------34",
             block.getScoresFor("1ABO"));
-    assertEquals("99999999999999999999999999985-------32--------35",
+    AssertJUnit.assertEquals("99999999999999999999999999985-------32--------35",
             block.getScoresFor("1FYN"));
-    assertEquals("99999999999999999999999999974-------2---------24",
+    AssertJUnit.assertEquals("99999999999999999999999999974-------2---------24",
             block.getScoresFor("1QCF"));
-    assertEquals("999999999999999999999999999851000110321100001134",
+    AssertJUnit.assertEquals("999999999999999999999999999851000110321100001134",
             block.getConsensus());
   }
 
@@ -144,31 +144,31 @@ public class TCoffeeScoreFileTest
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
             FormatAdapter.FILE);
 
-    assertEquals(
+    AssertJUnit.assertEquals(
             "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
             parser.getScoresFor("1PHT"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
             parser.getScoresFor("1BB9"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
             parser.getScoresFor("1UHC"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
             parser.getScoresFor("1YCS"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
             parser.getScoresFor("1OOT"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
             parser.getScoresFor("1ABO"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
             parser.getScoresFor("1FYN"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
             parser.getScoresFor("1QCF"));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
             parser.getScoresFor("cons"));
   }
@@ -179,33 +179,33 @@ public class TCoffeeScoreFileTest
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
             FormatAdapter.FILE);
-    assertTrue(parser.getWarningMessage(), parser.isValid());
+    AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
     List<String> scores = parser.getScoresList();
-    assertEquals(
+    AssertJUnit.assertEquals(
             "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
             scores.get(0));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
             scores.get(1));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
             scores.get(2));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
             scores.get(3));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
             scores.get(4));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
             scores.get(5));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
             scores.get(6));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
             scores.get(7));
-    assertEquals(
+    AssertJUnit.assertEquals(
             "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
             scores.get(8));
 
@@ -217,28 +217,28 @@ public class TCoffeeScoreFileTest
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
             FormatAdapter.FILE);
-    assertTrue(parser.getWarningMessage(), parser.isValid());
+    AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
     byte[][] scores = parser.getScoresArray();
 
-    assertEquals(9, scores[0][0]);
-    assertEquals(9, scores[1][0]);
-    assertEquals(9, scores[2][0]);
-    assertEquals(9, scores[3][0]);
-    assertEquals(9, scores[4][0]);
-    assertEquals(9, scores[5][0]);
-    assertEquals(9, scores[6][0]);
-    assertEquals(9, scores[7][0]);
-    assertEquals(9, scores[8][0]);
-
-    assertEquals(5, scores[0][36]);
-    assertEquals(4, scores[1][36]);
-    assertEquals(5, scores[2][36]);
-    assertEquals(4, scores[3][36]);
-    assertEquals(-1, scores[4][36]);
-    assertEquals(4, scores[5][36]);
-    assertEquals(3, scores[6][36]);
-    assertEquals(2, scores[7][36]);
-    assertEquals(3, scores[8][36]);
+    AssertJUnit.assertEquals(9, scores[0][0]);
+    AssertJUnit.assertEquals(9, scores[1][0]);
+    AssertJUnit.assertEquals(9, scores[2][0]);
+    AssertJUnit.assertEquals(9, scores[3][0]);
+    AssertJUnit.assertEquals(9, scores[4][0]);
+    AssertJUnit.assertEquals(9, scores[5][0]);
+    AssertJUnit.assertEquals(9, scores[6][0]);
+    AssertJUnit.assertEquals(9, scores[7][0]);
+    AssertJUnit.assertEquals(9, scores[8][0]);
+
+    AssertJUnit.assertEquals(5, scores[0][36]);
+    AssertJUnit.assertEquals(4, scores[1][36]);
+    AssertJUnit.assertEquals(5, scores[2][36]);
+    AssertJUnit.assertEquals(4, scores[3][36]);
+    AssertJUnit.assertEquals(-1, scores[4][36]);
+    AssertJUnit.assertEquals(4, scores[5][36]);
+    AssertJUnit.assertEquals(3, scores[6][36]);
+    AssertJUnit.assertEquals(2, scores[7][36]);
+    AssertJUnit.assertEquals(3, scores[8][36]);
 
   }
 
@@ -247,9 +247,9 @@ public class TCoffeeScoreFileTest
   {
     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
     TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
-    assertTrue(result.isValid());
-    assertEquals(5, result.getHeight());
-    assertEquals(84, result.getWidth());
+    AssertJUnit.assertTrue(result.isValid());
+    AssertJUnit.assertEquals(5, result.getHeight());
+    AssertJUnit.assertEquals(84, result.getWidth());
   }
 
 }