JAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refactored test suite with TestNG

diff --cc test/jalview/analysis/AlignmentUtilsTests.java
index 10fb81f,a503460..d44a6bc
--- 1/test/jalview/analysis/AlignmentUtilsTests.java
--- 2/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@@ -20,11 -20,12 +20,13 @@@
   */
  package jalview.analysis;
  
- import static org.junit.Assert.assertEquals;
- import static org.junit.Assert.assertFalse;
- import static org.junit.Assert.assertNull;
- import static org.junit.Assert.assertSame;
- import static org.junit.Assert.assertTrue;
++
+ import static org.testng.AssertJUnit.assertEquals;
+ import static org.testng.AssertJUnit.assertFalse;
+ import static org.testng.AssertJUnit.assertNull;
+ import static org.testng.AssertJUnit.assertSame;
+ import static org.testng.AssertJUnit.assertTrue;
+ 
  import jalview.datamodel.AlignedCodonFrame;
  import jalview.datamodel.Alignment;
  import jalview.datamodel.AlignmentAnnotation;

diff --cc test/jalview/datamodel/AlignmentTest.java
Simple merge

diff --cc test/jalview/io/JSONFileTest.java
index bce9795,33e67ce..2e28e3a
--- 1/test/jalview/io/JSONFileTest.java
--- 2/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@@ -1,7 -1,9 +1,8 @@@
  package jalview.io;
  
  
- import static org.junit.Assert.assertNotNull;
+ import static org.testng.AssertJUnit.assertNotNull;
+ 
 -import jalview.datamodel.Alignment;
  import jalview.datamodel.AlignmentAnnotation;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.Annotation;

diff --cc test/jalview/io/PhylipFileTests.java
index d6f28fa,9db4763..d335731
--- 1/test/jalview/io/PhylipFileTests.java
--- 2/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@@ -1,8 -1,9 +1,9 @@@
  package jalview.io;
  
- import static org.junit.Assert.assertNotNull;
- import static org.junit.Assert.assertTrue;
+ import static org.testng.AssertJUnit.assertNotNull;
+ import static org.testng.AssertJUnit.assertTrue;
+ 
 -import jalview.datamodel.Alignment;
 +import jalview.datamodel.AlignmentI;
  import jalview.datamodel.SequenceI;
  
  import java.io.IOException;

diff --cc test/jalview/io/RNAMLfileTest.java
Simple merge

diff --cc test/jalview/io/StockholmFileTest.java
index 3c78275,1c46d1f..45de531
--- 1/test/jalview/io/StockholmFileTest.java
--- 2/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@@ -20,9 -20,11 +20,10 @@@
   */
  package jalview.io;
  
- import static org.junit.Assert.assertEquals;
- import static org.junit.Assert.assertNotNull;
- import static org.junit.Assert.assertTrue;
+ import static org.testng.AssertJUnit.assertEquals;
+ import static org.testng.AssertJUnit.assertNotNull;
+ import static org.testng.AssertJUnit.assertTrue;
+ 
 -import jalview.datamodel.Alignment;
  import jalview.datamodel.AlignmentAnnotation;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.Annotation;

diff --cc test/jalview/util/MappingUtilsTest.java
index 8fc4507,0f2baf4..9985fb3
--- 1/test/jalview/util/MappingUtilsTest.java
--- 2/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@@ -1,10 -1,12 +1,12 @@@
  package jalview.util;
  
- import static org.junit.Assert.assertEquals;
- import static org.junit.Assert.assertSame;
- import static org.junit.Assert.assertTrue;
++
+ import static org.testng.AssertJUnit.assertEquals;
+ import static org.testng.AssertJUnit.assertSame;
+ import static org.testng.AssertJUnit.assertTrue;
+ 
  import jalview.api.AlignViewportI;
  import jalview.datamodel.AlignedCodonFrame;
 -import jalview.datamodel.Alignment;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.ColumnSelection;
  import jalview.datamodel.SearchResults;