Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 6e18324..0151a12 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import java.util.Locale;
-
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
@@ -30,20 +28,13 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.PDBEntry.Type;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Vector;
 
 import org.testng.Assert;
@@ -51,6 +42,13 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.bin.Cache;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
 import junit.extensions.PA;
 
 public class SequenceTest
@@ -62,6 +60,12 @@ public class SequenceTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @BeforeMethod(alwaysRun = true)
+  public void loadProperties()
+  {
+    Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+  }
+
   Sequence seq;
 
   @BeforeMethod(alwaysRun = true)
@@ -123,9 +127,13 @@ public class SequenceTest
     assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
     // test DNA with X
     assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
+    // short sequence is nucleotide only if 50% is nucleotide and remaining N/X
+    // is either N or X only
+    assertTrue(new Sequence("prot", "ACGTACGTACGTXN").isProtein());
     // test DNA with N
     assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
     // test RNA with X
+    assertFalse(new Sequence("prot", "ACGUACGUACGUACTGACAXX").isProtein());
     assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
     assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
   }