JAL-4386 - Implementation of substitution matrix and test cases.

[jalview.git] / test / jalview / gui / AnnotationChooserTest.java

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index f3c0dee..c8208ca 100644 (file)
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -325,7 +325,7 @@ public class AnnotationChooserTest
 
     types = AnnotationChooser.getAnnotationTypes(parentPanel.getAlignment(),
             false);
-    assertEquals("Not six annotation types", 7, types.size());
+    assertEquals("Not six annotation types", 8, types.size());
     assertTrue("IUPRED missing", types.contains("IUPRED"));
     assertTrue("JMol missing", types.contains("JMol"));
     assertTrue("Beauty missing", types.contains("Beauty"));
@@ -365,12 +365,13 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // Occupancy
-    assertTrue(anns[4].visible); // IUPred for seq0
-    assertTrue(anns[5].visible); // Beauty
-    assertFalse(anns[6].visible); // JMol for seq3 - not selected but hidden
-    assertTrue(anns[7].visible); // IUPRED for seq2
-    assertFalse(anns[8].visible); // JMol for seq1 - selected and hidden
+    assertTrue(anns[3].visible); // SS Consensus
+    assertTrue(anns[4].visible); // Occupancy
+    assertTrue(anns[5].visible); // IUPred for seq0
+    assertTrue(anns[6].visible); // Beauty
+    assertFalse(anns[7].visible); // JMol for seq3 - not selected but hidden
+    assertTrue(anns[8].visible); // IUPRED for seq2
+    assertFalse(anns[9].visible); // JMol for seq1 - selected and hidden
   }
 
   /**
@@ -404,12 +405,13 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // Occupancy
-    assertTrue(anns[4].visible); // IUPred for seq0
-    assertTrue(anns[5].visible); // Beauty
-    assertTrue(anns[6].visible); // JMol for seq3 not in selection group
-    assertTrue(anns[7].visible); // IUPRED for seq2
-    assertFalse(anns[8].visible); // JMol for seq1 in selection group
+    assertTrue(anns[3].visible); // SS ßConsensus
+    assertTrue(anns[4].visible); // Occupancy
+    assertTrue(anns[5].visible); // IUPred for seq0
+    assertTrue(anns[6].visible); // Beauty
+    assertTrue(anns[7].visible); // JMol for seq3 not in selection group
+    assertTrue(anns[8].visible); // IUPRED for seq2
+    assertFalse(anns[9].visible); // JMol for seq1 in selection group
   }
 
   /**
@@ -615,12 +617,13 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // Occupancy
-    assertTrue(anns[4].visible); // IUPred for seq0
-    assertTrue(anns[5].visible); // Beauty
-    assertFalse(anns[6].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // IUPRED for seq2
-    assertFalse(anns[8].visible); // JMol for seq1
+    assertTrue(anns[3].visible); // Consensus
+    assertTrue(anns[4].visible); // Occupancy
+    assertTrue(anns[5].visible); // IUPred for seq0
+    assertTrue(anns[6].visible); // Beauty
+    assertFalse(anns[7].visible); // JMol for seq3
+    assertTrue(anns[8].visible); // IUPRED for seq2
+    assertFalse(anns[9].visible); // JMol for seq1
   }
 
   /**
@@ -658,12 +661,13 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // Occupancy
-    assertTrue(anns[4].visible); // IUPred for seq0
-    assertTrue(anns[5].visible); // Beauty
-    assertTrue(anns[6].visible); // JMol for seq3 not in selection group
-    assertTrue(anns[7].visible); // IUPRED for seq2
-    assertFalse(anns[8].visible); // JMol for seq1 in selection group
+    assertTrue(anns[3].visible); // Consensus
+    assertTrue(anns[4].visible); // Occupancy
+    assertTrue(anns[5].visible); // IUPred for seq0
+    assertTrue(anns[6].visible); // Beauty
+    assertTrue(anns[7].visible); // JMol for seq3 not in selection group
+    assertTrue(anns[8].visible); // IUPRED for seq2
+    assertFalse(anns[9].visible); // JMol for seq1 in selection group
   }
 
   /**
@@ -805,12 +809,13 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // Occupancy
-    assertFalse(anns[4].visible); // IUPRED
-    assertTrue(anns[5].visible); // Beauty (not seq-related)
-    assertFalse(anns[6].visible); // JMol
-    assertFalse(anns[7].visible); // IUPRED
-    assertFalse(anns[8].visible); // JMol
+    assertTrue(anns[3].visible); // SS Consensus
+    assertTrue(anns[4].visible); // Occupancy
+    assertFalse(anns[5].visible); // IUPRED
+    assertTrue(anns[6].visible); // Beauty (not seq-related)
+    assertFalse(anns[7].visible); // JMol
+    assertFalse(anns[8].visible); // IUPRED
+    assertFalse(anns[9].visible); // JMol
 
     // reset - should all be visible
     testee.resetOriginalState();