JAL-4386 Fixed failed test cases

diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java
index a732254..aa3c834 100644 (file)
--- a/test/jalview/bin/CommandsTest2.java
+++ b/test/jalview/bin/CommandsTest2.java
@@ -167,14 +167,14 @@ public class CommandsTest2
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
-            15, 8, 1 },
+            15, 7, 1 },
         { "--gui --nonews --nosplash --debug "
                 + "--append=examples/uniref50.fa "
                 + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
-            15, 5, 1 },
+            15, 4, 1 },
         { "--gui --nonews --nosplash --debug "
                 + "--append=examples/uniref50.fa "
                 + "--colour=gecos-flower "
@@ -182,7 +182,7 @@ public class CommandsTest2
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
                 + "--noshowssannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
-            15, 5, 1 },
+            15, 4, 1 },
         { "--gui --nonews --nosplash --debug "
                 + "--append=examples/uniref50.fa "
                 + "--colour=gecos-flower "
@@ -208,7 +208,7 @@ public class CommandsTest2
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
-            16, 20, 3 },
+            16, 19, 3 },
         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
             16, 0, 2 },
         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
@@ -217,14 +217,14 @@ public class CommandsTest2
                 + "--structureviewer=none "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
-            16, 11, 0 },
+            16, 10, 0 },
         { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
                 + "--allstructures "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--noallstructures " + "--structureviewer=none "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
-            16, 11, 2 },
+            16, 10, 2 },
         /*
          */
         //

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index c8208ca..f3c0dee 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", 8, types.size());
+    assertEquals("Not six annotation types", 7, types.size());
     assertTrue("IUPRED missing", types.contains("IUPRED"));
     assertTrue("JMol missing", types.contains("JMol"));
     assertTrue("Beauty missing", types.contains("Beauty"));
@@ -365,13 +365,12 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    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
+    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
   }
 
   /**
@@ -405,13 +404,12 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    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
+    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
   }
 
   /**
@@ -617,13 +615,12 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    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
+    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
   }
 
   /**
@@ -661,13 +658,12 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    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
+    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
   }
 
   /**
@@ -809,13 +805,12 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    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
+    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
 
     // reset - should all be visible
     testee.resetOriginalState();

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 91c8bbc..dd5cd4c 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -394,27 +394,27 @@ public class StructureChooserTest
         { "examples/uniref50.fa", "FER1_SPIOL",
             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
-            true, false, null, 15, 8, 0, null },
+            true, false, null, 15, 7, 0, null },
         { "examples/uniref50.fa", "FER1_SPIOL",
             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
-            true, false, null, 15, 8, 0, null },
+            true, false, null, 15, 7, 0, null },
         { "examples/uniref50.fa", "FER1_SPIOL",
             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
-            false, false, null, 15, 5, 0, null },
+            false, false, null, 15, 4, 0, null },
         { "examples/uniref50.fa", "FER1_SPIOL",
             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
-            true, false, ViewerType.JMOL, 15, 8, 1, null },
+            true, false, ViewerType.JMOL, 15, 7, 1, null },
         { "examples/uniref50.fa", "FER1_SPIOL",
             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
-            true, false, ViewerType.JMOL, 15, 8, 1, null },
+            true, false, ViewerType.JMOL, 15, 7, 1, null },
         { "examples/uniref50.fa", "FER1_SPIOL",
             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
-            false, false, ViewerType.JMOL, 15, 5, 1, null }, };
+            false, false, ViewerType.JMOL, 15, 4, 1, null }, };
   }
 
 }