From: Renia Correya <rcorreya001@dundee.ac.uk>
Date: Tue, 3 Sep 2024 11:14:12 +0000 (+0530)
Subject: Correction in tests
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fspike%2FJAL-4386_merge_with_develop;p=jalview.git

Correction in tests
---

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 863356e..1cf9a80 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -83,29 +83,25 @@ public class AlignmentUtilsTests
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-
-    AlignmentAnnotation ann1 = new AlignmentAnnotation(
-            "Secondary Structure", "Secondary Structure",
+    
+    AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure",
+            new Annotation[] {});
+    AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred",
             new Annotation[] {});
-    AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
-            "jnetpred", new Annotation[] {});
     AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
             new Annotation[] {});
     AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
             new Annotation[] {});
+    
+    AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] {ann1, ann3, ann4};
 
-    AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] { ann1, ann3,
-        ann4 };
-
-    AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] { ann2, ann3,
-        ann4 };
-
-    AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] { ann3, ann4 };
-
+    AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] {ann2, ann3, ann4};
+    
+    AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] {ann3, ann4};
+    
     AlignmentAnnotation[] anns4 = new AlignmentAnnotation[0];
-
-    AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] { ann1, ann2,
-        ann3, ann4 };
+    
+    AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] {ann1, ann2, ann3, ann4};
   }
 
   @Test(groups = { "Functional" })
@@ -2785,180 +2781,133 @@ public class AlignmentUtilsTests
         Assert.assertEquals(expectedSSPresent, AlignmentUtils.isSecondaryStructurePresent(annotations));
     }
 
-  @Test(
-    groups = "Functional",
-    dataProvider = "SecondaryStructureAnnotations")
-  public void testSecondaryStructurePresentAndSources(
-          AlignmentAnnotation[] annotations, boolean expectedSSPresent,
-          ArrayList<String> expectedSSSources)
-  {
-    Assert.assertEquals(expectedSSPresent,
-            AlignmentUtils.isSecondaryStructurePresent(annotations));
-    Assert.assertEquals(expectedSSSources,
-            AlignmentUtils.getSecondaryStructureSources(annotations));
-  }
-
-  @DataProvider(name = "SecondaryStructureAnnotations")
-  public static Object[][] provideSecondaryStructureAnnotations()
-  {
-    AlignmentAnnotation ann1 = new AlignmentAnnotation(
-            "Secondary Structure", "Secondary Structure",
-            new Annotation[] {});
-    AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
-            "jnetpred", new Annotation[] {});
-    AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
-            new Annotation[] {});
-    AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
-            new Annotation[] {});
-
-    List<String> ssSources1 = new ArrayList<>(
-            Arrays.asList("3D Structures"));
-    List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
-    List<String> ssSources3 = new ArrayList<>(
-            Arrays.asList("3D Structures", "JPred"));
-    List<String> ssSources4 = new ArrayList<>();
-
-    return new Object[][] {
-        { new AlignmentAnnotation[]
-        { ann1, ann3, ann4 }, true, ssSources1 },
-        { new AlignmentAnnotation[]
-        { ann2, ann3, ann4 }, true, ssSources2 },
-        { new AlignmentAnnotation[]
-        { ann3, ann4 }, false, ssSources4 },
-        { new AlignmentAnnotation[] {}, false, ssSources4 },
-        { new AlignmentAnnotation[]
-        { ann1, ann2, ann3, ann4 }, true, ssSources3 } };
-  }
-
-  @Test(dataProvider = "SecondaryStructureAnnotationColours")
-  public void testSecondaryStructureAnnotationColour(char symbol,
-          Color expectedColor)
-  {
-    Color actualColor = AlignmentUtils
-            .getSecondaryStructureAnnotationColour(symbol);
-    Assert.assertEquals(actualColor, expectedColor);
-  }
-
-  @DataProvider(name = "SecondaryStructureAnnotationColours")
-  public static Object[][] provideSecondaryStructureAnnotationColours()
-  {
-    return new Object[][] { { 'C', Color.gray }, { 'E', Color.green },
-        { 'H', Color.red },
-        { '-', Color.gray } };
-  }
-
-  @Test(dataProvider = "SSAnnotationPresence")
-  public void testIsSSAnnotationPresent(
-          Map<SequenceI, List<AlignmentAnnotation>> annotations,
-          boolean expectedPresence)
-  {
-    boolean actualPresence = AlignmentUtils
-            .isSSAnnotationPresent(annotations);
-    Assert.assertEquals(actualPresence, expectedPresence);
-  }
-
-  @DataProvider(name = "SSAnnotationPresence")
-  public static Object[][] provideSSAnnotationPresence()
-  {
-    Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
-    SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
-    List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
-    annotationsList1.add(new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure", new Annotation[] {}));
-    annotations1.put(seq1, annotationsList1); // Annotation present secondary
-                                              // structure for seq1
-
-    Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
-    SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
-    List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
-    annotationsList2.add(new AlignmentAnnotation("Other Annotation",
-            "Other Annotation", new Annotation[] {}));
-    annotations2.put(seq2, annotationsList2); // Annotation not related to any
-                                              // of secondary structure for seq2
-
-    Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
-    // Empty annotation map
-
-    Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
-    SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
-    List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
-    annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred",
-            new Annotation[] {}));
-    annotations4.put(seq4, annotationsList4); // Annotation present from JPred
-                                              // for seq4
-
-    return new Object[][] { { annotations1, true }, // Annotations present
-                                                    // secondary structure
-                                                    // present
-        { annotations2, false }, // No annotations related to any of the
-                                 // secondary structure present
-        { annotations3, false }, // Empty annotation map
-        { annotations4, true }, // Annotations present from JPred secondary
-                                // structure present
-    };
-  }
+    @DataProvider(name = "SecondaryStructureAnnotations")
+    public static Object[][] provideSecondaryStructureAnnotations() {
+        AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{});
+        AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{});
+        AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
+        AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
+
+        List<String> ssSources1 = new ArrayList<>(Arrays.asList("3D Structures"));
+        List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
+        List<String> ssSources3 = new ArrayList<>(Arrays.asList("3D Structures", "JPred"));
+        List<String> ssSources4 = new ArrayList<>();
+
+        return new Object[][]{
+            {new AlignmentAnnotation[]{ann1, ann3, ann4}, true, ssSources1},
+            {new AlignmentAnnotation[]{ann2, ann3, ann4}, true, ssSources2},
+            {new AlignmentAnnotation[]{ann3, ann4}, false, ssSources4},
+            {new AlignmentAnnotation[]{}, false, ssSources4},
+            {new AlignmentAnnotation[]{ann1, ann2, ann3, ann4}, true, ssSources3}
+        };
+    }
+    
+    @Test(dataProvider = "SecondaryStructureAnnotationColours")
+    public void testSecondaryStructureAnnotationColour(char symbol, Color expectedColor) {
+        Color actualColor = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol);
+        Assert.assertEquals(actualColor, expectedColor);
+    }
 
-  @Test
-  public void testGetSSSourceFromAnnotationDescription(
-          AlignmentAnnotation[] annotations, String expectedSSSource)
-  {
-    List<String> actualSSSource = AlignmentUtils
-            .extractSSSourceInAlignmentAnnotation(annotations);
-    Assert.assertEquals(actualSSSource, expectedSSSource);
-  }
+    @DataProvider(name = "SecondaryStructureAnnotationColours")
+    public static Object[][] provideSecondaryStructureAnnotationColours() {
+        return new Object[][]{
+            {'C', Color.gray},
+            {'E', Color.green},
+            {'H', Color.red},
+            {'-', Color.gray}
+        };
+    }
+    
+    @Test(dataProvider = "SSAnnotationPresence")
+    public void testIsSSAnnotationPresent(Map<SequenceI, List<AlignmentAnnotation>> annotations, boolean expectedPresence) {
+        boolean actualPresence = AlignmentUtils.isSSAnnotationPresent(annotations);
+        Assert.assertEquals(actualPresence, expectedPresence);
+    }
 
-  @DataProvider(name = "SSSourceFromAnnotationDescription")
-  public static Object[][] provideSSSourceFromAnnotationDescription()
-  {
-    Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
-    SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
-    List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
-    annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output",
-            new Annotation[] {}));
-    annotations1.put(seq1, annotationsList1); // Annotation present from JPred
-                                              // for seq1
-
-    Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
-    SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
-    List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
-    annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure for af-q43517-f1A", new Annotation[] {}));
-    annotations2.put(seq2, annotationsList2); // Annotation present secondary
-                                              // structure from Alphafold for
-                                              // seq2
-
-    Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
-    // Empty annotation map
-
-    Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
-    SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
-    List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
-    annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure for 4zhpA", new Annotation[] {}));
-    annotations4.put(seq4, annotationsList4); // Annotation present secondary
-                                              // structure from pdb for seq4
-
-    Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
-    SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
-    List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
-    annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
-            new Annotation[] {}));
-    annotations5.put(seq5, annotationsList5); // Annotation present secondary
-                                              // structure from Swiss model for
-                                              // seq5
-
-    // JPred Output - JPred
-    // Secondary Structure for af-q43517-f1A - Alphafold
-    // Secondary Structure for 4zhpA - Experimental
-    // Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P -
-    // Swiss Model
-
-    return new Object[][] { { annotations1, "JPred" },
-        { annotations2, "Alphafold" },
-        { annotations3, null },
-        { annotations4, "PDB" },
-        { annotations5, "Swiss Model" } };
-  }
+    @DataProvider(name = "SSAnnotationPresence")
+    public static Object[][] provideSSAnnotationPresence() {
+        Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+        SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+        List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+        annotationsList1.add(new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{}));
+        annotations1.put(seq1, annotationsList1); // Annotation present secondary structure for seq1
+
+        Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+        SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+        List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+        annotationsList2.add(new AlignmentAnnotation("Other Annotation", "Other Annotation", new Annotation[]{}));
+        annotations2.put(seq2, annotationsList2); // Annotation not related to any of secondary structure for seq2
+
+        Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+        // Empty annotation map
+        
+        Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+        SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+        List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+        annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{}));
+        annotations4.put(seq4, annotationsList4); // Annotation present from JPred for seq4
+
+
+        return new Object[][]{
+            {annotations1, true}, // Annotations present secondary structure present
+            {annotations2, false}, // No annotations related to any of the secondary structure present
+            {annotations3, false},  // Empty annotation map
+            {annotations4, true}, // Annotations present from JPred secondary structure present
+        };
+    }
+    
+    @Test
+    public void testGetSSSourceFromAnnotationDescription(AlignmentAnnotation[] annotations, String expectedSSSource) {
+        List<String> actualSSSource = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+        Assert.assertEquals(actualSSSource, expectedSSSource);
+    }
+    
+    @DataProvider(name = "SSSourceFromAnnotationDescription")
+    public static Object[][] provideSSSourceFromAnnotationDescription() {
+        Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+        SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+        List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+        annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output", new Annotation[]{}));
+        annotations1.put(seq1, annotationsList1); // Annotation present from JPred for seq1
+
+        Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+        SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+        List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+        annotationsList2.add(new AlignmentAnnotation("Secondary Structure", 
+                "Secondary Structure for af-q43517-f1A", new Annotation[]{}));
+        annotations2.put(seq2, annotationsList2); // Annotation present secondary structure from Alphafold for seq2
+
+        Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+        // Empty annotation map
+        
+        Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+        SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+        List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+        annotationsList4.add(new AlignmentAnnotation("Secondary Structure", 
+                "Secondary Structure for 4zhpA", new Annotation[]{}));
+        annotations4.put(seq4, annotationsList4); // Annotation present secondary structure from pdb for seq4
+        
+        Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
+        SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
+        List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
+        annotationsList5.add(new AlignmentAnnotation("Secondary Structure", 
+                "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P", 
+                new Annotation[]{}));
+        annotations5.put(seq5, annotationsList5); // Annotation present secondary structure from Swiss model for seq5
+        
+
+        //JPred Output - JPred
+        //Secondary Structure for af-q43517-f1A - Alphafold
+        //Secondary Structure for 4zhpA - Experimental
+        //Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P - Swiss Model
+        
+        return new Object[][]{
+            {annotations1, "JPred"}, 
+            {annotations2, "Alphafold"}, 
+            {annotations3, null},  
+            {annotations4, "PDB"},
+            {annotations5, "Swiss Model"}
+        };
+    }   
 
 }