{
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" })
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"}
+ };
+ }
}
git://source.jalview.org / jalview.git / commitdiff