import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.SortedMap;
import java.util.TreeMap;
+import org.testng.Assert;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import jalview.datamodel.AlignedCodonFrame;
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+
+ 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[] {});
+
+ AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] {ann1, 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};
}
@Test(groups = { "Functional" })
&& al.getAlignmentAnnotation().length == 2);
}
+
+ @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
+ };
+ }
+//
+// @Test(dataProvider = "SSSourceFromAnnotationDescription")
+// public void testGetSSSourceFromAnnotationDescription(Map<SequenceI, List<AlignmentAnnotation>> annotations, String expectedSSSource) {
+// String actualSSSource = AlignmentUtils.getSSSourceFromAnnotationDescription(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 / blobdiff