1 package jalview.renderer.seqfeatures;
3 import static org.testng.Assert.assertEquals;
4 import static org.testng.Assert.assertFalse;
5 import static org.testng.Assert.assertTrue;
7 import jalview.api.AlignViewportI;
8 import jalview.api.FeatureColourI;
9 import jalview.datamodel.SequenceFeature;
10 import jalview.datamodel.SequenceI;
11 import jalview.gui.AlignFrame;
12 import jalview.io.DataSourceType;
13 import jalview.io.FileLoader;
14 import jalview.schemes.FeatureColour;
16 import java.awt.Color;
17 import java.util.Arrays;
18 import java.util.List;
21 import org.testng.annotations.Test;
23 public class FeatureRendererTest
26 @Test(groups = "Functional")
27 public void testFindAllFeatures()
29 String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
30 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
31 DataSourceType.PASTE);
32 AlignViewportI av = af.getViewport();
33 FeatureRenderer fr = new FeatureRenderer(av);
38 fr.findAllFeatures(true);
39 assertTrue(fr.getRenderOrder().isEmpty());
40 assertTrue(fr.getFeatureGroups().isEmpty());
42 List<SequenceI> seqs = av.getAlignment().getSequences();
44 // add a non-positional feature - should be ignored by FeatureRenderer
45 SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
47 seqs.get(0).addSequenceFeature(sf1);
48 fr.findAllFeatures(true);
49 // ? bug - types and groups added for non-positional features
50 List<String> types = fr.getRenderOrder();
51 List<String> groups = fr.getFeatureGroups();
52 assertEquals(types.size(), 0);
53 assertFalse(types.contains("Type"));
54 assertEquals(groups.size(), 0);
55 assertFalse(groups.contains("Group"));
57 // add some positional features
58 seqs.get(1).addSequenceFeature(
59 new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
60 seqs.get(2).addSequenceFeature(
61 new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
62 // bug in findAllFeatures - group not checked for a known feature type
63 seqs.get(2).addSequenceFeature(
64 new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
66 seqs.get(3).addSequenceFeature(
67 new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
68 // null value for type produces NullPointerException
69 fr.findAllFeatures(true);
70 types = fr.getRenderOrder();
71 groups = fr.getFeatureGroups();
72 assertEquals(types.size(), 2);
73 assertFalse(types.contains("Type"));
74 assertTrue(types.contains("Pfam"));
75 assertTrue(types.contains("Rfam"));
76 assertEquals(groups.size(), 2);
77 assertFalse(groups.contains("Group"));
78 assertTrue(groups.contains("PfamGroup"));
79 assertTrue(groups.contains("RfamGroup"));
80 assertFalse(groups.contains(null)); // null group is ignored
83 * check min-max values
85 Map<String, float[][]> minMax = fr.getMinMax();
86 assertEquals(minMax.size(), 1); // non-positional and NaN not stored
87 assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
88 assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
90 // increase max for Pfam, add scores for Rfam
91 seqs.get(0).addSequenceFeature(
92 new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
93 seqs.get(1).addSequenceFeature(
94 new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
95 fr.findAllFeatures(true);
96 // note minMax is not a defensive copy, shouldn't expose this
97 assertEquals(minMax.size(), 2);
98 assertEquals(minMax.get("Pfam")[0][0], 1f);
99 assertEquals(minMax.get("Pfam")[0][1], 8f);
100 assertEquals(minMax.get("Rfam")[0][0], 6f);
101 assertEquals(minMax.get("Rfam")[0][1], 6f);
104 * check render order (last is on top)
106 List<String> renderOrder = fr.getRenderOrder();
107 assertEquals(renderOrder, Arrays.asList("Rfam", "Pfam"));
110 * change render order (todo: an easier way)
111 * nb here last comes first in the data array
113 Object[][] data = new Object[2][];
114 FeatureColourI colour = new FeatureColour(Color.RED);
115 data[0] = new Object[] { "Rfam", colour, true };
116 data[1] = new Object[] { "Pfam", colour, false };
117 fr.setFeaturePriority(data);
118 assertEquals(fr.getRenderOrder(), Arrays.asList("Pfam", "Rfam"));
119 assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
122 * add a new feature type: should go on top of render order as visible,
123 * other feature ordering and visibility should be unchanged
125 seqs.get(2).addSequenceFeature(
126 new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
127 fr.findAllFeatures(true);
128 assertEquals(fr.getRenderOrder(),
129 Arrays.asList("Pfam", "Rfam", "Metal"));
130 assertEquals(fr.getDisplayedFeatureTypes(),
131 Arrays.asList("Rfam", "Metal"));