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"));
134 @Test(groups = "Functional")
135 public void testFindFeaturesAtRes()
137 String seqData = ">s1\nabcdefghijklmnopqrstuvwxyz\n";
138 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
139 DataSourceType.PASTE);
140 AlignViewportI av = af.getViewport();
141 FeatureRenderer fr = new FeatureRenderer(av);
142 SequenceI seq = av.getAlignment().getSequenceAt(0);
147 List<SequenceFeature> features = fr.findFeaturesAtRes(seq, 3);
148 assertTrue(features.isEmpty());
153 SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
154 "Group"); // non-positional
155 seq.addSequenceFeature(sf1);
156 SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 5, 15, 1f,
158 seq.addSequenceFeature(sf2);
159 SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
161 seq.addSequenceFeature(sf3);
162 SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
163 null); // null group is always treated as visible
164 seq.addSequenceFeature(sf4);
167 * add contact features
169 SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 4,
171 seq.addSequenceFeature(sf5);
172 SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 4,
174 seq.addSequenceFeature(sf6);
175 SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 4,
177 seq.addSequenceFeature(sf7);
180 * let feature renderer discover features (and make visible)
182 fr.findAllFeatures(true);
183 features = fr.findFeaturesAtRes(seq, 12); // all positional
184 assertEquals(features.size(), 6);
185 assertTrue(features.contains(sf2));
186 assertTrue(features.contains(sf3));
187 assertTrue(features.contains(sf4));
188 assertTrue(features.contains(sf5));
189 assertTrue(features.contains(sf6));
190 assertTrue(features.contains(sf7));
193 * at a non-contact position
195 features = fr.findFeaturesAtRes(seq, 11);
196 assertEquals(features.size(), 3);
197 assertTrue(features.contains(sf2));
198 assertTrue(features.contains(sf3));
199 assertTrue(features.contains(sf4));
202 * make "Type2" not displayed
204 Object[][] data = new Object[4][];
205 FeatureColourI colour = new FeatureColour(Color.RED);
206 data[0] = new Object[] { "Type1", colour, true };
207 data[1] = new Object[] { "Type2", colour, false };
208 data[2] = new Object[] { "Type3", colour, true };
209 data[3] = new Object[] { "Disulphide Bond", colour, true };
210 fr.setFeaturePriority(data);
211 features = fr.findFeaturesAtRes(seq, 12);
212 assertEquals(features.size(), 5); // no sf2
213 assertTrue(features.contains(sf3));
214 assertTrue(features.contains(sf4));
215 assertTrue(features.contains(sf5));
216 assertTrue(features.contains(sf6));
217 assertTrue(features.contains(sf7));
220 * make "Group2" not displayed
222 fr.setGroupVisibility("Group2", false);
223 features = fr.findFeaturesAtRes(seq, 12);
224 assertEquals(features.size(), 3); // no sf2, sf3, sf6
225 assertTrue(features.contains(sf4));
226 assertTrue(features.contains(sf5));
227 assertTrue(features.contains(sf7));