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package jalview.io; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertTrue; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import java.util.List; |
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import java.util.Map; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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import jalview.api.FeatureColourI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.MappedFeatures; |
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import jalview.datamodel.Mapping; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.JvOptionPane; |
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import jalview.io.gff.GffConstants; |
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import jalview.renderer.seqfeatures.FeatureRenderer; |
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import jalview.schemes.FeatureColour; |
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import jalview.util.MapList; |
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import jalview.viewmodel.seqfeatures.FeatureRendererModel; |
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import junit.extensions.PA; |
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| 100% |
Uncovered Elements: 0 (218) |
Complexity: 15 |
Complexity Density: 0.07 |
|
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public class SequenceAnnotationReportTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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1 |
@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
57 |
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} |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testAppendFeature_disulfideBond() |
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{ |
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SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
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StringBuilder sb = new StringBuilder(); |
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sb.append("123456"); |
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SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1, |
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3, 1.2f, "group"); |
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sar.appendFeature(sb, 2, null, sf, null, 0); |
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assertEquals("123456", sb.toString()); |
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sar.appendFeature(sb, 1, null, sf, null, 0); |
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assertEquals("123456disulfide bond 1:3", sb.toString()); |
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sar.appendFeature(sb, 3, null, sf, null, 0); |
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assertEquals("123456disulfide bond 1:3<br/>disulfide bond 1:3", |
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sb.toString()); |
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} |
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| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testAppendFeatures_longText() |
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{ |
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SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
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StringBuilder sb = new StringBuilder(); |
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String longString = "Abcd".repeat(50); |
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SequenceFeature sf = new SequenceFeature("sequence", longString, 1, 3, |
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"group"); |
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sar.appendFeature(sb, 1, null, sf, null, 0); |
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assertTrue(sb.length() < 100); |
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List<SequenceFeature> sfl = new ArrayList<>(); |
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sb.setLength(0); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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sfl.add(sf); |
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int n = sar.appendFeatures(sb, 1, sfl, |
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new FeatureRenderer(null), 200); |
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String s = sb.toString(); |
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assertTrue(s.length() < 200); |
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assertEquals(n, 7); |
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} |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
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@Test(groups = "Functional")... |
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public void testAppendFeature_status() |
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{ |
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SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
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StringBuilder sb = new StringBuilder(); |
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SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, |
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Float.NaN, "group"); |
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sf.setStatus("Confirmed"); |
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sar.appendFeature(sb, 1, null, sf, null, 0); |
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assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString()); |
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} |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testAppendFeature_withScore() |
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{ |
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SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
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StringBuilder sb = new StringBuilder(); |
134 |
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SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f, |
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"group"); |
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FeatureRendererModel fr = new FeatureRenderer(null); |
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Map<String, float[][]> minmax = fr.getMinMax(); |
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sar.appendFeature(sb, 1, fr, sf, null, 0); |
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assertEquals("METAL 1 3; Fe2-S", sb.toString()); |
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minmax.put("METAL", new float[][] { { 0f, 1f }, null }); |
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sar.appendFeature(sb, 1, fr, sf, null, 0); |
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assertEquals("METAL 1 3; Fe2-S<br/>METAL 1 3; Fe2-S Score=1.3", |
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sb.toString()); |
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minmax.put("METAL", new float[][] { { 2f, 2f }, null }); |
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sb.setLength(0); |
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sar.appendFeature(sb, 1, fr, sf, null, 0); |
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assertEquals("METAL 1 3; Fe2-S", sb.toString()); |
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} |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testAppendFeature_noScore() |
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{ |
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SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
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StringBuilder sb = new StringBuilder(); |
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SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, |
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Float.NaN, "group"); |
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sar.appendFeature(sb, 1, null, sf, null, 0); |
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assertEquals("METAL 1 3; Fe2-S", sb.toString()); |
173 |
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} |
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175 |
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176 |
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177 |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
|
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178 |
1 |
@Test(groups = "Functional")... |
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public void testAppendFeature_colouredByAttribute() |
180 |
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{ |
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SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
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StringBuilder sb = new StringBuilder(); |
183 |
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SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, |
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Float.NaN, "group"); |
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sf.setValue("clinical_significance", "Benign"); |
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189 |
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190 |
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FeatureRendererModel fr = new FeatureRenderer(null); |
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sar.appendFeature(sb, 1, fr, sf, null, 0); |
192 |
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assertEquals("METAL 1 3; Fe2-S", sb.toString()); |
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194 |
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195 |
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196 |
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197 |
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FeatureColourI fc = new FeatureColour(null, Color.white, Color.black, |
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null, 5, 10); |
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fc.setAttributeName("Pfam"); |
200 |
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fr.setColour("METAL", fc); |
201 |
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sb.setLength(0); |
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sar.appendFeature(sb, 1, fr, sf, null, 0); |
203 |
1 |
assertEquals("METAL 1 3; Fe2-S", sb.toString()); |
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206 |
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207 |
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fc.setAttributeName("clinical_significance"); |
209 |
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sb.setLength(0); |
210 |
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sar.appendFeature(sb, 1, fr, sf, null, 0); |
211 |
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assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign", |
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sb.toString()); |
213 |
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} |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
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215 |
1 |
@Test(groups = "Functional")... |
216 |
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public void testAppendFeature_withScoreStatusAttribute() |
217 |
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{ |
218 |
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SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
219 |
1 |
StringBuilder sb = new StringBuilder(); |
220 |
1 |
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f, |
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"group"); |
222 |
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sf.setStatus("Confirmed"); |
223 |
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sf.setValue("clinical_significance", "Benign"); |
224 |
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225 |
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FeatureRendererModel fr = new FeatureRenderer(null); |
226 |
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Map<String, float[][]> minmax = fr.getMinMax(); |
227 |
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FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue, |
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null, 12, 22); |
229 |
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fc.setAttributeName("clinical_significance"); |
230 |
1 |
fr.setColour("METAL", fc); |
231 |
1 |
minmax.put("METAL", new float[][] { { 0f, 1f }, null }); |
232 |
1 |
sar.appendFeature(sb, 1, fr, sf, null, 0); |
233 |
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234 |
1 |
assertEquals( |
235 |
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"METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign", |
236 |
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sb.toString()); |
237 |
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} |
238 |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
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239 |
1 |
@Test(groups = "Functional")... |
240 |
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public void testAppendFeature_DescEqualsType() |
241 |
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{ |
242 |
1 |
SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
243 |
1 |
StringBuilder sb = new StringBuilder(); |
244 |
1 |
SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3, |
245 |
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Float.NaN, "group"); |
246 |
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247 |
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248 |
1 |
sar.appendFeature(sb, 1, null, sf, null, 0); |
249 |
1 |
assertEquals("METAL 1 3", sb.toString()); |
250 |
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251 |
1 |
sb.setLength(0); |
252 |
1 |
sf.setDescription("Metal"); |
253 |
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254 |
1 |
sar.appendFeature(sb, 1, null, sf, null, 0); |
255 |
1 |
assertEquals("METAL 1 3; Metal", sb.toString()); |
256 |
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} |
257 |
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|
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
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258 |
1 |
@Test(groups = "Functional")... |
259 |
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public void testAppendFeature_stripHtml() |
260 |
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{ |
261 |
1 |
SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
262 |
1 |
StringBuilder sb = new StringBuilder(); |
263 |
1 |
SequenceFeature sf = new SequenceFeature("METAL", |
264 |
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"<html><body>hello<em>world</em></body></html>", 1, 3, |
265 |
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Float.NaN, "group"); |
266 |
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267 |
1 |
sar.appendFeature(sb, 1, null, sf, null, 0); |
268 |
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269 |
1 |
assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString()); |
270 |
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271 |
1 |
sb.setLength(0); |
272 |
1 |
sf.setDescription("<br>&kHD>6"); |
273 |
1 |
sar.appendFeature(sb, 1, null, sf, null, 0); |
274 |
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275 |
1 |
assertEquals("METAL 1 3; <br>&kHD>6", sb.toString()); |
276 |
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} |
277 |
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| 100% |
Uncovered Elements: 0 (57) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
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278 |
1 |
@Test(groups = "Functional")... |
279 |
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public void testCreateSequenceAnnotationReport() |
280 |
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{ |
281 |
1 |
SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
282 |
1 |
StringBuilder sb = new StringBuilder(); |
283 |
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284 |
1 |
SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL"); |
285 |
1 |
seq.setDescription("SeqDesc"); |
286 |
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287 |
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288 |
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289 |
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290 |
1 |
seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5, |
291 |
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10, 1f, null)); |
292 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, true, null); |
293 |
1 |
assertEquals("<i>SeqDesc</i>", sb.toString()); |
294 |
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295 |
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296 |
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297 |
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298 |
1 |
seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f, |
299 |
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null)); |
300 |
1 |
sb.setLength(0); |
301 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, true, null); |
302 |
1 |
String expected = "<i>SeqDesc<br/>Type1 ; Nonpos Score=1.0</i>"; |
303 |
1 |
assertEquals(expected, sb.toString()); |
304 |
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305 |
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306 |
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307 |
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|
308 |
1 |
sb.setLength(0); |
309 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, false, null); |
310 |
1 |
assertEquals("<i>SeqDesc</i>", sb.toString()); |
311 |
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312 |
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313 |
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314 |
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315 |
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316 |
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317 |
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318 |
1 |
seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f, |
319 |
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null)); |
320 |
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321 |
1 |
FeatureRendererModel fr = new FeatureRenderer(null); |
322 |
1 |
Map<String, float[][]> minmax = fr.getMinMax(); |
323 |
1 |
minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } }); |
324 |
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|
325 |
1 |
sb.setLength(0); |
326 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, true, fr); |
327 |
1 |
expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>"; |
328 |
1 |
assertEquals(expected, sb.toString()); |
329 |
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330 |
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331 |
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332 |
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333 |
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|
334 |
1 |
SequenceFeature sf = new SequenceFeature("Metal", "Desc", 0, 0, 5f, |
335 |
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null); |
336 |
1 |
sf.setValue("linkonly", Boolean.TRUE); |
337 |
1 |
seq.addSequenceFeature(sf); |
338 |
1 |
sb.setLength(0); |
339 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, true, fr); |
340 |
1 |
assertEquals(expected, sb.toString()); |
341 |
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|
342 |
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343 |
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|
344 |
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345 |
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|
346 |
1 |
SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0, |
347 |
|
5f, null); |
348 |
1 |
sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign"); |
349 |
1 |
seq.addSequenceFeature(sf2); |
350 |
1 |
sb.setLength(0); |
351 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, true, fr); |
352 |
1 |
expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana</i>"; |
353 |
1 |
assertEquals(expected, sb.toString()); |
354 |
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|
355 |
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|
356 |
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|
357 |
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|
358 |
1 |
seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1")); |
359 |
1 |
seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419")); |
360 |
|
|
361 |
|
|
362 |
1 |
sb.setLength(0); |
363 |
1 |
sar.createSequenceAnnotationReport(sb, seq, false, true, fr); |
364 |
1 |
assertEquals(expected, sb.toString()); |
365 |
|
|
366 |
|
|
367 |
1 |
sb.setLength(0); |
368 |
1 |
FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink, |
369 |
|
null, 2, 3); |
370 |
1 |
fc.setAttributeName("clinical_significance"); |
371 |
1 |
fr.setColour("Variant", fc); |
372 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, true, fr); |
373 |
1 |
expected = "<i>SeqDesc<br/>UNIPROT P30419<br/>PDB 3iu1<br/>Metal ; Desc<br/>" |
374 |
|
+ "Type1 ; Nonpos<br/>Variant ; Havana; clinical_significance=benign</i>"; |
375 |
1 |
assertEquals(expected, sb.toString()); |
376 |
|
|
377 |
1 |
sb.setLength(0); |
378 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, false, fr); |
379 |
1 |
expected = "<i>SeqDesc<br/>UNIPROT P30419<br/>PDB 3iu1</i>"; |
380 |
1 |
assertEquals(expected, sb.toString()); |
381 |
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|
382 |
|
|
383 |
|
|
384 |
|
|
385 |
1 |
sb.setLength(0); |
386 |
1 |
sf2.setDescription( |
387 |
|
"This is a very long description which should be truncated"); |
388 |
1 |
sar.createSequenceAnnotationReport(sb, seq, false, true, fr); |
389 |
1 |
expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; This is a very long description which sh...; clinical_significance=benign</i>"; |
390 |
1 |
assertEquals(expected, sb.toString()); |
391 |
|
|
392 |
|
|
393 |
|
} |
394 |
|
|
395 |
|
|
396 |
|
|
397 |
|
|
398 |
|
|
399 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (17) |
Complexity: 3 |
Complexity Density: 0.23 |
1PASS
|
|
400 |
1 |
@Test(groups = "Functional")... |
401 |
|
public void testCreateSequenceAnnotationReport_withEllipsis() |
402 |
|
{ |
403 |
1 |
SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
404 |
1 |
StringBuilder sb = new StringBuilder(); |
405 |
|
|
406 |
1 |
SequenceI seq = new Sequence("s1", "ABC"); |
407 |
|
|
408 |
1 |
int maxSources = (int) PA.getValue(sar, "MAX_SOURCES"); |
409 |
42 |
for (int i = 0; i <= maxSources; i++) |
410 |
|
{ |
411 |
41 |
seq.addDBRef(new DBRefEntry("PDB" + i, "0", "3iu1")); |
412 |
|
} |
413 |
|
|
414 |
1 |
int maxRefs = (int) PA.getValue(sar, "MAX_REFS_PER_SOURCE"); |
415 |
6 |
for (int i = 0; i <= maxRefs; i++) |
416 |
|
{ |
417 |
5 |
seq.addDBRef(new DBRefEntry("Uniprot", "0", "P3041" + i)); |
418 |
|
} |
419 |
|
|
420 |
1 |
sar.createSequenceAnnotationReport(sb, seq, true, true, null, true); |
421 |
1 |
String report = sb.toString(); |
422 |
1 |
assertTrue(report |
423 |
|
.startsWith( |
424 |
|
"<i><br/>UNIPROT P30410, P30411, P30412, P30413,...<br/>PDB0 3iu1")); |
425 |
1 |
assertTrue(report |
426 |
|
.endsWith( |
427 |
|
"<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>")); |
428 |
|
} |
429 |
|
|
430 |
|
|
431 |
|
|
432 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (24) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
433 |
1 |
@Test(groups = "Functional")... |
434 |
|
public void testAppendFeature_virtualFeature() |
435 |
|
{ |
436 |
|
|
437 |
|
|
438 |
|
|
439 |
1 |
SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT"); |
440 |
1 |
SequenceI peptide = new Sequence("Peptide/8-14", "PLRFQMD"); |
441 |
1 |
MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 }, |
442 |
|
3, 1); |
443 |
1 |
Mapping mapping = new Mapping(peptide, map); |
444 |
|
|
445 |
|
|
446 |
|
|
447 |
|
|
448 |
1 |
List<SequenceFeature> features = new ArrayList<>(); |
449 |
|
|
450 |
1 |
SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106, |
451 |
|
Float.NaN, null); |
452 |
1 |
features.add(sf); |
453 |
1 |
MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features); |
454 |
|
|
455 |
1 |
StringBuilder sb = new StringBuilder(); |
456 |
1 |
SequenceAnnotationReport sar = new SequenceAnnotationReport(false); |
457 |
1 |
sar.appendFeature(sb, 1, null, sf, mf, 0); |
458 |
|
|
459 |
|
|
460 |
|
|
461 |
|
|
462 |
1 |
assertEquals("variant 9; G,C", sb.toString()); |
463 |
|
|
464 |
|
|
465 |
|
|
466 |
|
|
467 |
|
|
468 |
1 |
sf.setValue("alleles", "G,C"); |
469 |
1 |
sb = new StringBuilder(); |
470 |
1 |
sar.appendFeature(sb, 1, null, sf, mf, 0); |
471 |
1 |
assertEquals("variant 9; G,C p.Leu9Phe", sb.toString()); |
472 |
|
|
473 |
|
|
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
1 |
SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, |
479 |
|
2.3f, "Uniprot"); |
480 |
1 |
features.clear(); |
481 |
1 |
features.add(sf2); |
482 |
1 |
mapping = new Mapping(peptide, map); |
483 |
1 |
mf = new MappedFeatures(mapping, peptide, 113, 't', features); |
484 |
1 |
sb = new StringBuilder(); |
485 |
1 |
sar.appendFeature(sb, 1, null, sf2, mf, 0); |
486 |
1 |
assertEquals("metal 110 115; Fe Score=2.3", sb.toString()); |
487 |
|
} |
488 |
|
} |