X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRendererTest.java;h=2e04ecb663b96a353cfe0bcd700fa4829f28ad95;hb=39845a5bd6ca82da33a9c800ec7282de4e2a96f1;hp=7c9927f86c8e550c12989ec19b1add2f18be90e2;hpb=356260e6aa37640091849355ed97cd4103cc4c6c;p=jalview.git diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java index 7c9927f..2e04ecb 100644 --- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java @@ -22,17 +22,24 @@ package jalview.renderer.seqfeatures; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertNotNull; import static org.testng.Assert.assertNull; +import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import jalview.analysis.GeneticCodes; import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; +import jalview.bin.Jalview; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.features.FeatureMatcher; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.Desktop; import jalview.io.DataSourceType; import jalview.io.FileLoader; import jalview.schemes.FeatureColour; @@ -285,8 +292,8 @@ public class FeatureRendererTest * give "Type3" features a graduated colour scheme * - first with no threshold */ - FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f, - 10f); + FeatureColourI gc = new FeatureColour(Color.green, Color.yellow, + Color.red, null, 0f, 10f); fr.getFeatureColours().put("Type3", gc); features = fr.findFeaturesAtColumn(seq, 8); assertTrue(features.contains(sf4)); @@ -328,18 +335,18 @@ public class FeatureRendererTest SequenceI seq = av.getAlignment().getSequenceAt(0); SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN, "group1"); - seq.addSequenceFeature(sf1); SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f, "group2"); - seq.addSequenceFeature(sf2); SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f, "group3"); - seq.addSequenceFeature(sf3); SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f, "group4"); - seq.addSequenceFeature(sf4); SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f, "group4"); + seq.addSequenceFeature(sf1); + seq.addSequenceFeature(sf2); + seq.addSequenceFeature(sf3); + seq.addSequenceFeature(sf4); seq.addSequenceFeature(sf5); fr.findAllFeatures(true); @@ -365,17 +372,17 @@ public class FeatureRendererTest assertTrue(features.contains(sf5)); /* - * hide groups 2 and 3 makes no difference to this method + * features in hidden groups are removed */ fr.setGroupVisibility("group2", false); fr.setGroupVisibility("group3", false); features = seq.getSequenceFeatures(); fr.filterFeaturesForDisplay(features); - assertEquals(features.size(), 3); + assertEquals(features.size(), 2); assertTrue(features.contains(sf1) || features.contains(sf4)); assertFalse(features.contains(sf1) && features.contains(sf4)); - assertTrue(features.contains(sf2) || features.contains(sf3)); - assertFalse(features.contains(sf2) && features.contains(sf3)); + assertFalse(features.contains(sf2)); + assertFalse(features.contains(sf3)); assertTrue(features.contains(sf5)); /* @@ -428,8 +435,8 @@ public class FeatureRendererTest * graduated colour by score, no threshold, no score * */ - FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, - Color.green, 1f, 11f); + FeatureColourI gc = new FeatureColour(Color.red, Color.yellow, + Color.red, Color.green, 1f, 11f); fr.getFeatureColours().put("Cath", gc); assertEquals(fr.getColour(sf1), Color.green); @@ -453,7 +460,8 @@ public class FeatureRendererTest * threshold is min-max; now score 6 is 1/6 of the way from 5 to 11 * or from yellow(255, 255, 0) to red(255, 0, 0) */ - gc = new FeatureColour(Color.yellow, Color.red, Color.green, 5f, 11f); + gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green, + 5f, 11f); fr.getFeatureColours().put("Cath", gc); gc.setAutoScaled(false); // this does little other than save a checkbox setting! assertEquals(fr.getColour(sf2), new Color(255, 213, 0)); @@ -476,7 +484,8 @@ public class FeatureRendererTest * colour by feature attribute value * first with no value held */ - gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f); + gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green, + 1f, 11f); fr.getFeatureColours().put("Cath", gc); gc.setAttributeName("AF"); assertEquals(fr.getColour(sf2), Color.green); @@ -574,7 +583,7 @@ public class FeatureRendererTest /* * feature score outwith colour threshold (score > 2) */ - FeatureColourI fc = new FeatureColour(Color.white, Color.black, + FeatureColourI fc = new FeatureColour(null, Color.white, Color.black, Color.white, 0, 10); fc.setAboveThreshold(true); fc.setThreshold(2f); @@ -602,4 +611,69 @@ public class FeatureRendererTest filter.and(FeatureMatcher.byScore(Condition.LE, "0.4")); assertFalse(fr.isVisible(sf)); // feature doesn't match filter } + + @Test(groups = "Functional") + public void testFindComplementFeaturesAtResidue() + { + Jalview.main( + new String[] + { "-nonews", "-props", "test/jalview/testProps.jvprops" }); + + // codons for MCWHSE + String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(cdsSeq, + DataSourceType.PASTE); + af.showTranslation_actionPerformed( + GeneticCodes.getInstance().getStandardCodeTable()); + af.closeMenuItem_actionPerformed(true); + + /* + * find the complement frames (ugly) + */ + AlignFrame[] frames = Desktop.getAlignFrames(); + assertEquals(frames.length, 2); + AlignViewport av1 = frames[0].getViewport(); + AlignViewport av2 = frames[1].getViewport(); + AlignViewport cds = av1.getAlignment().isNucleotide() ? av1 : av2; + AlignViewport peptide = cds == av1 ? av2 : av1; + assertNotNull(cds); + assertNotNull(peptide); + + /* + * add features to CDS at first codon, positions 2-3 + */ + SequenceI seq1 = cds.getAlignment().getSequenceAt(0); + SequenceFeature sf1 = new SequenceFeature("sequence_variant", "G,GT", 2, + 2, "ensembl"); + seq1.addSequenceFeature(sf1); + SequenceFeature sf2 = new SequenceFeature("sequence_variant", "C, CA", + 3, 3, "ensembl"); + seq1.addSequenceFeature(sf2); + + /* + * 'find' mapped features from the peptide position + * - first with CDS features _not_ shown on peptide alignment + */ + SequenceI seq2 = peptide.getAlignment().getSequenceAt(0); + FeatureRenderer frC = new FeatureRenderer(cds); + frC.featuresAdded(); + MappedFeatures mf = frC.findComplementFeaturesAtResidue(seq2, 1); + assertNotNull(mf); + assertEquals(mf.features.size(), 2); + assertSame(mf.features.get(0), sf1); + assertSame(mf.features.get(1), sf2); + + /* + * add exon feature and verify it is only returned once for a + * peptide position, even though it is on all 3 codon positions + */ + SequenceFeature sf3 = new SequenceFeature("exon", "exon1", 4, 12, + "ensembl"); + seq1.addSequenceFeature(sf3); + frC.featuresAdded(); + mf = frC.findComplementFeaturesAtResidue(seq2, 3); + assertNotNull(mf); + assertEquals(mf.features.size(), 1); + assertSame(mf.features.get(0), sf3); + } }