X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRendererTest.java;h=723f3b8c9dcf3cc7e8404cc1d0bf0908bfda2801;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=745eec337a3f73f29023057162597751e6d7bb18;hpb=1c08dfb40bd5ebbd485883b1a6b58254fdf11181;p=jalview.git diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java index 745eec3..723f3b8 100644 --- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.renderer.seqfeatures; import static org.testng.Assert.assertEquals; @@ -9,14 +29,15 @@ import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; 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.io.DataSourceType; import jalview.io.FileLoader; import jalview.schemes.FeatureColour; import jalview.util.matcher.Condition; -import jalview.util.matcher.KeyedMatcher; -import jalview.util.matcher.KeyedMatcherSet; -import jalview.util.matcher.KeyedMatcherSetI; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; import java.awt.Color; import java.util.ArrayList; @@ -67,9 +88,8 @@ public class FeatureRendererTest seqs.get(2).addSequenceFeature( new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup")); // bug in findAllFeatures - group not checked for a known feature type - seqs.get(2).addSequenceFeature( - new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, - "RfamGroup")); + seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9, + Float.NaN, "RfamGroup")); // existing feature type with null group seqs.get(3).addSequenceFeature( new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null)); @@ -122,13 +142,14 @@ public class FeatureRendererTest * change render order (todo: an easier way) * nb here last comes first in the data array */ - Object[][] data = new Object[3][]; + FeatureSettingsBean[] data = new FeatureSettingsBean[3]; FeatureColourI colour = new FeatureColour(Color.RED); - data[0] = new Object[] { "Rfam", colour, true }; - data[1] = new Object[] { "Pfam", colour, false }; - data[2] = new Object[] { "Scop", colour, false }; + data[0] = new FeatureSettingsBean("Rfam", colour, null, true); + data[1] = new FeatureSettingsBean("Pfam", colour, null, false); + data[2] = new FeatureSettingsBean("Scop", colour, null, false); fr.setFeaturePriority(data); - assertEquals(fr.getRenderOrder(), Arrays.asList("Scop", "Pfam", "Rfam")); + assertEquals(fr.getRenderOrder(), + Arrays.asList("Scop", "Pfam", "Rfam")); assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam")); /* @@ -223,12 +244,13 @@ public class FeatureRendererTest /* * make "Type2" not displayed */ - Object[][] data = new Object[4][]; FeatureColourI colour = new FeatureColour(Color.RED); - data[0] = new Object[] { "Type1", colour, true }; - data[1] = new Object[] { "Type2", colour, false }; - data[2] = new Object[] { "Type3", colour, true }; - data[3] = new Object[] { "Disulphide Bond", colour, true }; + FeatureSettingsBean[] data = new FeatureSettingsBean[4]; + data[0] = new FeatureSettingsBean("Type1", colour, null, true); + data[1] = new FeatureSettingsBean("Type2", colour, null, false); + data[2] = new FeatureSettingsBean("Type3", colour, null, true); + data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null, + true); fr.setFeaturePriority(data); features = fr.findFeaturesAtColumn(seq, 15); @@ -258,13 +280,13 @@ public class FeatureRendererTest features = fr.findFeaturesAtColumn(seq, 5); assertEquals(features.size(), 1); assertTrue(features.contains(sf8)); - + /* * 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)); @@ -306,18 +328,18 @@ 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); @@ -343,18 +365,26 @@ 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)); + + /* + * no filtering if transparency is applied + */ + fr.setTransparency(0.5f); + features = seq.getSequenceFeatures(); + fr.filterFeaturesForDisplay(features); + assertEquals(features.size(), 5); } @Test(groups = "Functional") @@ -376,12 +406,13 @@ public class FeatureRendererTest /* * hide feature type, then unhide + * - feature type visibility should not affect the result */ - Object[][] data = new Object[1][]; - data[0] = new Object[] { "Cath", fc, false }; + FeatureSettingsBean[] data = new FeatureSettingsBean[1]; + data[0] = new FeatureSettingsBean("Cath", fc, null, false); fr.setFeaturePriority(data); - assertNull(fr.getColour(sf1)); - data[0] = new Object[] { "Cath", fc, true }; + assertEquals(fr.getColour(sf1), Color.red); + data[0] = new FeatureSettingsBean("Cath", fc, null, true); fr.setFeaturePriority(data); assertEquals(fr.getColour(sf1), Color.red); @@ -397,8 +428,8 @@ 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); @@ -410,7 +441,7 @@ public class FeatureRendererTest // score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0) Color expected = new Color(255, 128, 0); assertEquals(fr.getColour(sf2), expected); - + /* * above threshold, score is above threshold - no change */ @@ -422,7 +453,8 @@ 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)); @@ -445,7 +477,8 @@ 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); @@ -466,14 +499,14 @@ public class FeatureRendererTest // with filter on AF < 4 gc.setAboveThreshold(false); assertEquals(fr.getColour(sf2), expected); - KeyedMatcherSetI filter = new KeyedMatcherSet(); - filter.and(new KeyedMatcher(Condition.LT, 4f, "AF")); + FeatureMatcherSetI filter = new FeatureMatcherSet(); + filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF")); fr.setFeatureFilter("Cath", filter); assertNull(fr.getColour(sf2)); // with filter on 'Consequence contains missense' - filter = new KeyedMatcherSet(); - filter.and(new KeyedMatcher(Condition.Contains, "missense", + filter = new FeatureMatcherSet(); + filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense", "Consequence")); fr.setFeatureFilter("Cath", filter); // if feature has no Consequence attribute, no colour @@ -485,10 +518,10 @@ public class FeatureRendererTest sf2.setValue("Consequence", "Missense variant"); assertEquals(fr.getColour(sf2), expected); - // with filter on CSQ.Feature contains "ENST01234" - filter = new KeyedMatcherSet(); - filter.and(new KeyedMatcher(Condition.Matches, "ENST01234", "CSQ", - "Feature")); + // with filter on CSQ:Feature contains "ENST01234" + filter = new FeatureMatcherSet(); + filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234", + "CSQ", "Feature")); fr.setFeatureFilter("Cath", filter); // if feature has no CSQ data, no colour assertNull(fr.getColour(sf2)); @@ -504,4 +537,71 @@ public class FeatureRendererTest csqData.put("Feature", "ENST01234"); assertEquals(fr.getColour(sf2), expected); } + + @Test(groups = "Functional") + public void testIsVisible() + { + String seqData = ">s1\nMLQGIFPRS\n"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, + DataSourceType.PASTE); + AlignViewportI av = af.getViewport(); + FeatureRenderer fr = new FeatureRenderer(av); + SequenceI seq = av.getAlignment().getSequenceAt(0); + SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f, + "Group"); + sf.setValue("AC", "11"); + sf.setValue("CLIN_SIG", "Likely Pathogenic"); + seq.addSequenceFeature(sf); + + assertFalse(fr.isVisible(null)); + + /* + * initial state FeatureRenderer hasn't 'found' feature + * and so its feature type has not yet been set visible + */ + assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL")); + assertFalse(fr.isVisible(sf)); + + fr.findAllFeatures(true); + assertTrue(fr.isVisible(sf)); + + /* + * feature group not visible + */ + fr.setGroupVisibility("Group", false); + assertFalse(fr.isVisible(sf)); + fr.setGroupVisibility("Group", true); + assertTrue(fr.isVisible(sf)); + + /* + * feature score outwith colour threshold (score > 2) + */ + FeatureColourI fc = new FeatureColour(null, Color.white, Color.black, + Color.white, 0, 10); + fc.setAboveThreshold(true); + fc.setThreshold(2f); + fr.setColour("METAL", fc); + assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2 + fc.setBelowThreshold(true); + assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2 + + /* + * colour with threshold on attribute AC (value is 11) + */ + fc.setAttributeName("AC"); + assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2 + fc.setAboveThreshold(true); + assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2 + + fc.setAttributeName("AF"); // attribute AF is absent in sf + assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold + + FeatureMatcherSetI filter = new FeatureMatcherSet(); + filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic", + "CLIN_SIG")); + fr.setFeatureFilter("METAL", filter); + assertTrue(fr.isVisible(sf)); // feature matches filter + filter.and(FeatureMatcher.byScore(Condition.LE, "0.4")); + assertFalse(fr.isVisible(sf)); // feature doesn't match filter + } }