X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRendererTest.java;h=11b129e200eef979cc6124adc64ec7ba66c08b8c;hb=bab38275a499a24b8964181a6eb03262b720ee18;hp=745eec337a3f73f29023057162597751e6d7bb18;hpb=9e926ac4305fd9dff38b6e079e55b4f50664d544;p=jalview.git diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java index 745eec3..11b129e 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); @@ -258,7 +280,7 @@ 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 @@ -355,6 +377,14 @@ public class FeatureRendererTest assertTrue(features.contains(sf2) || features.contains(sf3)); assertFalse(features.contains(sf2) && 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); @@ -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 */ @@ -466,14 +497,14 @@ 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 +516,10 @@ 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));