/* * 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.io; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertTrue; import jalview.api.FeatureColourI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.JvOptionPane; import jalview.io.gff.GffConstants; import jalview.renderer.seqfeatures.FeatureRenderer; import jalview.schemes.FeatureColour; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.awt.Color; import java.util.Map; import junit.extensions.PA; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class SequenceAnnotationReportTest { @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @Test(groups = "Functional") public void testAppendFeature_disulfideBond() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); sb.append("123456"); SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1, 3, 1.2f, "group"); // residuePos == 2 does not match start or end of feature, nothing done: sar.appendFeature(sb, 2, null, sf); assertEquals("123456", sb.toString()); // residuePos == 1 matches start of feature, text appended (but no
) // feature score is not included sar.appendFeature(sb, 1, null, sf); assertEquals("123456disulfide bond 1:3", sb.toString()); // residuePos == 3 matches end of feature, text appended //
is prefixed once sb.length() > 6 sar.appendFeature(sb, 3, null, sf); assertEquals("123456disulfide bond 1:3
disulfide bond 1:3", sb.toString()); } @Test(groups = "Functional") public void testAppendFeature_status() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, Float.NaN, "group"); sf.setStatus("Confirmed"); sar.appendFeature(sb, 1, null, sf); assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString()); } @Test(groups = "Functional") public void testAppendFeature_withScore() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f, "group"); FeatureRendererModel fr = new FeatureRenderer(null); Map minmax = fr.getMinMax(); sar.appendFeature(sb, 1, fr, sf); /* * map has no entry for this feature type - score is not shown: */ assertEquals("METAL 1 3; Fe2-S", sb.toString()); /* * map has entry for this feature type - score is shown: */ minmax.put("METAL", new float[][] { { 0f, 1f }, null }); sar.appendFeature(sb, 1, fr, sf); //
is appended to a buffer > 6 in length assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3", sb.toString()); /* * map has min == max for this feature type - score is not shown: */ minmax.put("METAL", new float[][] { { 2f, 2f }, null }); sb.setLength(0); sar.appendFeature(sb, 1, fr, sf); assertEquals("METAL 1 3; Fe2-S", sb.toString()); } @Test(groups = "Functional") public void testAppendFeature_noScore() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, Float.NaN, "group"); sar.appendFeature(sb, 1, null, sf); assertEquals("METAL 1 3; Fe2-S", sb.toString()); } /** * A specific attribute value is included if it is used to colour the feature */ @Test(groups = "Functional") public void testAppendFeature_colouredByAttribute() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, Float.NaN, "group"); sf.setValue("clinical_significance", "Benign"); /* * first with no colour by attribute */ FeatureRendererModel fr = new FeatureRenderer(null); sar.appendFeature(sb, 1, fr, sf); assertEquals("METAL 1 3; Fe2-S", sb.toString()); /* * then with colour by an attribute the feature lacks */ FeatureColourI fc = new FeatureColour(Color.white, Color.black, 5, 10); fc.setAttributeName("Pfam"); fr.setColour("METAL", fc); sb.setLength(0); sar.appendFeature(sb, 1, fr, sf); assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change /* * then with colour by an attribute the feature has */ fc.setAttributeName("clinical_significance"); sb.setLength(0); sar.appendFeature(sb, 1, fr, sf); assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign", sb.toString()); } @Test(groups = "Functional") public void testAppendFeature_withScoreStatusAttribute() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f, "group"); sf.setStatus("Confirmed"); sf.setValue("clinical_significance", "Benign"); FeatureRendererModel fr = new FeatureRenderer(null); Map minmax = fr.getMinMax(); FeatureColourI fc = new FeatureColour(Color.white, Color.blue, 12, 22); fc.setAttributeName("clinical_significance"); fr.setColour("METAL", fc); minmax.put("METAL", new float[][] { { 0f, 1f }, null }); sar.appendFeature(sb, 1, fr, sf); assertEquals( "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign", sb.toString()); } @Test(groups = "Functional") public void testAppendFeature_DescEqualsType() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3, Float.NaN, "group"); // description is not included if it duplicates type: sar.appendFeature(sb, 1, null, sf); assertEquals("METAL 1 3", sb.toString()); sb.setLength(0); sf.setDescription("Metal"); // test is case-sensitive: sar.appendFeature(sb, 1, null, sf); assertEquals("METAL 1 3; Metal", sb.toString()); } @Test(groups = "Functional") public void testAppendFeature_stripHtml() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceFeature sf = new SequenceFeature("METAL", "helloworld", 1, 3, Float.NaN, "group"); sar.appendFeature(sb, 1, null, sf); // !! strips off but not ?? assertEquals("METAL 1 3; helloworld", sb.toString()); sb.setLength(0); sf.setDescription("
&kHD>6"); sar.appendFeature(sb, 1, null, sf); // if no tag, html-encodes > and < (only): assertEquals("METAL 1 3; <br>&kHD>6", sb.toString()); } @Test(groups = "Functional") public void testCreateSequenceAnnotationReport() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL"); seq.setDescription("SeqDesc"); sar.createSequenceAnnotationReport(sb, seq, true, true, null); /* * positional features are ignored */ seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5, 10, 1f, null)); assertEquals("
SeqDesc
", sb.toString()); /* * non-positional feature */ seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f, null)); sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, null); String expected = "
SeqDesc
Type1 ; Nonpos Score=1.0
"; assertEquals(expected, sb.toString()); /* * non-positional features not wanted */ sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, false, null); assertEquals("
SeqDesc
", sb.toString()); /* * add non-pos feature with score inside min-max range for feature type * minmax holds { [positionalMin, positionalMax], [nonPosMin, nonPosMax] } * score is only appended for positional features so ignored here! * minMax are not recorded for non-positional features */ seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f, null)); FeatureRendererModel fr = new FeatureRenderer(null); Map minmax = fr.getMinMax(); minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } }); sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, fr); expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos
"; assertEquals(expected, sb.toString()); /* * 'linkonly' features are ignored; this is obsolete, as linkonly * is only set by DasSequenceFetcher, and DAS is history */ SequenceFeature sf = new SequenceFeature("Metal", "Desc", 0, 0, 5f, null); sf.setValue("linkonly", Boolean.TRUE); seq.addSequenceFeature(sf); sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, fr); assertEquals(expected, sb.toString()); // unchanged! /* * 'clinical_significance' attribute only included when * used for feature colouring */ SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0, 5f, null); sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign"); seq.addSequenceFeature(sf2); sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, fr); expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana
"; assertEquals(expected, sb.toString()); /* * add dbrefs */ seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1")); seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419")); // with showDbRefs = false sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, false, true, fr); assertEquals(expected, sb.toString()); // unchanged // with showDbRefs = true, colour Variant features by clinical_significance sb.setLength(0); FeatureColourI fc = new FeatureColour(Color.green, Color.pink, 2, 3); fc.setAttributeName("clinical_significance"); fr.setColour("Variant", fc); sar.createSequenceAnnotationReport(sb, seq, true, true, fr); expected = "
SeqDesc
UNIPROT P30419
PDB 3iu1
Metal ; Desc
" + "Type1 ; Nonpos
Variant ; Havana; clinical_significance=benign
"; assertEquals(expected, sb.toString()); // with showNonPositionalFeatures = false sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, false, fr); expected = "
SeqDesc
UNIPROT P30419
PDB 3iu1
"; assertEquals(expected, sb.toString()); // see other tests for treatment of status and html } /** * Test that exercises an abbreviated sequence details report, with ellipsis * where there are more than 40 different sources, or more than 4 dbrefs for a * single source */ @Test(groups = "Functional") public void testCreateSequenceAnnotationReport_withEllipsis() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); SequenceI seq = new Sequence("s1", "ABC"); int maxSources = (int) PA.getValue(sar, "MAX_SOURCES"); for (int i = 0; i <= maxSources; i++) { seq.addDBRef(new DBRefEntry("PDB" + i, "0", "3iu1")); } int maxRefs = (int) PA.getValue(sar, "MAX_REFS_PER_SOURCE"); for (int i = 0; i <= maxRefs; i++) { seq.addDBRef(new DBRefEntry("Uniprot", "0", "P3041" + i)); } sar.createSequenceAnnotationReport(sb, seq, true, true, null, true); String report = sb.toString(); assertTrue(report .startsWith("
UNIPROT P30410, P30411, P30412, P30413,...
PDB0 3iu1")); assertTrue(report .endsWith("
PDB7 3iu1
PDB8,...
(Output Sequence Details to list all database references)
")); } }