From b785b473bee76eb532b6552fe61f4817b095cdbb Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Wed, 4 Mar 2020 02:14:11 +0000 Subject: [PATCH] JAL-3468 Fixed tests and added test for max-length of feature set tooltip --- test/jalview/io/SequenceAnnotationReportTest.java | 64 ++++++++++++++++----- 1 file changed, 50 insertions(+), 14 deletions(-) diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java index 7f4f3a3..42183ca 100644 --- a/test/jalview/io/SequenceAnnotationReportTest.java +++ b/test/jalview/io/SequenceAnnotationReportTest.java @@ -35,6 +35,8 @@ import jalview.schemes.FeatureColour; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.awt.Color; +import java.util.ArrayList; +import java.util.List; import java.util.Map; import org.testng.annotations.BeforeClass; @@ -65,19 +67,51 @@ public class SequenceAnnotationReportTest sar.appendFeature(sb, 2, null, sf, null); assertEquals("123456", sb.toString()); - // residuePos == 1 matches start of feature, text appended (but no
) + // residuePos == 1 matches start of feature, text appended (but no
) // feature score is not included sar.appendFeature(sb, 1, null, sf, null); assertEquals("123456disulfide bond 1:3", sb.toString()); // residuePos == 3 matches end of feature, text appended - //
is prefixed once sb.length() > 6 + //
is prefixed once sb.length() > 6 sar.appendFeature(sb, 3, null, sf, null); - assertEquals("123456disulfide bond 1:3
disulfide bond 1:3", + assertEquals("123456disulfide bond 1:3
disulfide bond 1:3", sb.toString()); } @Test(groups = "Functional") + public void testAppendFeatures_longText() + { + SequenceAnnotationReport sar = new SequenceAnnotationReport(null); + StringBuilder sb = new StringBuilder(); + String longString = "Abcd".repeat(50); + SequenceFeature sf = new SequenceFeature("sequence", longString, 1, 3, + "group"); + + sar.appendFeature(sb, 1, null, sf, null); + assertTrue(sb.length() < 100); + + List sfl = new ArrayList<>(); + sb.setLength(0); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + sfl.add(sf); + int n = sar.appendFeaturesLengthLimit(sb, 1, sfl, + new FeatureRenderer(null), 200); // text should terminate before 200 characters + String s = sb.toString(); + assertTrue(s.length() < 200); + assertEquals(n, 7); // should be 7 features left over + + } + + @Test(groups = "Functional") public void testAppendFeature_status() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); @@ -111,8 +145,8 @@ public class SequenceAnnotationReportTest */ minmax.put("METAL", new float[][] { { 0f, 1f }, null }); sar.appendFeature(sb, 1, fr, sf, null); - //
is appended to a buffer > 6 in length - assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3", + //
is appended to a buffer > 6 in length + assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3", sb.toString()); /* @@ -263,7 +297,7 @@ public class SequenceAnnotationReportTest null)); sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, null); - String expected = "SeqDesc
Type1 ; Nonpos Score=1.0"; + String expected = "SeqDesc
Type1 ; Nonpos Score=1.0"; assertEquals(expected, sb.toString()); /* @@ -288,7 +322,7 @@ public class SequenceAnnotationReportTest sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, fr); - expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos"; + expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos"; assertEquals(expected, sb.toString()); /* @@ -313,7 +347,7 @@ public class SequenceAnnotationReportTest seq.addSequenceFeature(sf2); sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, fr); - expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana"; + expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana"; assertEquals(expected, sb.toString()); /* @@ -334,13 +368,13 @@ public class SequenceAnnotationReportTest 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"; + 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"; + expected = "SeqDesc
UNIPROT P30419
PDB 3iu1"; assertEquals(expected, sb.toString()); /* @@ -350,7 +384,7 @@ public class SequenceAnnotationReportTest sf2.setDescription( "This is a very long description which should be truncated"); sar.createSequenceAnnotationReport(sb, seq, false, true, fr); - expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; This is a very long description which sh...; clinical_significance=benign"; + expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; This is a very long description which sh...; clinical_significance=benign"; assertEquals(expected, sb.toString()); // see other tests for treatment of status and html @@ -384,8 +418,10 @@ public class SequenceAnnotationReportTest sar.createSequenceAnnotationReport(sb, seq, true, true, null, true); String report = sb.toString(); assertTrue(report - .startsWith("
UNIPROT P30410, P30411, P30412, P30413,...
PDB0 3iu1")); + .startsWith( + "
UNIPROT P30410, P30411, P30412, P30413,...
PDB0 3iu1")); assertTrue(report - .endsWith("
PDB7 3iu1
PDB8,...
(Output Sequence Details to list all database references)")); + .endsWith( + "
PDB7 3iu1
PDB8,...
(Output Sequence Details to list all database references)")); } } -- 1.7.10.2