X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;fp=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=270de2d8fbe47eb2dd5a1fdab06f5d74304b84c9;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=f3a75868ef43c42d215ef499383a69c07a9a2976;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java index f3a7586..270de2d 100644 --- a/test/jalview/io/SequenceAnnotationReportTest.java +++ b/test/jalview/io/SequenceAnnotationReportTest.java @@ -287,19 +287,20 @@ public class SequenceAnnotationReportTest /* * positional features are ignored */ - seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5, - 10, 1f, null)); + seq.addSequenceFeature( + new SequenceFeature("Domain", "Ferredoxin", 5, 10, 1f, null)); sar.createSequenceAnnotationReport(sb, seq, true, true, null); - assertEquals("SeqDesc", sb.toString()); + assertEquals("SeqDesc\n" + "\n" + "", sb.toString()); /* * non-positional feature */ - seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f, - null)); + 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
"; + String expected = "SeqDesc\n" + "\n" + + "
Type1 ; Nonpos Score=1.0
"; assertEquals(expected, sb.toString()); /* @@ -307,7 +308,7 @@ public class SequenceAnnotationReportTest */ sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, false, null); - assertEquals("SeqDesc", sb.toString()); + assertEquals("SeqDesc\n\n", sb.toString()); /* * add non-pos feature with score inside min-max range for feature type @@ -315,8 +316,8 @@ public class SequenceAnnotationReportTest * 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)); + seq.addSequenceFeature( + new SequenceFeature("Metal", "Desc", 0, 0, 5f, null)); FeatureRendererModel fr = new FeatureRenderer(null); Map minmax = fr.getMinMax(); @@ -324,7 +325,8 @@ public class SequenceAnnotationReportTest sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, fr); - expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos
"; + expected = "SeqDesc\n" + "\n" + + "
Metal ; Desc
Type1 ; Nonpos
"; assertEquals(expected, sb.toString()); /* @@ -343,13 +345,14 @@ public class SequenceAnnotationReportTest * 'clinical_significance' attribute is only included in description * when used for feature colouring */ - SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0, - 5f, null); + 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
"; + expected = "SeqDesc\n" + "\n" + + "
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana
"; assertEquals(expected, sb.toString()); /* @@ -370,13 +373,15 @@ 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\n" + "
\n" + "UNIPROT P30419
\n" + + "PDB 3iu1\n" + + "
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\n" + "
\n" + "UNIPROT P30419
\n" + + "PDB 3iu1\n" + "
"; assertEquals(expected, sb.toString()); /* @@ -386,7 +391,8 @@ 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\n" + "\n" + + "
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 @@ -419,12 +425,13 @@ 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")); - assertTrue(report - .endsWith( - "
PDB7 3iu1
PDB8,...
(Output Sequence Details to list all database references)
")); + assertTrue(report.startsWith("\n" + "
\n" + "UNIPROT P30410,\n" + + " P30411,\n" + " P30412,\n" + " P30413,...
\n" + + "PDB0 3iu1
\n" + "PDB1 3iu1
")); + assertTrue(report.endsWith("PDB5 3iu1
\n" + "PDB6 3iu1
\n" + + "PDB7 3iu1
\n" + "PDB8,...
\n" + + "(Output Sequence Details to list all database references)\n" + + "
")); } /** @@ -475,8 +482,8 @@ public class SequenceAnnotationReportTest * feature at 11-12 on peptide maps to 110-115 on CDS * here we test for tooltip at 113 (t) */ - SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, - 2.3f, "Uniprot"); + SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, 2.3f, + "Uniprot"); features.clear(); features.add(sf2); mapping = new Mapping(peptide, map);