X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=7f4f3a335aa4274bc0b522e69a12d9cda9cba181;hb=2350ea66072d77b929d89e5ba42599c0e8d3ea53;hp=0b5dfdda390449a21a9d72de37336426db090fa9;hpb=586b87fca07c53c935ffe67827e498eb80fad4bf;p=jalview.git
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 0b5dfdd..7f4f3a3 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -248,14 +248,13 @@ public class SequenceAnnotationReportTest
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());
+ sar.createSequenceAnnotationReport(sb, seq, true, true, null);
+ assertEquals("SeqDesc", sb.toString());
/*
* non-positional feature
@@ -264,7 +263,7 @@ 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());
/*
@@ -272,7 +271,7 @@ public class SequenceAnnotationReportTest
*/
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, false, null);
- assertEquals("
SeqDesc", sb.toString());
+ assertEquals("SeqDesc", sb.toString());
/*
* add non-pos feature with score inside min-max range for feature type
@@ -289,7 +288,7 @@ 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());
/*
@@ -305,8 +304,8 @@ public class SequenceAnnotationReportTest
assertEquals(expected, sb.toString()); // unchanged!
/*
- * 'clinical_significance' attribute only included when
- * used for feature colouring
+ * 'clinical_significance' attribute is only included in description
+ * when used for feature colouring
*/
SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
5f, null);
@@ -314,7 +313,7 @@ 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());
/*
@@ -335,13 +334,23 @@ 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
"
+ 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());
+
+ /*
+ * long feature description is truncated with ellipsis
+ */
+ sb.setLength(0);
+ 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";
assertEquals(expected, sb.toString());
// see other tests for treatment of status and html