sar.appendFeature(sb, 2, null, sf, null, 0);
assertEquals("123456", sb.toString());
sar.appendFeature(sb, 2, null, sf, null, 0);
assertEquals("123456", sb.toString());
// feature score is not included
sar.appendFeature(sb, 1, null, sf, null, 0);
assertEquals("123456disulfide bond 1:3", sb.toString());
// residuePos == 3 matches end of feature, text appended
// feature score is not included
sar.appendFeature(sb, 1, null, sf, null, 0);
assertEquals("123456disulfide bond 1:3", sb.toString());
// residuePos == 3 matches end of feature, text appended
sar.appendFeature(sb, 3, null, sf, null, 0);
sar.appendFeature(sb, 3, null, sf, null, 0);
*/
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
sar.appendFeature(sb, 1, fr, sf, null, 0);
*/
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
sar.appendFeature(sb, 1, fr, sf, null, 0);
- // <br/> is appended to a buffer > 6 in length
- assertEquals("METAL 1 3; Fe2-S<br/>METAL 1 3; Fe2-S Score=1.3",
+ // <br> is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
null));
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, null);
null));
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, null);
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
seq.addSequenceFeature(sf2);
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
seq.addSequenceFeature(sf2);
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
fc.setAttributeName("clinical_significance");
fr.setColour("Variant", fc);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
fc.setAttributeName("clinical_significance");
fr.setColour("Variant", fc);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "<i>SeqDesc<br/>UNIPROT P30419<br/>PDB 3iu1<br/>Metal ; Desc<br/>"
- + "Type1 ; Nonpos<br/>Variant ; Havana; clinical_significance=benign</i>";
+ expected = "<i>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1<br>Metal ; Desc<br>"
+ + "Type1 ; Nonpos<br>Variant ; Havana; clinical_significance=benign</i>";
assertEquals(expected, sb.toString());
// with showNonPositionalFeatures = false
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
assertEquals(expected, sb.toString());
// with showNonPositionalFeatures = false
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
sf2.setDescription(
"This is a very long description which should be truncated");
sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
sf2.setDescription(
"This is a very long description which should be truncated");
sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
assertEquals(expected, sb.toString());
// see other tests for treatment of status and html
assertEquals(expected, sb.toString());
// see other tests for treatment of status and html
- "<i><br/>UNIPROT P30410, P30411, P30412, P30413,...<br/>PDB0 3iu1"));
+ "<i><br>UNIPROT P30410, P30411, P30412, P30413,...<br>PDB0 3iu1"));