import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.GffConstants;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.FeatureColour;
+import jalview.util.MapList;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import junit.extensions.PA;
SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
sb.append("123456");
- SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
- 3, 1.2f, "group");
+ 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, null, 0);
sfl.add(sf);
sfl.add(sf);
sfl.add(sf);
- int n = sar.appendFeatures(sb, 1, sfl,
- new FeatureRenderer(null), 200); // text should terminate before 200 characters
+ int n = sar.appendFeatures(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
/*
* 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("<i>SeqDesc</i>", sb.toString());
+ assertEquals("<i>SeqDesc\n" + "\n" + "</i>", 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 = "<i>SeqDesc<br/>Type1 ; Nonpos Score=1.0</i>";
+ String expected = "<i>SeqDesc\n" + "\n"
+ + "<br/>Type1 ; Nonpos Score=1.0</i>";
assertEquals(expected, sb.toString());
/*
*/
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, false, null);
- assertEquals("<i>SeqDesc</i>", sb.toString());
+ assertEquals("<i>SeqDesc\n\n</i>", sb.toString());
/*
* add non-pos feature with score inside min-max range for feature type
* 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<String, float[][]> minmax = fr.getMinMax();
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
+ expected = "<i>SeqDesc\n" + "\n"
+ + "<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
assertEquals(expected, sb.toString());
-
+
/*
* 'linkonly' features are ignored; this is obsolete, as linkonly
* is only set by DasSequenceFetcher, and DAS is history
* '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 = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana</i>";
+ expected = "<i>SeqDesc\n" + "\n"
+ + "<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana</i>";
assertEquals(expected, sb.toString());
/*
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\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
+ + "PDB 3iu1\n"
+ + "<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);
- expected = "<i>SeqDesc<br/>UNIPROT P30419<br/>PDB 3iu1</i>";
+ expected = "<i>SeqDesc\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
+ + "PDB 3iu1\n" + "</i>";
assertEquals(expected, sb.toString());
/*
sf2.setDescription(
"This is a very long description which should be truncated");
sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
- expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; This is a very long description which sh...; clinical_significance=benign</i>";
+ expected = "<i>SeqDesc\n" + "\n"
+ + "<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; This is a very long description which sh...; clinical_significance=benign</i>";
assertEquals(expected, sb.toString());
// see other tests for treatment of status and html
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
-
+
SequenceI seq = new Sequence("s1", "ABC");
int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
{
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(
- "<i><br/>UNIPROT P30410, P30411, P30412, P30413,...<br/>PDB0 3iu1"));
- assertTrue(report
- .endsWith(
- "<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>"));
+ assertTrue(report.startsWith("<i>\n" + "<br/>\n" + "UNIPROT P30410,\n"
+ + " P30411,\n" + " P30412,\n" + " P30413,...<br/>\n"
+ + "PDB0 3iu1<br/>\n" + "PDB1 3iu1<br/>"));
+ assertTrue(report.endsWith("PDB5 3iu1<br/>\n" + "PDB6 3iu1<br/>\n"
+ + "PDB7 3iu1<br/>\n" + "PDB8,...<br/>\n"
+ + "(Output Sequence Details to list all database references)\n"
+ + "</i>"));
+ }
+
+ /**
+ * Test adding a linked feature to the tooltip
+ */
+ @Test(groups = "Functional")
+ public void testAppendFeature_virtualFeature()
+ {
+ /*
+ * map CDS to peptide sequence
+ */
+ SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+ SequenceI peptide = new Sequence("Peptide/8-14", "PLRFQMD");
+ MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+ 3, 1);
+ Mapping mapping = new Mapping(peptide, map);
+
+ /*
+ * assume variant feature found at CDS position 106 G>C
+ */
+ List<SequenceFeature> features = new ArrayList<>();
+ // vary ttg (Leu) to ttc (Phe)
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+ Float.NaN, null);
+ features.add(sf);
+ MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+ StringBuilder sb = new StringBuilder();
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+ sar.appendFeature(sb, 1, null, sf, mf, 0);
+
+ /*
+ * linked feature shown in tooltip in protein coordinates
+ */
+ assertEquals("variant 9; G,C", sb.toString());
+
+ /*
+ * adding "alleles" attribute to variant allows peptide consequence
+ * to be calculated and added to the tooltip
+ */
+ sf.setValue("alleles", "G,C");
+ sb = new StringBuilder();
+ sar.appendFeature(sb, 1, null, sf, mf, 0);
+ assertEquals("variant 9; G,C p.Leu9Phe", sb.toString());
+
+ /*
+ * now a virtual peptide feature on CDS
+ * 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");
+ features.clear();
+ features.add(sf2);
+ mapping = new Mapping(peptide, map);
+ mf = new MappedFeatures(mapping, peptide, 113, 't', features);
+ sb = new StringBuilder();
+ sar.appendFeature(sb, 1, null, sf2, mf, 0);
+ assertEquals("metal 110 115; Fe Score=2.3", sb.toString());
}
}
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