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;
3, 1.2f, "group");
// residuePos == 2 does not match start or end of feature, nothing done:
- sar.appendFeature(sb, 2, null, sf);
+ sar.appendFeature(sb, 2, null, sf, null);
assertEquals("123456", sb.toString());
- // residuePos == 1 matches start of feature, text appended (but no <br>)
+ // residuePos == 1 matches start of feature, text appended (but no <br/>)
// feature score is not included
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
assertEquals("123456disulfide bond 1:3", sb.toString());
// residuePos == 3 matches end of feature, text appended
- // <br> is prefixed once sb.length() > 6
- sar.appendFeature(sb, 3, null, sf);
- assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
+ // <br/> is prefixed once sb.length() > 6
+ sar.appendFeature(sb, 3, null, sf, null);
+ assertEquals("123456disulfide bond 1:3<br/>disulfide bond 1:3",
sb.toString());
}
@Test(groups = "Functional")
+ public void testAppendFeatures_longText()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuilder sb = new StringBuilder();
+ String longString = // java11!"Abcd".repeat(50);
+ "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+ + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+ + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+ + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+ + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd";
+
+ SequenceFeature sf = new SequenceFeature("sequence", longString, 1, 3,
+ "group");
+
+ sar.appendFeature(sb, 1, null, sf, null);
+ assertTrue(sb.length() < 100);
+
+ List<SequenceFeature> 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);
Float.NaN, "group");
sf.setStatus("Confirmed");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
}
FeatureRendererModel fr = new FeatureRenderer(null);
Map<String, float[][]> minmax = fr.getMinMax();
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
/*
* map has no entry for this feature type - score is not shown:
*/
* map has entry for this feature type - score is shown:
*/
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
- sar.appendFeature(sb, 1, fr, sf);
- // <br> is appended to a buffer > 6 in length
- assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
+ sar.appendFeature(sb, 1, fr, sf, null);
+ // <br/> is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S<br/>METAL 1 3; Fe2-S Score=1.3",
sb.toString());
/*
*/
minmax.put("METAL", new float[][] { { 2f, 2f }, null });
sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
}
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
Float.NaN, "group");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
}
* first with no colour by attribute
*/
FeatureRendererModel fr = new FeatureRenderer(null);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
/*
fc.setAttributeName("Pfam");
fr.setColour("METAL", fc);
sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
/*
*/
fc.setAttributeName("clinical_significance");
sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
sb.toString());
}
fc.setAttributeName("clinical_significance");
fr.setColour("METAL", fc);
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
assertEquals(
"METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
Float.NaN, "group");
// description is not included if it duplicates type:
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
assertEquals("METAL 1 3", sb.toString());
sb.setLength(0);
sf.setDescription("Metal");
// test is case-sensitive:
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
assertEquals("METAL 1 3; Metal", sb.toString());
}
"<html><body>hello<em>world</em></body></html>", 1, 3,
Float.NaN, "group");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
// !! strips off </body> but not <body> ??
assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
sb.setLength(0);
sf.setDescription("<br>&kHD>6");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
// if no <html> tag, html-encodes > and < (only):
assertEquals("METAL 1 3; <br>&kHD>6", sb.toString());
}
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("<i><br>SeqDesc</i>", sb.toString());
+ sar.createSequenceAnnotationReport(sb, seq, true, true, null);
+ assertEquals("<i>SeqDesc</i>", sb.toString());
/*
* non-positional feature
null));
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, null);
- String expected = "<i><br>SeqDesc<br>Type1 ; Nonpos Score=1.0</i>";
+ String expected = "<i>SeqDesc<br/>Type1 ; Nonpos Score=1.0</i>";
assertEquals(expected, sb.toString());
/*
*/
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, false, null);
- assertEquals("<i><br>SeqDesc</i>", sb.toString());
+ assertEquals("<i>SeqDesc</i>", sb.toString());
/*
* add non-pos feature with score inside min-max range for feature type
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos</i>";
+ expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
assertEquals(expected, sb.toString());
/*
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);
seq.addSequenceFeature(sf2);
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana</i>";
+ expected = "<i>SeqDesc<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><br>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);
- expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1</i>";
+ expected = "<i>SeqDesc<br/>UNIPROT P30419<br/>PDB 3iu1</i>";
+ 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 = "<i>SeqDesc<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
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"));
+ .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>"));
+ .endsWith(
+ "<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>"));
}
}
git://source.jalview.org / jalview.git / blobdiff