package jalview.io;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.io.gff.GffConstants;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.FeatureColour;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-import java.util.Hashtable;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceAnnotationReportTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testAppendFeature_disulfideBond()
{
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 = "Abcd".repeat(50);
+ 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());
}
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
"group");
- Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
- sar.appendFeature(sb, 1, minmax, sf);
+ FeatureRendererModel fr = new FeatureRenderer(null);
+ Map<String, float[][]> minmax = fr.getMinMax();
+ 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, minmax, 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, minmax, 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());
}
+ /**
+ * A specific attribute value is included if it is used to colour the feature
+ */
@Test(groups = "Functional")
- public void testAppendFeature_clinicalSignificance()
+ public void testAppendFeature_colouredByAttribute()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
StringBuilder sb = new StringBuilder();
Float.NaN, "group");
sf.setValue("clinical_significance", "Benign");
- sar.appendFeature(sb, 1, null, sf);
- assertEquals("METAL 1 3; Fe2-S; Benign", sb.toString());
+ /*
+ * first with no colour by attribute
+ */
+ FeatureRendererModel fr = new FeatureRenderer(null);
+ sar.appendFeature(sb, 1, fr, sf, null);
+ assertEquals("METAL 1 3; Fe2-S", sb.toString());
+
+ /*
+ * then with colour by an attribute the feature lacks
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
+ null, 5, 10);
+ fc.setAttributeName("Pfam");
+ fr.setColour("METAL", fc);
+ sb.setLength(0);
+ sar.appendFeature(sb, 1, fr, sf, null);
+ assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
+
+ /*
+ * then with colour by an attribute the feature has
+ */
+ fc.setAttributeName("clinical_significance");
+ sb.setLength(0);
+ sar.appendFeature(sb, 1, fr, sf, null);
+ assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
+ sb.toString());
}
@Test(groups = "Functional")
- public void testAppendFeature_withScoreStatusClinicalSignificance()
+ public void testAppendFeature_withScoreStatusAttribute()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
StringBuilder sb = new StringBuilder();
"group");
sf.setStatus("Confirmed");
sf.setValue("clinical_significance", "Benign");
- Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+
+ FeatureRendererModel fr = new FeatureRenderer(null);
+ Map<String, float[][]> minmax = fr.getMinMax();
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue,
+ null, 12, 22);
+ fc.setAttributeName("clinical_significance");
+ fr.setColour("METAL", fc);
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
- sar.appendFeature(sb, 1, minmax, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
- assertEquals("METAL 1 3; Fe2-S Score=1.3; (Confirmed); Benign",
+ assertEquals(
+ "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
sb.toString());
}
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());
}
+
+ @Test(groups = "Functional")
+ public void testCreateSequenceAnnotationReport()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuilder sb = new StringBuilder();
+
+ SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
+ seq.setDescription("SeqDesc");
+
+ /*
+ * positional features are ignored
+ */
+ seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5,
+ 10, 1f, null));
+ sar.createSequenceAnnotationReport(sb, seq, true, true, null);
+ assertEquals("<i>SeqDesc</i>", sb.toString());
+
+ /*
+ * non-positional feature
+ */
+ 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>";
+ assertEquals(expected, sb.toString());
+
+ /*
+ * non-positional features not wanted
+ */
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, false, null);
+ assertEquals("<i>SeqDesc</i>", sb.toString());
+
+ /*
+ * add non-pos feature with score inside min-max range for feature type
+ * minmax holds { [positionalMin, positionalMax], [nonPosMin, nonPosMax] }
+ * 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));
+
+ FeatureRendererModel fr = new FeatureRenderer(null);
+ Map<String, float[][]> minmax = fr.getMinMax();
+ minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } });
+
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
+ expected = "<i>SeqDesc<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
+ */
+ SequenceFeature sf = new SequenceFeature("Metal", "Desc", 0, 0, 5f,
+ null);
+ sf.setValue("linkonly", Boolean.TRUE);
+ seq.addSequenceFeature(sf);
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
+ assertEquals(expected, sb.toString()); // unchanged!
+
+ /*
+ * 'clinical_significance' attribute is only included in description
+ * when used for feature colouring
+ */
+ 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>";
+ assertEquals(expected, sb.toString());
+
+ /*
+ * add dbrefs
+ */
+ seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1"));
+ seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419"));
+
+ // with showDbRefs = false
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
+ assertEquals(expected, sb.toString()); // unchanged
+
+ // with showDbRefs = true, colour Variant features by clinical_significance
+ sb.setLength(0);
+ FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink,
+ null, 2, 3);
+ 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>";
+ 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>";
+ 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
+ }
+
+ /**
+ * Test that exercises an abbreviated sequence details report, with ellipsis
+ * where there are more than 40 different sources, or more than 4 dbrefs for a
+ * single source
+ */
+ @Test(groups = "Functional")
+ public void testCreateSequenceAnnotationReport_withEllipsis()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuilder sb = new StringBuilder();
+
+ SequenceI seq = new Sequence("s1", "ABC");
+
+ int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
+ for (int i = 0; i <= maxSources; i++)
+ {
+ 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>"));
+ }
}