JAL-3567 unit tests for linked feature tooltips

[jalview.git] / test / jalview / io / SequenceAnnotationReportTest.java

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 7e00caa..772ed2b 100644 (file)
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -33,6 +33,8 @@ import org.testng.annotations.Test;
 
 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;
@@ -40,6 +42,7 @@ import jalview.gui.JvOptionPane;
 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;
 
@@ -423,4 +426,63 @@ public class SequenceAnnotationReportTest
             .endsWith(
                     "<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</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());
+  }
 }