X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=772ed2bb7570050645da2caaa3a1eaf236430d0c;hb=339d1bf247a3b0d000044892bee3d5668a8d9b11;hp=42183ca8816cdb03d35cf92264b6609006d4f67b;hpb=b785b473bee76eb532b6552fe61f4817b095cdbb;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 42183ca..772ed2b 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -23,8 +23,18 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+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 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;
@@ -32,16 +42,8 @@ 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 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
@@ -57,24 +59,24 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_disulfideBond()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     sb.append("123456");
     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);
+    sar.appendFeature(sb, 2, null, sf, null, 0);
     assertEquals("123456", sb.toString());
 
     // residuePos == 1 matches start of feature, text appended (but no <br/>)
     // feature score is not included
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     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, null);
+    sar.appendFeature(sb, 3, null, sf, null, 0);
     assertEquals("123456disulfide bond 1:3<br/>disulfide bond 1:3",
             sb.toString());
   }
@@ -82,13 +84,13 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeatures_longText()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     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);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertTrue(sb.length() < 100);
 
     List<SequenceFeature> sfl = new ArrayList<>();
@@ -103,7 +105,7 @@ public class SequenceAnnotationReportTest
     sfl.add(sf);
     sfl.add(sf);
     sfl.add(sf);
-    int n = sar.appendFeaturesLengthLimit(sb, 1, sfl,
+    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);
@@ -114,27 +116,27 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_status()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
     sf.setStatus("Confirmed");
 
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_withScore()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
             "group");
 
     FeatureRendererModel fr = new FeatureRenderer(null);
     Map<String, float[][]> minmax = fr.getMinMax();
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     /*
      * map has no entry for this feature type - score is not shown:
      */
@@ -144,7 +146,7 @@ public class SequenceAnnotationReportTest
      * map has entry for this feature type - score is shown:
      */
     minmax.put("METAL", new float[][] { { 0f, 1f }, null });
-    sar.appendFeature(sb, 1, fr, sf, 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",
             sb.toString());
@@ -154,19 +156,19 @@ public class SequenceAnnotationReportTest
      */
     minmax.put("METAL", new float[][] { { 2f, 2f }, null });
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_noScore()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
 
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
@@ -176,7 +178,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_colouredByAttribute()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
@@ -186,7 +188,7 @@ public class SequenceAnnotationReportTest
      * first with no colour by attribute
      */
     FeatureRendererModel fr = new FeatureRenderer(null);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
 
     /*
@@ -197,7 +199,7 @@ public class SequenceAnnotationReportTest
     fc.setAttributeName("Pfam");
     fr.setColour("METAL", fc);
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
 
     /*
@@ -205,7 +207,7 @@ public class SequenceAnnotationReportTest
      */
     fc.setAttributeName("clinical_significance");
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
             sb.toString());
   }
@@ -213,7 +215,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_withScoreStatusAttribute()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
             "group");
@@ -227,7 +229,7 @@ public class SequenceAnnotationReportTest
     fc.setAttributeName("clinical_significance");
     fr.setColour("METAL", fc);
     minmax.put("METAL", new float[][] { { 0f, 1f }, null });
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
 
     assertEquals(
             "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
@@ -237,38 +239,38 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_DescEqualsType()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
             Float.NaN, "group");
 
     // description is not included if it duplicates type:
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("Metal");
     // test is case-sensitive:
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3; Metal", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_stripHtml()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL",
             "<html><body>hello<em>world</em></body></html>", 1, 3,
             Float.NaN, "group");
 
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     // !! 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, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     // if no <html> tag, html-encodes > and < (only):
     assertEquals("METAL 1 3; &lt;br&gt;&kHD&gt;6", sb.toString());
   }
@@ -276,7 +278,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testCreateSequenceAnnotationReport()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
 
     SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
@@ -398,7 +400,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testCreateSequenceAnnotationReport_withEllipsis()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
   
     SequenceI seq = new Sequence("s1", "ABC");
@@ -424,4 +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());
+  }
 }