X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=0b5dfdda390449a21a9d72de37336426db090fa9;hb=e51f922b88b1f316e27cf4c19eef437ff592d74d;hp=9e61bec5632803554dce391211eca358de59d6b7;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 9e61bec..0b5dfdd 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -23,22 +23,25 @@ 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.HashMap;
-import java.util.Hashtable;
+import java.awt.Color;
 import java.util.Map;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceAnnotationReportTest
 {
 
@@ -59,17 +62,17 @@ public class SequenceAnnotationReportTest
             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>)
     // 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);
+    sar.appendFeature(sb, 3, null, sf, null);
     assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
             sb.toString());
   }
@@ -83,7 +86,7 @@ public class SequenceAnnotationReportTest
             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());
   }
 
@@ -95,8 +98,9 @@ public class SequenceAnnotationReportTest
     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:
      */
@@ -106,7 +110,7 @@ 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, minmax, sf);
+    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());
@@ -116,7 +120,7 @@ public class SequenceAnnotationReportTest
      */
     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());
   }
 
@@ -128,12 +132,15 @@ public class SequenceAnnotationReportTest
     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();
@@ -141,12 +148,36 @@ public class SequenceAnnotationReportTest
             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();
@@ -154,11 +185,18 @@ public class SequenceAnnotationReportTest
             "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());
   }
 
@@ -171,13 +209,13 @@ public class SequenceAnnotationReportTest
             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());
   }
 
@@ -190,13 +228,13 @@ public class SequenceAnnotationReportTest
             "<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; &lt;br&gt;&kHD&gt;6", sb.toString());
   }
@@ -226,7 +264,7 @@ public class SequenceAnnotationReportTest
             null));
     sb.setLength(0);
     sar.createSequenceAnnotationReport(sb, seq, true, true, null);
-    String expected = "<i><br>SeqDesc<br>Type1 ; Nonpos</i>";
+    String expected = "<i><br>SeqDesc<br>Type1 ; Nonpos Score=1.0</i>";
     assertEquals(expected, sb.toString());
 
     /*
@@ -244,10 +282,13 @@ public class SequenceAnnotationReportTest
      */
     seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f,
             null));
-    Map<String, float[][]> minmax = new HashMap<String, float[][]>();
+
+    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, minmax);
+    sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
     expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos</i>";
     assertEquals(expected, sb.toString());
     
@@ -260,19 +301,20 @@ public class SequenceAnnotationReportTest
     sf.setValue("linkonly", Boolean.TRUE);
     seq.addSequenceFeature(sf);
     sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, true, minmax);
+    sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
     assertEquals(expected, sb.toString()); // unchanged!
 
     /*
-     * 'clinical_significance' currently being specially included
+     * 'clinical_significance' attribute only included 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, minmax);
-    expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana; benign</i>";
+    sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
+    expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana</i>";
     assertEquals(expected, sb.toString());
 
     /*
@@ -280,18 +322,25 @@ public class SequenceAnnotationReportTest
      */
     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, minmax);
+    sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
     assertEquals(expected, sb.toString()); // unchanged
-    // with showDbRefs = true
+
+    // with showDbRefs = true, colour Variant features by clinical_significance
     sb.setLength(0);
-    sar.createSequenceAnnotationReport(sb, seq, true, true, minmax);
-    expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana; benign</i>";
+    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><br>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, minmax);
+    sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
     expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1</i>";
     assertEquals(expected, sb.toString());