X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=0b5dfdda390449a21a9d72de37336426db090fa9;hb=e51f922b88b1f316e27cf4c19eef437ff592d74d;hp=13921573f7d9709686aead99117dfda162c7437a;hpb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 1392157..0b5dfdd 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -21,16 +21,37 @@
 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.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()
   {
@@ -41,17 +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());
   }
@@ -65,7 +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());
   }
 
@@ -77,8 +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:
      */
@@ -88,7 +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());
@@ -98,7 +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());
   }
 
@@ -110,12 +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();
@@ -123,12 +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();
@@ -136,11 +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());
   }
 
@@ -153,13 +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());
   }
 
@@ -172,14 +228,155 @@ 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());
   }
+
+  @Test(groups = "Functional")
+  public void testCreateSequenceAnnotationReport()
+  {
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    StringBuilder sb = new StringBuilder();
+
+    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());
+
+    /*
+     * 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><br>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><br>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><br>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 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, fr);
+    expected = "<i><br>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><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, fr);
+    expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1</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>"));
+  }
 }