Merge branch 'feature/JAL-3468featureDescriptionEllipsis' into develop

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

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 0b5dfdd..42183ca 100644 (file)
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -35,6 +35,8 @@ import jalview.schemes.FeatureColour;
 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;
@@ -65,19 +67,51 @@ public class SequenceAnnotationReportTest
     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, null);
     assertEquals("123456disulfide bond 1:3", sb.toString());
 
     // residuePos == 3 matches end of feature, text appended
-    // <br> is prefixed once sb.length() > 6
+    // <br/> is prefixed once sb.length() > 6
     sar.appendFeature(sb, 3, null, sf, null);
-    assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
+    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);
@@ -111,8 +145,8 @@ public class SequenceAnnotationReportTest
      */
     minmax.put("METAL", new float[][] { { 0f, 1f }, null });
     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",
+    // <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());
 
     /*
@@ -248,14 +282,13 @@ public class SequenceAnnotationReportTest
     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());
+    sar.createSequenceAnnotationReport(sb, seq, true, true, null);
+    assertEquals("<i>SeqDesc</i>", sb.toString());
 
     /*
      * non-positional feature
@@ -264,7 +297,7 @@ public class SequenceAnnotationReportTest
             null));
     sb.setLength(0);
     sar.createSequenceAnnotationReport(sb, seq, true, true, null);
-    String expected = "<i><br>SeqDesc<br>Type1 ; Nonpos Score=1.0</i>";
+    String expected = "<i>SeqDesc<br/>Type1 ; Nonpos Score=1.0</i>";
     assertEquals(expected, sb.toString());
 
     /*
@@ -272,7 +305,7 @@ public class SequenceAnnotationReportTest
      */
     sb.setLength(0);
     sar.createSequenceAnnotationReport(sb, seq, true, false, null);
-    assertEquals("<i><br>SeqDesc</i>", sb.toString());
+    assertEquals("<i>SeqDesc</i>", sb.toString());
 
     /*
      * add non-pos feature with score inside min-max range for feature type
@@ -289,7 +322,7 @@ public class SequenceAnnotationReportTest
 
     sb.setLength(0);
     sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
-    expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos</i>";
+    expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
     assertEquals(expected, sb.toString());
     
     /*
@@ -305,8 +338,8 @@ public class SequenceAnnotationReportTest
     assertEquals(expected, sb.toString()); // unchanged!
 
     /*
-     * 'clinical_significance' attribute only included when
-     * used for feature colouring
+     * 'clinical_significance' attribute is only included in description 
+     * when used for feature colouring
      */
     SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
             5f, null);
@@ -314,7 +347,7 @@ public class SequenceAnnotationReportTest
     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>";
+    expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana</i>";
     assertEquals(expected, sb.toString());
 
     /*
@@ -335,13 +368,23 @@ public class SequenceAnnotationReportTest
     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>";
+    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><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1</i>";
+    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
@@ -375,8 +418,10 @@ public class SequenceAnnotationReportTest
     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"));
+            .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>"));
+            .endsWith(
+                    "<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>"));
   }
 }