X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=111fadb38f41354e8fb36ff03d3bfb5ad6d8ba48;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=cf3c7e5ed4027d0fb977666aea2453536139cfc7;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index cf3c7e5..111fadb 100644
--- 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;
@@ -62,22 +64,60 @@ 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>)
+    // 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);
-    assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
+    // <br/> is prefixed once sb.length() > 6
+    sar.appendFeature(sb, 3, null, sf, null);
+    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 = // java11!"Abcd".repeat(50);
+            "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+                    + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+                    + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+                    + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd"
+                    + "abcdabcdabcdabcdabcdabcdabcdabcdabcdabcd";
+
+    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);
@@ -86,7 +126,7 @@ 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());
   }
 
@@ -100,7 +140,7 @@ public class SequenceAnnotationReportTest
 
     FeatureRendererModel fr = new FeatureRenderer(null);
     Map<String, float[][]> minmax = fr.getMinMax();
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     /*
      * map has no entry for this feature type - score is not shown:
      */
@@ -110,9 +150,9 @@ 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);
-    // <br> is appended to a buffer > 6 in length
-    assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
+    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());
 
     /*
@@ -120,7 +160,7 @@ public class SequenceAnnotationReportTest
      */
     minmax.put("METAL", new float[][] { { 2f, 2f }, null });
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
@@ -132,7 +172,7 @@ 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());
   }
 
@@ -152,7 +192,7 @@ public class SequenceAnnotationReportTest
      * first with no colour by attribute
      */
     FeatureRendererModel fr = new FeatureRenderer(null);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
 
     /*
@@ -163,7 +203,7 @@ public class SequenceAnnotationReportTest
     fc.setAttributeName("Pfam");
     fr.setColour("METAL", fc);
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
 
     /*
@@ -171,7 +211,7 @@ public class SequenceAnnotationReportTest
      */
     fc.setAttributeName("clinical_significance");
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
             sb.toString());
   }
@@ -193,7 +233,7 @@ 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);
+    sar.appendFeature(sb, 1, fr, sf, null);
 
     assertEquals(
             "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
@@ -209,13 +249,13 @@ 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());
   }
 
@@ -228,13 +268,13 @@ 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());
   }
@@ -248,14 +288,13 @@ 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 +303,7 @@ 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 +311,7 @@ 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 +328,7 @@ 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 +344,8 @@ 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 +353,7 @@ 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 +374,23 @@ 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 +424,10 @@ 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>"));
   }
 }