Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 772ed2b..270de2d 100644 (file)
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -69,15 +69,15 @@ public class SequenceAnnotationReportTest
     sar.appendFeature(sb, 2, null, sf, null, 0);
     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, 0);
     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, 0);
-    assertEquals("123456disulfide bond 1:3<br/>disulfide bond 1:3",
+    assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
             sb.toString());
   }
 
@@ -147,8 +147,8 @@ public class SequenceAnnotationReportTest
      */
     minmax.put("METAL", new float[][] { { 0f, 1f }, 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",
+    // <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());
 
     /*
@@ -287,19 +287,20 @@ public class SequenceAnnotationReportTest
     /*
      * positional features are ignored
      */
-    seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5,
-            10, 1f, null));
+    seq.addSequenceFeature(
+            new SequenceFeature("Domain", "Ferredoxin", 5, 10, 1f, null));
     sar.createSequenceAnnotationReport(sb, seq, true, true, null);
-    assertEquals("<i>SeqDesc</i>", sb.toString());
+    assertEquals("<i>SeqDesc\n" + "\n" + "</i>", sb.toString());
 
     /*
      * non-positional feature
      */
-    seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f,
-            null));
+    seq.addSequenceFeature(
+            new SequenceFeature("Type1", "Nonpos", 0, 0, 1f, null));
     sb.setLength(0);
     sar.createSequenceAnnotationReport(sb, seq, true, true, null);
-    String expected = "<i>SeqDesc<br/>Type1 ; Nonpos Score=1.0</i>";
+    String expected = "<i>SeqDesc\n" + "\n"
+            + "<br/>Type1 ; Nonpos Score=1.0</i>";
     assertEquals(expected, sb.toString());
 
     /*
@@ -307,7 +308,7 @@ public class SequenceAnnotationReportTest
      */
     sb.setLength(0);
     sar.createSequenceAnnotationReport(sb, seq, true, false, null);
-    assertEquals("<i>SeqDesc</i>", sb.toString());
+    assertEquals("<i>SeqDesc\n\n</i>", sb.toString());
 
     /*
      * add non-pos feature with score inside min-max range for feature type
@@ -315,8 +316,8 @@ public class SequenceAnnotationReportTest
      * 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));
+    seq.addSequenceFeature(
+            new SequenceFeature("Metal", "Desc", 0, 0, 5f, null));
 
     FeatureRendererModel fr = new FeatureRenderer(null);
     Map<String, float[][]> minmax = fr.getMinMax();
@@ -324,7 +325,8 @@ public class SequenceAnnotationReportTest
 
     sb.setLength(0);
     sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
-    expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
+    expected = "<i>SeqDesc\n" + "\n"
+            + "<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
     assertEquals(expected, sb.toString());
     
     /*
@@ -343,13 +345,14 @@ public class SequenceAnnotationReportTest
      * 'clinical_significance' attribute is only included in description 
      * when used for feature colouring
      */
-    SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
-            5f, null);
+    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>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana</i>";
+    expected = "<i>SeqDesc\n" + "\n"
+            + "<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana</i>";
     assertEquals(expected, sb.toString());
 
     /*
@@ -370,13 +373,15 @@ public class SequenceAnnotationReportTest
     fc.setAttributeName("clinical_significance");
     fr.setColour("Variant", fc);
     sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
-    expected = "<i>SeqDesc<br/>UNIPROT P30419<br/>PDB 3iu1<br/>Metal ; Desc<br/>"
-            + "Type1 ; Nonpos<br/>Variant ; Havana; clinical_significance=benign</i>";
+    expected = "<i>SeqDesc\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
+            + "PDB 3iu1\n"
+            + "<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>SeqDesc<br/>UNIPROT P30419<br/>PDB 3iu1</i>";
+    expected = "<i>SeqDesc\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
+            + "PDB 3iu1\n" + "</i>";
     assertEquals(expected, sb.toString());
 
     /*
@@ -386,7 +391,8 @@ public class SequenceAnnotationReportTest
     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>";
+    expected = "<i>SeqDesc\n" + "\n"
+            + "<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
@@ -419,12 +425,13 @@ 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"));
-    assertTrue(report
-            .endsWith(
-                    "<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>"));
+    assertTrue(report.startsWith("<i>\n" + "<br/>\n" + "UNIPROT P30410,\n"
+            + " P30411,\n" + " P30412,\n" + " P30413,...<br/>\n"
+            + "PDB0 3iu1<br/>\n" + "PDB1 3iu1<br/>"));
+    assertTrue(report.endsWith("PDB5 3iu1<br/>\n" + "PDB6 3iu1<br/>\n"
+            + "PDB7 3iu1<br/>\n" + "PDB8,...<br/>\n"
+            + "(Output Sequence Details to list all database references)\n"
+            + "</i>"));
   }
 
   /**
@@ -475,8 +482,8 @@ public class SequenceAnnotationReportTest
      * 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");
+    SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, 2.3f,
+            "Uniprot");
     features.clear();
     features.add(sf2);
     mapping = new Mapping(peptide, map);