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 bb5d1c4..270de2d 100644 (file)
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -62,22 +62,22 @@ public class SequenceAnnotationReportTest
     SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     sb.append("123456");
-    SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1, 3,
-            1.2f, "group");
+    SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
+            3, 1.2f, "group");
 
     // residuePos == 2 does not match start or end of feature, nothing done:
     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());
   }
 
@@ -105,12 +105,8 @@ public class SequenceAnnotationReportTest
     sfl.add(sf);
     sfl.add(sf);
     sfl.add(sf);
-    int n = sar.appendFeatures(sb, 1, sfl, new FeatureRenderer(null), 200); // text
-                                                                            // should
-                                                                            // terminate
-                                                                            // before
-                                                                            // 200
-                                                                            // characters
+    int n = sar.appendFeatures(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
@@ -151,8 +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());
 
     /*
@@ -332,7 +328,7 @@ public class SequenceAnnotationReportTest
     expected = "<i>SeqDesc\n" + "\n"
             + "<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
@@ -412,7 +408,7 @@ public class SequenceAnnotationReportTest
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
-
+  
     SequenceI seq = new Sequence("s1", "ABC");
 
     int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
@@ -420,13 +416,13 @@ public class SequenceAnnotationReportTest
     {
       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>\n" + "<br/>\n" + "UNIPROT P30410,\n"