X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=64595456d125fac84bb707373e3d4d316fb8a6cd;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=772ed2bb7570050645da2caaa3a1eaf236430d0c;hpb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 772ed2b..6459545 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -62,8 +62,8 @@ 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);
@@ -105,8 +105,12 @@ 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
@@ -287,16 +291,16 @@ 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());
 
     /*
      * 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>";
@@ -315,8 +319,8 @@ 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();
@@ -326,7 +330,7 @@ public class SequenceAnnotationReportTest
     sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
     expected = "<i>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
@@ -343,8 +347,8 @@ 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);
@@ -402,7 +406,7 @@ 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");
@@ -410,21 +414,19 @@ 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><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><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>"));
   }
 
   /**
@@ -475,8 +477,8 @@ 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);