From 5d003f492184b893aa4c2f437c6021626b573c45 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 5 Apr 2022 18:37:11 +0100
Subject: [PATCH] JAL-3981 patch tests and remove errant imports

---
 src/jalview/io/SequenceAnnotationReport.java      |    5 +--
 test/jalview/io/SequenceAnnotationReportTest.java |   35 +++++++++++++--------
 2 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index c831366..95bd1cc 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,17 +20,14 @@
  */
 package jalview.io;
 
-import java.util.Locale;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
-import com.google.common.collect.Lists;
-
 import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 6459545..bb5d1c4 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -294,7 +294,7 @@ public class SequenceAnnotationReportTest
     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
@@ -303,7 +303,8 @@ public class SequenceAnnotationReportTest
             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());
 
     /*
@@ -311,7 +312,7 @@ 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
@@ -328,7 +329,8 @@ 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());
 
     /*
@@ -353,7 +355,8 @@ public class SequenceAnnotationReportTest
     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());
 
     /*
@@ -374,13 +377,15 @@ 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());
 
     /*
@@ -390,7 +395,8 @@ 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
@@ -423,10 +429,13 @@ 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>"));
   }
 
   /**
-- 
1.7.10.2