Merge branch 'develop' into trialMerge

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

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index f551571..1392157 100644 (file)
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -15,7 +35,7 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_disulfideBond()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     sb.append("123456");
     SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
             3, 1.2f, "group");
@@ -40,11 +60,11 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_status()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
     sf.setStatus("Confirmed");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
   }
@@ -53,7 +73,7 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_withScore()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
             "group");
 
@@ -86,10 +106,10 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_noScore()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
@@ -98,11 +118,11 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_clinicalSignificance()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
     sf.setValue("clinical_significance", "Benign");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3; Fe2-S; Benign", sb.toString());
   }
@@ -111,7 +131,7 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_withScoreStatusClinicalSignificance()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
             "group");
     sf.setStatus("Confirmed");
@@ -128,10 +148,10 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_DescEqualsType()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
             Float.NaN, "group");
-  
+
     // description is not included if it duplicates type:
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3", sb.toString());
@@ -147,15 +167,14 @@ public class SequenceAnnotationReportTest
   public void testAppendFeature_stripHtml()
   {
     SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
-    StringBuffer sb = new StringBuffer();
+    StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL",
             "<html><body>hello<em>world</em></body></html>", 1, 3,
             Float.NaN, "group");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     // !! strips off </body> but not <body> ??
-    assertEquals("METAL 1 3; <body>hello<em>world</em>",
-            sb.toString());
+    assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("<br>&kHD>6");