JAL-1925 update source version in license

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

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 7911188..6a47af0 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -40,19 +40,21 @@ public class TCoffeeScoreFileTest
   final static File ALIGN_FILE = new File(
           "test/jalview/io/tcoffee.fasta_aln");
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testReadHeader() throws IOException
   {
 
     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
             AppletFormatAdapter.FILE);
-    AssertJUnit.assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
+    AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
+            scoreFile.isValid());
 
     Header header = scoreFile.header;
     AssertJUnit.assertNotNull(header);
-    AssertJUnit.assertEquals(
-            "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
-            header.head);
+    AssertJUnit
+            .assertEquals(
+                    "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
+                    header.head);
     AssertJUnit.assertEquals(90, header.score);
     AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
     AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
@@ -65,7 +67,7 @@ public class TCoffeeScoreFileTest
     AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testWrongFile()
   {
     try
@@ -80,7 +82,7 @@ public class TCoffeeScoreFileTest
     }
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testHeightAndWidth() throws IOException
   {
     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
@@ -90,7 +92,7 @@ public class TCoffeeScoreFileTest
     AssertJUnit.assertEquals(83, result.getWidth());
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testReadBlock() throws IOException
   {
 
@@ -109,63 +111,81 @@ public class TCoffeeScoreFileTest
     Block block = TCoffeeScoreFile.readBlock(source, 0);
 
     AssertJUnit.assertNotNull(block);
-    AssertJUnit.assertEquals("999999999999999999999999998762112222543211112134",
+    AssertJUnit.assertEquals(
+            "999999999999999999999999998762112222543211112134",
             block.getScoresFor("1PHT"));
-    AssertJUnit.assertEquals("99999999999999999999999999987-------4322----2234",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------4322----2234",
             block.getScoresFor("1BB9"));
-    AssertJUnit.assertEquals("99999999999999999999999999987-------5321----2246",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------5321----2246",
             block.getScoresFor("1UHC"));
-    AssertJUnit.assertEquals("99999999999999999999999999986-------4321----1-35",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------4321----1-35",
             block.getScoresFor("1YCS"));
-    AssertJUnit.assertEquals("999999999999999999999999999861-------3------1135",
+    AssertJUnit.assertEquals(
+            "999999999999999999999999999861-------3------1135",
             block.getScoresFor("1OOT"));
-    AssertJUnit.assertEquals("99999999999999999999999999986-------422-------34",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------422-------34",
             block.getScoresFor("1ABO"));
-    AssertJUnit.assertEquals("99999999999999999999999999985-------32--------35",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999985-------32--------35",
             block.getScoresFor("1FYN"));
-    AssertJUnit.assertEquals("99999999999999999999999999974-------2---------24",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999974-------2---------24",
             block.getScoresFor("1QCF"));
-    AssertJUnit.assertEquals("999999999999999999999999999851000110321100001134",
+    AssertJUnit.assertEquals(
+            "999999999999999999999999999851000110321100001134",
             block.getConsensus());
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testParse() throws IOException
   {
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
             FormatAdapter.FILE);
 
-    AssertJUnit.assertEquals(
-            "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
-            parser.getScoresFor("1PHT"));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
-            parser.getScoresFor("1BB9"));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
-            parser.getScoresFor("1UHC"));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
-            parser.getScoresFor("1YCS"));
-    AssertJUnit.assertEquals(
-            "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
-            parser.getScoresFor("1OOT"));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
-            parser.getScoresFor("1ABO"));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
-            parser.getScoresFor("1FYN"));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
-            parser.getScoresFor("1QCF"));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
-            parser.getScoresFor("cons"));
+    AssertJUnit
+            .assertEquals(
+                    "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+                    parser.getScoresFor("1PHT"));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+                    parser.getScoresFor("1BB9"));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+                    parser.getScoresFor("1UHC"));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+                    parser.getScoresFor("1YCS"));
+    AssertJUnit
+            .assertEquals(
+                    "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+                    parser.getScoresFor("1OOT"));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+                    parser.getScoresFor("1ABO"));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+                    parser.getScoresFor("1FYN"));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+                    parser.getScoresFor("1QCF"));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+                    parser.getScoresFor("cons"));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetAsList() throws IOException
   {
 
@@ -173,37 +193,46 @@ public class TCoffeeScoreFileTest
             FormatAdapter.FILE);
     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
     List<String> scores = parser.getScoresList();
-    AssertJUnit.assertEquals(
-            "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
-            scores.get(0));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
-            scores.get(1));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
-            scores.get(2));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
-            scores.get(3));
-    AssertJUnit.assertEquals(
-            "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
-            scores.get(4));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
-            scores.get(5));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
-            scores.get(6));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
-            scores.get(7));
-    AssertJUnit.assertEquals(
-            "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
-            scores.get(8));
+    AssertJUnit
+            .assertEquals(
+                    "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+                    scores.get(0));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+                    scores.get(1));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+                    scores.get(2));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+                    scores.get(3));
+    AssertJUnit
+            .assertEquals(
+                    "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+                    scores.get(4));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+                    scores.get(5));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+                    scores.get(6));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+                    scores.get(7));
+    AssertJUnit
+            .assertEquals(
+                    "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+                    scores.get(8));
 
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetAsArray() throws IOException
   {
 
@@ -234,7 +263,7 @@ public class TCoffeeScoreFileTest
 
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testHeightAndWidthWithResidueNumbers() throws Exception
   {
     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";