JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / test / jalview / io / Gff3tests.java

diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java
index c8cf638..faa4d43 100644 (file)
--- a/test/jalview/io/Gff3tests.java
+++ b/test/jalview/io/Gff3tests.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
@@ -23,7 +43,7 @@ public class Gff3tests
           exonerateOutput = "examples/testdata/exonerateoutput.gff",
           simpleGff3file = "examples/testdata/simpleGff3.gff";
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testExonerateImport()
   {
     // exonerate does not tag sequences after features, so we have a more
@@ -34,8 +54,8 @@ public class Gff3tests
     AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
             FormatAdapter.FILE);
 
-    assertEquals("Unexpected number of DNA protein associations", 0,
-            af.getViewport().getAlignment().getCodonFrames().size());
+    assertEquals("Unexpected number of DNA protein associations", 0, af
+            .getViewport().getAlignment().getCodonFrames().size());
 
     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
 
@@ -45,19 +65,17 @@ public class Gff3tests
 
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void simpleGff3FileIdentify()
   {
-    assertEquals("Didn't recognise file correctly.",
-            IdentifyFile.GFF3File,
+    assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File,
             new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void simpleGff3FileClass() throws IOException
   {
-    AlignmentI dataset = new Alignment(new SequenceI[]
-    {});
+    AlignmentI dataset = new Alignment(new SequenceI[] {});
     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
             FormatAdapter.FILE);
 
@@ -66,7 +84,7 @@ public class Gff3tests
     checkDatasetfromSimpleGff3(dataset);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void simpleGff3FileLoader() throws IOException
   {
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@@ -77,11 +95,10 @@ public class Gff3tests
     checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void simpleGff3RelaxedIdMatching() throws IOException
   {
-    AlignmentI dataset = new Alignment(new SequenceI[]
-    {});
+    AlignmentI dataset = new Alignment(new SequenceI[] {});
     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
             FormatAdapter.FILE);
 
@@ -91,7 +108,7 @@ public class Gff3tests
     checkDatasetfromSimpleGff3(dataset);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void readGff3File() throws IOException
   {
     Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
@@ -123,17 +140,16 @@ public class Gff3tests
             placeholderseq.equals(seq1.getSequenceAsString()));
     assertFalse("dummy replacement buggy for seq2",
             placeholderseq.equals(seq2.getSequenceAsString()));
-    assertNotNull("No features added to seq1",
-            seq1.getSequenceFeatures());// != null);
+    assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
+                                                                           // null);
     assertEquals("Wrong number of features", 3,
             seq1.getSequenceFeatures().length);
     assertNull(seq2.getSequenceFeatures());
     assertEquals(
             "Wrong number of features",
             0,
-            seq2
-            .getSequenceFeatures() == null ? 0
-            : seq2.getSequenceFeatures().length);
+            seq2.getSequenceFeatures() == null ? 0 : seq2
+                    .getSequenceFeatures().length);
     assertTrue(
             "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null