Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

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

diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java
index c8cf638..e4a6119 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 ($$Version-Rel$$)
+ * 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;
@@ -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
@@ -34,30 +54,29 @@ 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);
 
-    assertTrue("Expected at least one DNA protein association", af
-            .getViewport().getAlignment().getDataset().getCodonFrames()
-            .size() > 0);
+    assertNotEquals("Expected at least one DNA protein association",
+            0, af.getViewport().getAlignment().getDataset()
+            .getCodonFrames().size(),
+            );
 
   }
 
-  @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 +85,7 @@ public class Gff3tests
     checkDatasetfromSimpleGff3(dataset);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void simpleGff3FileLoader() throws IOException
   {
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@@ -77,11 +96,10 @@ 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 +109,7 @@ public class Gff3tests
     checkDatasetfromSimpleGff3(dataset);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void readGff3File() throws IOException
   {
     Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
@@ -117,27 +135,27 @@ public class Gff3tests
     assertFalse(
             "Failed to replace dummy seq2 with real sequence",
             seq2 instanceof SequenceDummy
-                    && ((SequenceDummy) seq2).isDummy());
+            && ((SequenceDummy) seq2).isDummy(),
+            "Failed to replace dummy seq2 with real sequence");
     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
     assertFalse("dummy replacement buggy for seq1",
             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());
     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
-                    && dataset.getCodonFrame(seq1).size() > 0);
+            && dataset.getCodonFrame(seq1).size() > 0,
+            "Expected at least one CDNA/Protein mapping for seq1");
 
   }
   // @Test(groups ={ "Functional" })