Merge branch 'develop' into ben/gecos_colour_schemes

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

diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 53f18bf..27cfa5e 100644 (file)
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -1,5 +1,27 @@
+/*
+ * 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 java.util.Locale;
+
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotEquals;
@@ -31,14 +53,15 @@ public class FileFormatsTest
   public void testIsIdentifiable()
   {
     FileFormats formats = FileFormats.getInstance();
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Fasta
-            .getName())));
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.MMCif
-            .getName())));
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jnet
-            .getName())));
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jalview
-            .getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.Fasta.getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.MMCif.getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.Jnet.getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.Jalview.getName())));
+    // GenBank/ENA
     assertFalse(formats.isIdentifiable(null));
 
     /*
@@ -55,7 +78,7 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetReadableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getReadableFormats().toString(), expected);
   }
@@ -74,14 +97,14 @@ public class FileFormatsTest
   public void testDeregisterFileFormat()
   {
     String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
     formats.deregisterFileFormat(FileFormat.Fasta.getName());
     writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
@@ -90,7 +113,7 @@ public class FileFormatsTest
      */
     formats.registerFileFormat(FileFormat.Fasta);
     writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
   }
@@ -102,8 +125,10 @@ public class FileFormatsTest
     for (FileFormatI ff : FileFormat.values())
     {
       assertSame(ff, formats.forName(ff.getName()));
-      assertSame(ff, formats.forName(ff.getName().toUpperCase()));
-      assertSame(ff, formats.forName(ff.getName().toLowerCase()));
+      assertSame(ff,
+              formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
+      assertSame(ff,
+              formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
     }
     assertNull(formats.forName(null));
     assertNull(formats.forName("rubbish"));
@@ -144,8 +169,7 @@ public class FileFormatsTest
      * verify the list of file formats registered matches the enum values
      */
     FileFormats instance = FileFormats.getInstance();
-    Iterator<FileFormatI> formats = instance.getFormats()
-            .iterator();
+    Iterator<FileFormatI> formats = instance.getFormats().iterator();
     FileFormatI[] builtIn = FileFormat.values();
 
     for (FileFormatI ff : builtIn)